From inturu.srinivas2020 at vitstudent.ac.in Fri Sep 1 00:29:28 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Fri, 1 Sep 2023 10:59:28 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> Message-ID: Hi, I ran "make all" for petsc 3.13.4 by removing all occurrences of "-lut -licudata -licui18n -licuuc". When I ran "make test" got the following errors in petsc/3.13.4/linux-debug: TEST linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 # Running problem 5 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine on # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named MB108SMEC028 by vit Fri Sep 1 10:01:11 2023 # [0]PETSC ERROR: Configure options --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 --download-hypre=1 --download-fblaslapack=1 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -prob_id 5 # [0]PETSC ERROR: -tao_smonitor # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF # with errorcode 126076. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff in petsc/3.13.4/linux-opt TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 # Running problem 5 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine on # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by vit Fri Sep 1 10:34:12 2023 # [0]PETSC ERROR: Configure options --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt --with-debugging=0 --download-hypre=1 --with-x=0 --download-fblaslapack=1 --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -prob_id 5 # [0]PETSC ERROR: -tao_smonitor # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF # with errorcode 126076. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff. The same errors occurred for petsc 3.17.5 version. I am sharing the config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. Please find the attachment and do the needful. Thanks and regards Srinivas On Tue, Aug 29, 2023 at 10:56?PM Satish Balay wrote: > Well - you sent in libmesh log not petsc's configure.log/make.log for > petsc-3.17 > > Anyway - with petsc-3.13 - you have: > > >>>> > > Matlab: > Includes: -I/usr/local/MATLAB/R2020b/extern/include > /usr/local/MATLAB/R2020b > MatlabEngine: > Library: > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut > -licudata -licui18n -licuuc > Language used to compile PETSc: C > <<<<< > > With petsc-3.19 (and matlab-R2022a) - we are seeing: > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > >>> > Matlab: > Includes: > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > Libraries: > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > -leng -lmex -lmx -lmat > Executable: > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > mex: > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > matlab: > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > -glnxa64 > <<< > > I.e "-lut -licudata -licui18n -licuuc" are not preset here. This might be > a change wrt newer matlab versions. > > You can: > > - edit /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > and remove all occurrences of "-lut -licudata -licui18n -licuuc" > - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > And see if the build works now. > > Satish > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > I am sharing the log files while building petsc3.13.4 with matlab and > also > > the log file while building libmesh with petsc3.17.5 and matlab. Building > > petsc 3.17.5 with matlab was done successfully. But libmesh is not able > to > > find the petsc > > Please find the attachments. > > > > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay wrote: > > > > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or 3.19]. > > > > > > [you can gzip them to make the logs friendly to mailing list - or send > > > them to petsc-maint] > > > > > > And does test suite work with 3.17? [or 3.19?] > > > > > > Satish > > > > > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > > > > > I am sharing the make.log file while building petsc-3.13.4 with > Matlab. > > > > Please find the attachment and do the needful. > > > > > > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < > > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > > > > > I tried with petsc-3.17.5. During building of libmesh, the error > shows > > > > > petsc was not found > > > > > > > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay > > > wrote: > > > > > > > > > >> https://ibamr.github.io/linux says petsc-3.17 > > > > >> > > > > >> Here you are using 3.13 > > > > >> > > > > >> Can you retry with petsc-3.17.5? > > > > >> > > > > >> Satish > > > > >> > > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > > > > >> > > > > >> > Hello, > > > > >> > > > > > >> > I want to build PETSc with MATLAB for working on the simulation > > > using > > > > >> IBAMR > > > > >> > open software. While building the PETSc, using the following > > > > >> > > > > > >> > export PETSC_DIR=$PWD > > > > >> > export PETSC_ARCH=linux-debug > > > > >> > ./configure \ > > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > > >> > --with-debugging=1 \ > > > > >> > --download-hypre=1 \ > > > > >> > --download-fblaslapack=1 \ > > > > >> > --with-x=0 \ > > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >> > --with-matlab-engine=1 > > > > >> > > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >> > > > > > >> > make -j4 > > > > >> > make -j4 test > > > > >> > > > > > >> > I got the following error > > > > >> > CLINKER > > > > >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > >> > /usr/bin/ld: > > > > >> > > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >> > function `EvaluateResidual': > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > > >> > undefined reference to `PetscMatlabEnginePut' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > >> > /usr/bin/ld: > > > > >> > > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >> > function `EvaluateJacobian': > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > > >> > undefined reference to `PetscMatlabEnginePut' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > >> > /usr/bin/ld: > > > > >> > > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >> > function `TaoPounders': > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > >> > /usr/bin/ld: > > > > >> > > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >> > function `main': > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > > >> > undefined reference to `PetscMatlabEngineCreate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >> > /usr/bin/ld: > > > > >> > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > > >> > undefined reference to `PetscMatlabEngineDestroy' > > > > >> > > > > > >> > collect2: error: ld returned 1 exit status > > > > >> > make: *** [gmakefile.test:185: > > > > >> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > > >> Error 1 > > > > >> > make: *** Waiting for unfinished jobs.... > > > > >> > > > > > >> > Please help me to solve this issue > > > > >> > > > > > >> > Thank you > > > > >> > Srinivas > > > > >> > > > > > >> > > > > > >> > > > > >> > > > > > > > > > > > > > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3.13.4_logfiles.zip Type: application/zip Size: 5649 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 3.17.5_logfiles.zip Type: application/zip Size: 110244 bytes Desc: not available URL: From s.kramer at imperial.ac.uk Fri Sep 1 06:04:58 2023 From: s.kramer at imperial.ac.uk (Stephan Kramer) Date: Fri, 1 Sep 2023 12:04:58 +0100 Subject: [petsc-users] performance regression with GAMG In-Reply-To: References: <9716433a-7aa0-9284-141f-a1e2fccb310e@imperial.ac.uk> Message-ID: <99896e04-7ac2-9e92-0922-e78f2d0c710d@imperial.ac.uk> Hi Mark Sorry took a while to report back. We have tried your branch but hit a few issues, some of which we're not entirely sure are related. First switching off minimum degree ordering, and then switching to the old version of aggressive coarsening, as you suggested, got us back to the coarsening behaviour that we had previously, but then we also observed an even further worsening of the iteration count: it had previously gone up by 50% already (with the newer main petsc), but now was more than double "old" petsc. Took us a while to realize this was due to the default smoother changing from Cheby+SOR to Cheby+Jacobi. Switching this also back to the old default we get back to very similar coarsening levels (see below for more details if it is of interest) and iteration counts. So that's all very good news. However, we were also starting seeing memory errors (double free or corruption) when we switched off the minimum degree ordering. Because this was at an earlier version of your branch we then rebuild, hoping this was just an earlier bug that had been fixed, but then we were having MPI-lockup issues. We have now figured out the MPI issues are completely unrelated - some combination with a newer mpi build and firedrake on our cluster which also occur using main branches of everything. So switching back to an older MPI build we are hoping to now test your most recent version of adams/gamg-add-old-coarsening with these options and see whether the memory errors are still there. Will let you know Best wishes Stephan Kramer Coarsening details with various options for Level 6 of the test case: In our original setup (using "old" petsc), we had: ????????? rows=516, cols=516, bs=6 ????????? rows=12660, cols=12660, bs=6 ????????? rows=346974, cols=346974, bs=6 ????????? rows=19169670, cols=19169670, bs=3 Then with the newer main petsc we had ????????? rows=666, cols=666, bs=6 ????????? rows=7740, cols=7740, bs=6 ????????? rows=34902, cols=34902, bs=6 ????????? rows=736578, cols=736578, bs=6 ????????? rows=19169670, cols=19169670, bs=3 Then on your branch with minimum_degree_ordering False: ????????? rows=504, cols=504, bs=6 ????????? rows=2274, cols=2274, bs=6 ????????? rows=11010, cols=11010, bs=6 ????????? rows=35790, cols=35790, bs=6 ????????? rows=430686, cols=430686, bs=6 ????????? rows=19169670, cols=19169670, bs=3 And with minimum_degree_ordering False and use_aggressive_square_graph True: ????????? rows=498, cols=498, bs=6 ????????? rows=12672, cols=12672, bs=6 ????????? rows=346974, cols=346974, bs=6 ????????? rows=19169670, cols=19169670, bs=3 So that is indeed pretty much back to what it was before On 31/08/2023 23:40, Mark Adams wrote: > Hi Stephan, > > This branch is settling down. adams/gamg-add-old-coarsening > > I made the old, not minimum degree, ordering the default but kept the new > "aggressive" coarsening as the default, so I am hoping that just adding > "-pc_gamg_use_aggressive_square_graph true" to your regression tests will > get you back to where you were before. > Fingers crossed ... let me know if you have any success or not. > > Thanks, > Mark > > > On Tue, Aug 15, 2023 at 1:45?PM Mark Adams wrote: > >> Hi Stephan, >> >> I have a branch that you can try: adams/gamg-add-old-coarsening >> >> >> Things to test: >> * First, verify that nothing unintended changed by reproducing your bad >> results with this branch (the defaults are the same) >> * Try not using the minimum degree ordering that I suggested >> with: -pc_gamg_use_minimum_degree_ordering false >> -- I am eager to see if that is the main problem. >> * Go back to what I think is the old method: >> -pc_gamg_use_minimum_degree_ordering >> false -pc_gamg_use_aggressive_square_graph true >> >> When we get back to where you were, I would like to try to get modern >> stuff working. >> I did add a -pc_gamg_aggressive_mis_k <2> >> You could to another step of MIS coarsening with -pc_gamg_aggressive_mis_k >> 3 >> >> Anyway, lots to look at but, alas, AMG does have a lot of parameters. >> >> Thanks, >> Mark >> >> On Mon, Aug 14, 2023 at 4:26?PM Mark Adams wrote: >> >>> >>> On Mon, Aug 14, 2023 at 11:03?AM Stephan Kramer >>> wrote: >>> >>>> Many thanks for looking into this, Mark >>>>> My 3D tests were not that different and I see you lowered the >>>> threshold. >>>>> Note, you can set the threshold to zero, but your test is running so >>>> much >>>>> differently than mine there is something else going on. >>>>> Note, the new, bad, coarsening rate of 30:1 is what we tend to shoot >>>> for >>>>> in 3D. >>>>> >>>>> So it is not clear what the problem is. Some questions: >>>>> >>>>> * do you have a picture of this mesh to show me? >>>> It's just a standard hexahedral cubed sphere mesh with the refinement >>>> level giving the number of times each of the six sides have been >>>> subdivided: so Level_5 mean 2^5 x 2^5 squares which is extruded to 16 >>>> layers. So the total number of elements at Level_5 is 6 x 32 x 32 x 16 = >>>> 98304 hexes. And everything doubles in all 3 dimensions (so 2^3) going >>>> to the next Level >>>> >>> I see, and I assume these are pretty stretched elements. >>> >>> >>>>> * what do you mean by Q1-Q2 elements? >>>> Q2-Q1, basically Taylor hood on hexes, so (tri)quadratic for velocity >>>> and (tri)linear for pressure >>>> >>>> I guess you could argue we could/should just do good old geometric >>>> multigrid instead. More generally we do use this solver configuration a >>>> lot for tetrahedral Taylor Hood (P2-P1) in particular also for our >>>> adaptive mesh runs - would it be worth to see if we have the same >>>> performance issues with tetrahedral P2-P1? >>>> >>> No, you have a clear reproducer, if not minimal. >>> The first coarsening is very different. >>> >>> I am working on this and I see that I added a heuristic for thin bodies >>> where you order the vertices in greedy algorithms with minimum degree first. >>> This will tend to pick corners first, edges then faces, etc. >>> That may be the problem. I would like to understand it better (see below). >>> >>> >>> >>>>> It would be nice to see if the new and old codes are similar without >>>>> aggressive coarsening. >>>>> This was the intended change of the major change in this time frame as >>>> you >>>>> noticed. >>>>> If these jobs are easy to run, could you check that the old and new >>>>> versions are similar with "-pc_gamg_square_graph 0 ", ( and you only >>>> need >>>>> one time step). >>>>> All you need to do is check that the first coarse grid has about the >>>> same >>>>> number of equations (large). >>>> Unfortunately we're seeing some memory errors when we use this option, >>>> and I'm not entirely clear whether we're just running out of memory and >>>> need to put it on a special queue. >>>> >>>> The run with square_graph 0 using new PETSc managed to get through one >>>> solve at level 5, and is giving the following mg levels: >>>> >>>> rows=174, cols=174, bs=6 >>>> total: nonzeros=30276, allocated nonzeros=30276 >>>> -- >>>> rows=2106, cols=2106, bs=6 >>>> total: nonzeros=4238532, allocated nonzeros=4238532 >>>> -- >>>> rows=21828, cols=21828, bs=6 >>>> total: nonzeros=62588232, allocated nonzeros=62588232 >>>> -- >>>> rows=589824, cols=589824, bs=6 >>>> total: nonzeros=1082528928, allocated nonzeros=1082528928 >>>> -- >>>> rows=2433222, cols=2433222, bs=3 >>>> total: nonzeros=456526098, allocated nonzeros=456526098 >>>> >>>> comparing with square_graph 100 with new PETSc >>>> >>>> rows=96, cols=96, bs=6 >>>> total: nonzeros=9216, allocated nonzeros=9216 >>>> -- >>>> rows=1440, cols=1440, bs=6 >>>> total: nonzeros=647856, allocated nonzeros=647856 >>>> -- >>>> rows=97242, cols=97242, bs=6 >>>> total: nonzeros=65656836, allocated nonzeros=65656836 >>>> -- >>>> rows=2433222, cols=2433222, bs=3 >>>> total: nonzeros=456526098, allocated nonzeros=456526098 >>>> >>>> and old PETSc with square_graph 100 >>>> >>>> rows=90, cols=90, bs=6 >>>> total: nonzeros=8100, allocated nonzeros=8100 >>>> -- >>>> rows=1872, cols=1872, bs=6 >>>> total: nonzeros=1234080, allocated nonzeros=1234080 >>>> -- >>>> rows=47652, cols=47652, bs=6 >>>> total: nonzeros=23343264, allocated nonzeros=23343264 >>>> -- >>>> rows=2433222, cols=2433222, bs=3 >>>> total: nonzeros=456526098, allocated nonzeros=456526098 >>>> -- >>>> >>>> Unfortunately old PETSc with square_graph 0 did not complete a single >>>> solve before giving the memory error >>>> >>> OK, thanks for trying. >>> >>> I am working on this and I will give you a branch to test, but if you can >>> rebuild PETSc here is a quick test that might fix your problem. >>> In src/ksp/pc/impls/gamg/agg.c you will see: >>> >>> PetscCall(PetscSortIntWithArray(nloc, degree, permute)); >>> >>> If you can comment this out in the new code and compare with the old, >>> that might fix the problem. >>> >>> Thanks, >>> Mark >>> >>> >>>>> BTW, I am starting to think I should add the old method back as an >>>> option. >>>>> I did not think this change would cause large differences. >>>> Yes, I think that would be much appreciated. Let us know if we can do >>>> any testing >>>> >>>> Best wishes >>>> Stephan >>>> >>>> >>>>> Thanks, >>>>> Mark >>>>> >>>>> >>>>> >>>>> >>>>>> Note that we are providing the rigid body near nullspace, >>>>>> hence the bs=3 to bs=6. >>>>>> We have tried different values for the gamg_threshold but it doesn't >>>>>> really seem to significantly alter the coarsening amount in that first >>>>>> step. >>>>>> >>>>>> Do you have any suggestions for further things we should try/look at? >>>>>> Any feedback would be much appreciated >>>>>> >>>>>> Best wishes >>>>>> Stephan Kramer >>>>>> >>>>>> Full logs including log_view timings available from >>>>>> https://github.com/stephankramer/petsc-scaling/ >>>>>> >>>>>> In particular: >>>>>> >>>>>> >>>>>> >>>> https://github.com/stephankramer/petsc-scaling/blob/main/before/Level_5/output_2.dat >>>>>> >>>> https://github.com/stephankramer/petsc-scaling/blob/main/after/Level_5/output_2.dat >>>>>> >>>> https://github.com/stephankramer/petsc-scaling/blob/main/before/Level_6/output_2.dat >>>>>> >>>> https://github.com/stephankramer/petsc-scaling/blob/main/after/Level_6/output_2.dat >>>>>> >>>> https://github.com/stephankramer/petsc-scaling/blob/main/before/Level_7/output_2.dat >>>>>> >>>> https://github.com/stephankramer/petsc-scaling/blob/main/after/Level_7/output_2.dat >>>>>> >>>> From gsosajones at oakland.edu Fri Sep 1 07:26:53 2023 From: gsosajones at oakland.edu (Giselle Sosa Jones) Date: Fri, 1 Sep 2023 08:26:53 -0400 Subject: [petsc-users] Configuring PETSc on Mac M1 Message-ID: Hello, I am trying to install PETSc on my M1 Mac and I keep encountering the following error when configuring: Unknown Fortran name mangling: Are you sure the C and Fortran compilers are compatible? Perhaps one is 64 bit and one is 32 bit? Any ideas on how to fix this? All my compilers are 64 bit. I am using gfortran and gcc (installed with brew). Thank you in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Fri Sep 1 08:58:12 2023 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 1 Sep 2023 09:58:12 -0400 Subject: [petsc-users] Configuring PETSc on Mac M1 In-Reply-To: References: Message-ID: You need to send us configure.log so that we can see what the failure message is. Thanks, Matt On Fri, Sep 1, 2023 at 9:56?AM Giselle Sosa Jones wrote: > Hello, > > I am trying to install PETSc on my M1 Mac and I keep encountering the > following error when configuring: > > Unknown Fortran name mangling: Are you sure the C and Fortran compilers > are compatible? > > Perhaps one is 64 bit and one is 32 bit? > > > Any ideas on how to fix this? All my compilers are 64 bit. I am using > gfortran and gcc (installed with brew). > > Thank you in advance. > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Sep 1 09:00:46 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 1 Sep 2023 09:00:46 -0500 (CDT) Subject: [petsc-users] Configuring PETSc on Mac M1 In-Reply-To: References: Message-ID: please send the correspond configure.log for this failure - perhaps to petsc-maint [to avoid sending large files to petsc-users mailing list] BTW: We normally use xcode clang/clang++ with brew gfortran (with system blas/lapack) for MacOS builds Satish On Fri, 1 Sep 2023, Giselle Sosa Jones wrote: > Hello, > > I am trying to install PETSc on my M1 Mac and I keep encountering the > following error when configuring: > > Unknown Fortran name mangling: Are you sure the C and Fortran compilers are > compatible? > > Perhaps one is 64 bit and one is 32 bit? > > > Any ideas on how to fix this? All my compilers are 64 bit. I am using > gfortran and gcc (installed with brew). > > Thank you in advance. > From mail2amneet at gmail.com Fri Sep 1 09:18:46 2023 From: mail2amneet at gmail.com (Amneet Bhalla) Date: Fri, 1 Sep 2023 07:18:46 -0700 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> Message-ID: Hi Srinivas, As discussed earlier you don?t need libMesh for the WEC application. You can just work with PETSc 3.17.5 that builds with Matlab. Do you have a specific reason for wanting to build libMesh? Thanks, ?Amneet On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via petsc-users < petsc-users at mcs.anl.gov> wrote: > Hi, > > I ran "make all" for petsc 3.13.4 by removing all occurrences of "-lut > -licudata -licui18n -licuuc". When I ran "make test" got the following > errors > in petsc/3.13.4/linux-debug: > TEST > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named MB108SMEC028 by > vit Fri Sep 1 10:01:11 2023 > # [0]PETSC ERROR: Configure options > --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 > --download-hypre=1 --download-fblaslapack=1 --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # > -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 126076. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # > -------------------------------------------------------------------------- > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed > so no diff > > in petsc/3.13.4/linux-opt > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > vit Fri Sep 1 10:34:12 2023 > # [0]PETSC ERROR: Configure options > --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 > --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt --with-debugging=0 > --download-hypre=1 --with-x=0 --download-fblaslapack=1 > --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # > -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 126076. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # > -------------------------------------------------------------------------- > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed > so no diff. > > The same errors occurred for petsc 3.17.5 version. I am sharing the > config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. Please find > the attachment and do the needful. > > Thanks and regards > Srinivas > > On Tue, Aug 29, 2023 at 10:56?PM Satish Balay wrote: > >> Well - you sent in libmesh log not petsc's configure.log/make.log for >> petsc-3.17 >> >> Anyway - with petsc-3.13 - you have: >> >> >>>> >> >> Matlab: >> Includes: -I/usr/local/MATLAB/R2020b/extern/include >> /usr/local/MATLAB/R2020b >> MatlabEngine: >> Library: >> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut >> -licudata -licui18n -licuuc >> Language used to compile PETSc: C >> <<<<< >> >> With petsc-3.19 (and matlab-R2022a) - we are seeing: >> >> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >> >> >>> >> Matlab: >> Includes: >> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >> Libraries: >> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >> -leng -lmex -lmx -lmat >> Executable: >> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >> mex: >> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >> matlab: >> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >> -glnxa64 >> <<< >> >> I.e "-lut -licudata -licui18n -licuuc" are not preset here. This might be >> a change wrt newer matlab versions. >> >> You can: >> >> - edit /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >> and remove all occurrences of "-lut -licudata -licui18n -licuuc" >> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' >> >> And see if the build works now. >> >> Satish >> >> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >> >> > I am sharing the log files while building petsc3.13.4 with matlab and >> also >> > the log file while building libmesh with petsc3.17.5 and matlab. >> Building >> > petsc 3.17.5 with matlab was done successfully. But libmesh is not able >> to >> > find the petsc >> > Please find the attachments. >> > >> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay wrote: >> > >> > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or 3.19]. >> > > >> > > [you can gzip them to make the logs friendly to mailing list - or send >> > > them to petsc-maint] >> > > >> > > And does test suite work with 3.17? [or 3.19?] >> > > >> > > Satish >> > > >> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >> > > >> > > > I am sharing the make.log file while building petsc-3.13.4 with >> Matlab. >> > > > Please find the attachment and do the needful. >> > > > >> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < >> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >> > > > >> > > > > I tried with petsc-3.17.5. During building of libmesh, the error >> shows >> > > > > petsc was not found >> > > > > >> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay >> > > wrote: >> > > > > >> > > > >> https://ibamr.github.io/linux says petsc-3.17 >> > > > >> >> > > > >> Here you are using 3.13 >> > > > >> >> > > > >> Can you retry with petsc-3.17.5? >> > > > >> >> > > > >> Satish >> > > > >> >> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >> wrote: >> > > > >> >> > > > >> > Hello, >> > > > >> > >> > > > >> > I want to build PETSc with MATLAB for working on the simulation >> > > using >> > > > >> IBAMR >> > > > >> > open software. While building the PETSc, using the following >> > > > >> > >> > > > >> > export PETSC_DIR=$PWD >> > > > >> > export PETSC_ARCH=linux-debug >> > > > >> > ./configure \ >> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >> > > > >> > --with-debugging=1 \ >> > > > >> > --download-hypre=1 \ >> > > > >> > --download-fblaslapack=1 \ >> > > > >> > --with-x=0 \ >> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ >> > > > >> > --with-matlab-engine=1 >> > > > >> > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >> > > > >> > >> > > > >> > make -j4 >> > > > >> > make -j4 test >> > > > >> > >> > > > >> > I got the following error >> > > > >> > CLINKER >> > > > >> >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: >> in >> > > > >> > function `EvaluateResidual': >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >> > > > >> > undefined reference to `PetscMatlabEnginePut' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >> > > > >> > undefined reference to `PetscMatlabEngineGet' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: >> in >> > > > >> > function `EvaluateJacobian': >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >> > > > >> > undefined reference to `PetscMatlabEnginePut' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >> > > > >> > undefined reference to `PetscMatlabEngineGet' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: >> in >> > > > >> > function `TaoPounders': >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >> > > > >> > undefined reference to `PetscMatlabEngineGet' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: >> in >> > > > >> > function `main': >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >> > > > >> > undefined reference to `PetscMatlabEngineCreate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >> > > > >> > /usr/bin/ld: >> > > > >> > >> > > > >> >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >> > > > >> > undefined reference to `PetscMatlabEngineDestroy' >> > > > >> > >> > > > >> > collect2: error: ld returned 1 exit status >> > > > >> > make: *** [gmakefile.test:185: >> > > > >> > >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >> > > > >> Error 1 >> > > > >> > make: *** Waiting for unfinished jobs.... >> > > > >> > >> > > > >> > Please help me to solve this issue >> > > > >> > >> > > > >> > Thank you >> > > > >> > Srinivas >> > > > >> > >> > > > >> > >> > > > >> >> > > > >> >> > > > >> > > > >> > > >> > >> > >> > > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Fri Sep 1 09:49:43 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Fri, 1 Sep 2023 20:19:43 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> Message-ID: Hi Amneet, Without libmesh, even for PETSc with MATLAB is not working. It is showing error for both 3.13.4 and 3.17.5 versions. I am trying to install IBAMR in HPC cluster with libmesh and this is for general usage not only for WEC. This I tried without linking Matlab with PETSc. Here also I got the error while configuring libmesh 1.6.2 that PETSc was not found but --enable-petsc-required is specified. The reason for specifically asking for libmesh with PETSc and Matlab is in the cfd-mpc-wecs application for complicated geometries it is mentioned to build cfd-mpc-wecs with libmesh construct. For the past 10 days I am trying these various things and ended up with errors. I want to solve this and proceed further to do my research work. Please help me to solve this as soon as possible. Thanks and Regards Srinivas On Fri, Sep 1, 2023, 19:48 Amneet Bhalla wrote: > Hi Srinivas, > > As discussed earlier you don?t need libMesh for the WEC application. You > can just work with PETSc 3.17.5 that builds with Matlab. > > Do you have a specific reason for wanting to build libMesh? > > Thanks, > ?Amneet > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > >> Hi, >> >> I ran "make all" for petsc 3.13.4 by removing all occurrences of "-lut >> -licudata -licui18n -licuuc". When I ran "make test" got the following >> errors >> in petsc/3.13.4/linux-debug: >> TEST >> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >> # Running problem 5 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Error in external library >> # [0]PETSC ERROR: Unable to start MATLAB engine on >> # [0]PETSC ERROR: See >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named MB108SMEC028 >> by vit Fri Sep 1 10:01:11 2023 >> # [0]PETSC ERROR: Configure options >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >> # [0]PETSC ERROR: #2 main() line 126 in >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -prob_id 5 >> # [0]PETSC ERROR: -tao_smonitor >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >> # with errorcode 126076. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >> failed so no diff >> >> in petsc/3.13.4/linux-opt >> TEST >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >> # Running problem 5 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Error in external library >> # [0]PETSC ERROR: Unable to start MATLAB engine on >> # [0]PETSC ERROR: See >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >> vit Fri Sep 1 10:34:12 2023 >> # [0]PETSC ERROR: Configure options >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt --with-debugging=0 >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >> # [0]PETSC ERROR: #2 main() line 126 in >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -prob_id 5 >> # [0]PETSC ERROR: -tao_smonitor >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >> # with errorcode 126076. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >> failed so no diff. >> >> The same errors occurred for petsc 3.17.5 version. I am sharing the >> config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. Please find >> the attachment and do the needful. >> >> Thanks and regards >> Srinivas >> >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay wrote: >> >>> Well - you sent in libmesh log not petsc's configure.log/make.log for >>> petsc-3.17 >>> >>> Anyway - with petsc-3.13 - you have: >>> >>> >>>> >>> >>> Matlab: >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> /usr/local/MATLAB/R2020b >>> MatlabEngine: >>> Library: >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut >>> -licudata -licui18n -licuuc >>> Language used to compile PETSc: C >>> <<<<< >>> >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: >>> >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> >>> >>> >>> Matlab: >>> Includes: >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>> Libraries: >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> -leng -lmex -lmx -lmat >>> Executable: >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>> mex: >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>> matlab: >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>> -glnxa64 >>> <<< >>> >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. This might >>> be a change wrt newer matlab versions. >>> >>> You can: >>> >>> - edit >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables and >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' >>> >>> And see if the build works now. >>> >>> Satish >>> >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>> >>> > I am sharing the log files while building petsc3.13.4 with matlab and >>> also >>> > the log file while building libmesh with petsc3.17.5 and matlab. >>> Building >>> > petsc 3.17.5 with matlab was done successfully. But libmesh is not >>> able to >>> > find the petsc >>> > Please find the attachments. >>> > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay >>> wrote: >>> > >>> > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or 3.19]. >>> > > >>> > > [you can gzip them to make the logs friendly to mailing list - or >>> send >>> > > them to petsc-maint] >>> > > >>> > > And does test suite work with 3.17? [or 3.19?] >>> > > >>> > > Satish >>> > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>> > > >>> > > > I am sharing the make.log file while building petsc-3.13.4 with >>> Matlab. >>> > > > Please find the attachment and do the needful. >>> > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> > > > >>> > > > > I tried with petsc-3.17.5. During building of libmesh, the error >>> shows >>> > > > > petsc was not found >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay >>> > > wrote: >>> > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 >>> > > > >> >>> > > > >> Here you are using 3.13 >>> > > > >> >>> > > > >> Can you retry with petsc-3.17.5? >>> > > > >> >>> > > > >> Satish >>> > > > >> >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>> wrote: >>> > > > >> >>> > > > >> > Hello, >>> > > > >> > >>> > > > >> > I want to build PETSc with MATLAB for working on the >>> simulation >>> > > using >>> > > > >> IBAMR >>> > > > >> > open software. While building the PETSc, using the following >>> > > > >> > >>> > > > >> > export PETSC_DIR=$PWD >>> > > > >> > export PETSC_ARCH=linux-debug >>> > > > >> > ./configure \ >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>> > > > >> > --with-debugging=1 \ >>> > > > >> > --download-hypre=1 \ >>> > > > >> > --download-fblaslapack=1 \ >>> > > > >> > --with-x=0 \ >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > > >> > --with-matlab-engine=1 >>> > > > >> > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > >> > >>> > > > >> > make -j4 >>> > > > >> > make -j4 test >>> > > > >> > >>> > > > >> > I got the following error >>> > > > >> > CLINKER >>> > > > >> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >> > function `EvaluateResidual': >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>> > > > >> > undefined reference to `PetscMatlabEnginePut' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>> > > > >> > undefined reference to `PetscMatlabEngineGet' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >> > function `EvaluateJacobian': >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>> > > > >> > undefined reference to `PetscMatlabEnginePut' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>> > > > >> > undefined reference to `PetscMatlabEngineGet' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >> > function `TaoPounders': >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>> > > > >> > undefined reference to `PetscMatlabEngineGet' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >> > function `main': >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > >> > /usr/bin/ld: >>> > > > >> > >>> > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' >>> > > > >> > >>> > > > >> > collect2: error: ld returned 1 exit status >>> > > > >> > make: *** [gmakefile.test:185: >>> > > > >> > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>> > > > >> Error 1 >>> > > > >> > make: *** Waiting for unfinished jobs.... >>> > > > >> > >>> > > > >> > Please help me to solve this issue >>> > > > >> > >>> > > > >> > Thank you >>> > > > >> > Srinivas >>> > > > >> > >>> > > > >> > >>> > > > >> >>> > > > >> >>> > > > >>> > > > >>> > > >>> > >>> > >>> >> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Sep 1 10:08:27 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 1 Sep 2023 10:08:27 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> Message-ID: <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Here is the matlab test that runs in CI https://gitlab.com/petsc/petsc/-/jobs/4904566768 config/examples/arch-ci-linux-matlab-ilp64.py # Note: regular BLAS [with 32-bit integers] conflict with # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 Ah - so you need to use the ilp64 blas/lapack with matlab - to have a compatible build '--with-blaslapack-dir='+matlab_dir, Satish On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > Hi Amneet, > > Without libmesh, even for PETSc with MATLAB is not working. It is showing > error for both 3.13.4 and 3.17.5 versions. > > I am trying to install IBAMR in HPC cluster with libmesh and this is for > general usage not only for WEC. This I tried without linking Matlab with > PETSc. Here also I got the error while configuring libmesh 1.6.2 that PETSc > was not found but --enable-petsc-required is specified. > > The reason for specifically asking for libmesh with PETSc and Matlab is in > the cfd-mpc-wecs application for complicated geometries it is mentioned to > build cfd-mpc-wecs with libmesh construct. > > For the past 10 days I am trying these various things and ended up with > errors. > I want to solve this and proceed further to do my research work. > > Please help me to solve this as soon as possible. > > > Thanks and Regards > Srinivas > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla wrote: > > > Hi Srinivas, > > > > As discussed earlier you don?t need libMesh for the WEC application. You > > can just work with PETSc 3.17.5 that builds with Matlab. > > > > Do you have a specific reason for wanting to build libMesh? > > > > Thanks, > > ?Amneet > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via petsc-users > > wrote: > > > >> Hi, > >> > >> I ran "make all" for petsc 3.13.4 by removing all occurrences of "-lut > >> -licudata -licui18n -licuuc". When I ran "make test" got the following > >> errors > >> in petsc/3.13.4/linux-debug: > >> TEST > >> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > >> # Running problem 5 > >> # [0]PETSC ERROR: --------------------- Error Message > >> -------------------------------------------------------------- > >> # [0]PETSC ERROR: Error in external library > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > >> # [0]PETSC ERROR: See > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > >> shooting. > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named MB108SMEC028 > >> by vit Fri Sep 1 10:01:11 2023 > >> # [0]PETSC ERROR: Configure options > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >> # [0]PETSC ERROR: #2 main() line 126 in > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >> # [0]PETSC ERROR: PETSc Option Table entries: > >> # [0]PETSC ERROR: -prob_id 5 > >> # [0]PETSC ERROR: -tao_smonitor > >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire > >> error message to petsc-maint at mcs.anl.gov---------- > >> # > >> -------------------------------------------------------------------------- > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >> # with errorcode 126076. > >> # > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >> # You may or may not see output from other processes, depending on > >> # exactly when Open MPI kills them. > >> # > >> -------------------------------------------------------------------------- > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > >> failed so no diff > >> > >> in petsc/3.13.4/linux-opt > >> TEST > >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > >> # Running problem 5 > >> # [0]PETSC ERROR: --------------------- Error Message > >> -------------------------------------------------------------- > >> # [0]PETSC ERROR: Error in external library > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > >> # [0]PETSC ERROR: See > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > >> shooting. > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > >> vit Fri Sep 1 10:34:12 2023 > >> # [0]PETSC ERROR: Configure options > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt --with-debugging=0 > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >> # [0]PETSC ERROR: #2 main() line 126 in > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >> # [0]PETSC ERROR: PETSc Option Table entries: > >> # [0]PETSC ERROR: -prob_id 5 > >> # [0]PETSC ERROR: -tao_smonitor > >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire > >> error message to petsc-maint at mcs.anl.gov---------- > >> # > >> -------------------------------------------------------------------------- > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >> # with errorcode 126076. > >> # > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >> # You may or may not see output from other processes, depending on > >> # exactly when Open MPI kills them. > >> # > >> -------------------------------------------------------------------------- > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > >> failed so no diff. > >> > >> The same errors occurred for petsc 3.17.5 version. I am sharing the > >> config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. Please find > >> the attachment and do the needful. > >> > >> Thanks and regards > >> Srinivas > >> > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay wrote: > >> > >>> Well - you sent in libmesh log not petsc's configure.log/make.log for > >>> petsc-3.17 > >>> > >>> Anyway - with petsc-3.13 - you have: > >>> > >>> >>>> > >>> > >>> Matlab: > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > >>> /usr/local/MATLAB/R2020b > >>> MatlabEngine: > >>> Library: > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut > >>> -licudata -licui18n -licuuc > >>> Language used to compile PETSc: C > >>> <<<<< > >>> > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > >>> > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>> > >>> >>> > >>> Matlab: > >>> Includes: > >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > >>> Libraries: > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>> -leng -lmex -lmx -lmat > >>> Executable: > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > >>> mex: > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > >>> matlab: > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > >>> -glnxa64 > >>> <<< > >>> > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. This might > >>> be a change wrt newer matlab versions. > >>> > >>> You can: > >>> > >>> - edit > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables and > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > >>> > >>> And see if the build works now. > >>> > >>> Satish > >>> > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > >>> > >>> > I am sharing the log files while building petsc3.13.4 with matlab and > >>> also > >>> > the log file while building libmesh with petsc3.17.5 and matlab. > >>> Building > >>> > petsc 3.17.5 with matlab was done successfully. But libmesh is not > >>> able to > >>> > find the petsc > >>> > Please find the attachments. > >>> > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay > >>> wrote: > >>> > > >>> > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or 3.19]. > >>> > > > >>> > > [you can gzip them to make the logs friendly to mailing list - or > >>> send > >>> > > them to petsc-maint] > >>> > > > >>> > > And does test suite work with 3.17? [or 3.19?] > >>> > > > >>> > > Satish > >>> > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > >>> > > > >>> > > > I am sharing the make.log file while building petsc-3.13.4 with > >>> Matlab. > >>> > > > Please find the attachment and do the needful. > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of libmesh, the error > >>> shows > >>> > > > > petsc was not found > >>> > > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay > >>> > > wrote: > >>> > > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > >>> > > > >> > >>> > > > >> Here you are using 3.13 > >>> > > > >> > >>> > > > >> Can you retry with petsc-3.17.5? > >>> > > > >> > >>> > > > >> Satish > >>> > > > >> > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > >>> wrote: > >>> > > > >> > >>> > > > >> > Hello, > >>> > > > >> > > >>> > > > >> > I want to build PETSc with MATLAB for working on the > >>> simulation > >>> > > using > >>> > > > >> IBAMR > >>> > > > >> > open software. While building the PETSc, using the following > >>> > > > >> > > >>> > > > >> > export PETSC_DIR=$PWD > >>> > > > >> > export PETSC_ARCH=linux-debug > >>> > > > >> > ./configure \ > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > >>> > > > >> > --with-debugging=1 \ > >>> > > > >> > --download-hypre=1 \ > >>> > > > >> > --download-fblaslapack=1 \ > >>> > > > >> > --with-x=0 \ > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>> > > > >> > --with-matlab-engine=1 > >>> > > > >> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>> > > > >> > > >>> > > > >> > make -j4 > >>> > > > >> > make -j4 test > >>> > > > >> > > >>> > > > >> > I got the following error > >>> > > > >> > CLINKER > >>> > > > >> > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > >> > function `EvaluateResidual': > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > >> > function `EvaluateJacobian': > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > >> > function `TaoPounders': > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > >> > function `main': > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > >> > /usr/bin/ld: > >>> > > > >> > > >>> > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > >>> > > > >> > > >>> > > > >> > collect2: error: ld returned 1 exit status > >>> > > > >> > make: *** [gmakefile.test:185: > >>> > > > >> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > >>> > > > >> Error 1 > >>> > > > >> > make: *** Waiting for unfinished jobs.... > >>> > > > >> > > >>> > > > >> > Please help me to solve this issue > >>> > > > >> > > >>> > > > >> > Thank you > >>> > > > >> > Srinivas > >>> > > > >> > > >>> > > > >> > > >>> > > > >> > >>> > > > >> > >>> > > > > >>> > > > > >>> > > > >>> > > >>> > > >>> > >> > >> > >> *Disclaimer:This message was sent from Vellore Institute of Technology. > >> The contents of this email may contain legally protected confidential or > >> privileged information of ?Vellore Institute of Technology?. If you are > >> not the intended recipient, you should not disseminate, distribute or copy > >> this e-mail. Please notify the sender immediately and destroy all copies of > >> this message and any attachments. If you have received this email in error, > >> please promptly notify the sender by reply email and delete the original > >> email and any backup copies without reading them.* > >> > > > > From balay at mcs.anl.gov Fri Sep 1 10:12:43 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 1 Sep 2023 10:12:43 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Message-ID: Also: '-known-64-bit-blas-indices=1', Note: most externalpackages might not work in this mode. [we can't really over come such dependency/conflicts across packages] Satish On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > Here is the matlab test that runs in CI > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > config/examples/arch-ci-linux-matlab-ilp64.py > > # Note: regular BLAS [with 32-bit integers] conflict with > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > Ah - so you need to use the ilp64 blas/lapack with matlab - to have a compatible build > > '--with-blaslapack-dir='+matlab_dir, > > Satish > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > Hi Amneet, > > > > Without libmesh, even for PETSc with MATLAB is not working. It is showing > > error for both 3.13.4 and 3.17.5 versions. > > > > I am trying to install IBAMR in HPC cluster with libmesh and this is for > > general usage not only for WEC. This I tried without linking Matlab with > > PETSc. Here also I got the error while configuring libmesh 1.6.2 that PETSc > > was not found but --enable-petsc-required is specified. > > > > The reason for specifically asking for libmesh with PETSc and Matlab is in > > the cfd-mpc-wecs application for complicated geometries it is mentioned to > > build cfd-mpc-wecs with libmesh construct. > > > > For the past 10 days I am trying these various things and ended up with > > errors. > > I want to solve this and proceed further to do my research work. > > > > Please help me to solve this as soon as possible. > > > > > > Thanks and Regards > > Srinivas > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla wrote: > > > > > Hi Srinivas, > > > > > > As discussed earlier you don?t need libMesh for the WEC application. You > > > can just work with PETSc 3.17.5 that builds with Matlab. > > > > > > Do you have a specific reason for wanting to build libMesh? > > > > > > Thanks, > > > ?Amneet > > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via petsc-users > > > wrote: > > > > > >> Hi, > > >> > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences of "-lut > > >> -licudata -licui18n -licuuc". When I ran "make test" got the following > > >> errors > > >> in petsc/3.13.4/linux-debug: > > >> TEST > > >> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > > >> # Running problem 5 > > >> # [0]PETSC ERROR: --------------------- Error Message > > >> -------------------------------------------------------------- > > >> # [0]PETSC ERROR: Error in external library > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > >> # [0]PETSC ERROR: See > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > >> shooting. > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named MB108SMEC028 > > >> by vit Fri Sep 1 10:01:11 2023 > > >> # [0]PETSC ERROR: Configure options > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >> # [0]PETSC ERROR: #2 main() line 126 in > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > >> # [0]PETSC ERROR: -prob_id 5 > > >> # [0]PETSC ERROR: -tao_smonitor > > >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire > > >> error message to petsc-maint at mcs.anl.gov---------- > > >> # > > >> -------------------------------------------------------------------------- > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > >> # with errorcode 126076. > > >> # > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > >> # You may or may not see output from other processes, depending on > > >> # exactly when Open MPI kills them. > > >> # > > >> -------------------------------------------------------------------------- > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > >> failed so no diff > > >> > > >> in petsc/3.13.4/linux-opt > > >> TEST > > >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > > >> # Running problem 5 > > >> # [0]PETSC ERROR: --------------------- Error Message > > >> -------------------------------------------------------------- > > >> # [0]PETSC ERROR: Error in external library > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > >> # [0]PETSC ERROR: See > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > >> shooting. > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > > >> vit Fri Sep 1 10:34:12 2023 > > >> # [0]PETSC ERROR: Configure options > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt --with-debugging=0 > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >> # [0]PETSC ERROR: #2 main() line 126 in > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > >> # [0]PETSC ERROR: -prob_id 5 > > >> # [0]PETSC ERROR: -tao_smonitor > > >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire > > >> error message to petsc-maint at mcs.anl.gov---------- > > >> # > > >> -------------------------------------------------------------------------- > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > >> # with errorcode 126076. > > >> # > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > >> # You may or may not see output from other processes, depending on > > >> # exactly when Open MPI kills them. > > >> # > > >> -------------------------------------------------------------------------- > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > >> failed so no diff. > > >> > > >> The same errors occurred for petsc 3.17.5 version. I am sharing the > > >> config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. Please find > > >> the attachment and do the needful. > > >> > > >> Thanks and regards > > >> Srinivas > > >> > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay wrote: > > >> > > >>> Well - you sent in libmesh log not petsc's configure.log/make.log for > > >>> petsc-3.17 > > >>> > > >>> Anyway - with petsc-3.13 - you have: > > >>> > > >>> >>>> > > >>> > > >>> Matlab: > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > >>> /usr/local/MATLAB/R2020b > > >>> MatlabEngine: > > >>> Library: > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut > > >>> -licudata -licui18n -licuuc > > >>> Language used to compile PETSc: C > > >>> <<<<< > > >>> > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > >>> > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > >>> > > >>> >>> > > >>> Matlab: > > >>> Includes: > > >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > >>> Libraries: > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > >>> -leng -lmex -lmx -lmat > > >>> Executable: > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > >>> mex: > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > >>> matlab: > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > >>> -glnxa64 > > >>> <<< > > >>> > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. This might > > >>> be a change wrt newer matlab versions. > > >>> > > >>> You can: > > >>> > > >>> - edit > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables and > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > >>> > > >>> And see if the build works now. > > >>> > > >>> Satish > > >>> > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > >>> > > >>> > I am sharing the log files while building petsc3.13.4 with matlab and > > >>> also > > >>> > the log file while building libmesh with petsc3.17.5 and matlab. > > >>> Building > > >>> > petsc 3.17.5 with matlab was done successfully. But libmesh is not > > >>> able to > > >>> > find the petsc > > >>> > Please find the attachments. > > >>> > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay > > >>> wrote: > > >>> > > > >>> > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or 3.19]. > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to mailing list - or > > >>> send > > >>> > > them to petsc-maint] > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > >>> > > > > >>> > > Satish > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > >>> > > > > >>> > > > I am sharing the make.log file while building petsc-3.13.4 with > > >>> Matlab. > > >>> > > > Please find the attachment and do the needful. > > >>> > > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > >>> > > > > > >>> > > > > I tried with petsc-3.17.5. During building of libmesh, the error > > >>> shows > > >>> > > > > petsc was not found > > >>> > > > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay > > >>> > > wrote: > > >>> > > > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > >>> > > > >> > > >>> > > > >> Here you are using 3.13 > > >>> > > > >> > > >>> > > > >> Can you retry with petsc-3.17.5? > > >>> > > > >> > > >>> > > > >> Satish > > >>> > > > >> > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > >>> wrote: > > >>> > > > >> > > >>> > > > >> > Hello, > > >>> > > > >> > > > >>> > > > >> > I want to build PETSc with MATLAB for working on the > > >>> simulation > > >>> > > using > > >>> > > > >> IBAMR > > >>> > > > >> > open software. While building the PETSc, using the following > > >>> > > > >> > > > >>> > > > >> > export PETSC_DIR=$PWD > > >>> > > > >> > export PETSC_ARCH=linux-debug > > >>> > > > >> > ./configure \ > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > >>> > > > >> > --with-debugging=1 \ > > >>> > > > >> > --download-hypre=1 \ > > >>> > > > >> > --download-fblaslapack=1 \ > > >>> > > > >> > --with-x=0 \ > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>> > > > >> > --with-matlab-engine=1 > > >>> > > > >> > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>> > > > >> > > > >>> > > > >> > make -j4 > > >>> > > > >> > make -j4 test > > >>> > > > >> > > > >>> > > > >> > I got the following error > > >>> > > > >> > CLINKER > > >>> > > > >> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > >> > function `EvaluateResidual': > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > >> > function `EvaluateJacobian': > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > >> > function `TaoPounders': > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > >> > function `main': > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > >> > /usr/bin/ld: > > >>> > > > >> > > > >>> > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > > >>> > > > >> > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > >>> > > > >> > make: *** [gmakefile.test:185: > > >>> > > > >> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > >>> > > > >> Error 1 > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > >>> > > > >> > > > >>> > > > >> > Please help me to solve this issue > > >>> > > > >> > > > >>> > > > >> > Thank you > > >>> > > > >> > Srinivas > > >>> > > > >> > > > >>> > > > >> > > > >>> > > > >> > > >>> > > > >> > > >>> > > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > >>> > > >> > > >> > > >> *Disclaimer:This message was sent from Vellore Institute of Technology. > > >> The contents of this email may contain legally protected confidential or > > >> privileged information of ?Vellore Institute of Technology?. If you are > > >> not the intended recipient, you should not disseminate, distribute or copy > > >> this e-mail. Please notify the sender immediately and destroy all copies of > > >> this message and any attachments. If you have received this email in error, > > >> please promptly notify the sender by reply email and delete the original > > >> email and any backup copies without reading them.* > > >> > > > > > > > > From mfadams at lbl.gov Fri Sep 1 10:58:39 2023 From: mfadams at lbl.gov (Mark Adams) Date: Fri, 1 Sep 2023 11:58:39 -0400 Subject: [petsc-users] performance regression with GAMG In-Reply-To: <99896e04-7ac2-9e92-0922-e78f2d0c710d@imperial.ac.uk> References: <9716433a-7aa0-9284-141f-a1e2fccb310e@imperial.ac.uk> <99896e04-7ac2-9e92-0922-e78f2d0c710d@imperial.ac.uk> Message-ID: Fantastic! I fixed a memory free problem. You should be OK now. I am pretty sure you are good but I would like to wait to get any feedback from you. We should have a release at the end of the month and it would be nice to get this into it. Thanks, Mark On Fri, Sep 1, 2023 at 7:07?AM Stephan Kramer wrote: > Hi Mark > > Sorry took a while to report back. We have tried your branch but hit a > few issues, some of which we're not entirely sure are related. > > First switching off minimum degree ordering, and then switching to the > old version of aggressive coarsening, as you suggested, got us back to > the coarsening behaviour that we had previously, but then we also > observed an even further worsening of the iteration count: it had > previously gone up by 50% already (with the newer main petsc), but now > was more than double "old" petsc. Took us a while to realize this was > due to the default smoother changing from Cheby+SOR to Cheby+Jacobi. > Switching this also back to the old default we get back to very similar > coarsening levels (see below for more details if it is of interest) and > iteration counts. > > So that's all very good news. However, we were also starting seeing > memory errors (double free or corruption) when we switched off the > minimum degree ordering. Because this was at an earlier version of your > branch we then rebuild, hoping this was just an earlier bug that had > been fixed, but then we were having MPI-lockup issues. We have now > figured out the MPI issues are completely unrelated - some combination > with a newer mpi build and firedrake on our cluster which also occur > using main branches of everything. So switching back to an older MPI > build we are hoping to now test your most recent version of > adams/gamg-add-old-coarsening with these options and see whether the > memory errors are still there. Will let you know > > Best wishes > Stephan Kramer > > Coarsening details with various options for Level 6 of the test case: > > In our original setup (using "old" petsc), we had: > > rows=516, cols=516, bs=6 > rows=12660, cols=12660, bs=6 > rows=346974, cols=346974, bs=6 > rows=19169670, cols=19169670, bs=3 > > Then with the newer main petsc we had > > rows=666, cols=666, bs=6 > rows=7740, cols=7740, bs=6 > rows=34902, cols=34902, bs=6 > rows=736578, cols=736578, bs=6 > rows=19169670, cols=19169670, bs=3 > > Then on your branch with minimum_degree_ordering False: > > rows=504, cols=504, bs=6 > rows=2274, cols=2274, bs=6 > rows=11010, cols=11010, bs=6 > rows=35790, cols=35790, bs=6 > rows=430686, cols=430686, bs=6 > rows=19169670, cols=19169670, bs=3 > > And with minimum_degree_ordering False and use_aggressive_square_graph > True: > > rows=498, cols=498, bs=6 > rows=12672, cols=12672, bs=6 > rows=346974, cols=346974, bs=6 > rows=19169670, cols=19169670, bs=3 > > So that is indeed pretty much back to what it was before > > > > > > > > > On 31/08/2023 23:40, Mark Adams wrote: > > Hi Stephan, > > > > This branch is settling down. adams/gamg-add-old-coarsening > > > > I made the old, not minimum degree, ordering the default but kept the new > > "aggressive" coarsening as the default, so I am hoping that just adding > > "-pc_gamg_use_aggressive_square_graph true" to your regression tests will > > get you back to where you were before. > > Fingers crossed ... let me know if you have any success or not. > > > > Thanks, > > Mark > > > > > > On Tue, Aug 15, 2023 at 1:45?PM Mark Adams wrote: > > > >> Hi Stephan, > >> > >> I have a branch that you can try: adams/gamg-add-old-coarsening > >> > > >> > >> Things to test: > >> * First, verify that nothing unintended changed by reproducing your bad > >> results with this branch (the defaults are the same) > >> * Try not using the minimum degree ordering that I suggested > >> with: -pc_gamg_use_minimum_degree_ordering false > >> -- I am eager to see if that is the main problem. > >> * Go back to what I think is the old method: > >> -pc_gamg_use_minimum_degree_ordering > >> false -pc_gamg_use_aggressive_square_graph true > >> > >> When we get back to where you were, I would like to try to get modern > >> stuff working. > >> I did add a -pc_gamg_aggressive_mis_k <2> > >> You could to another step of MIS coarsening with > -pc_gamg_aggressive_mis_k > >> 3 > >> > >> Anyway, lots to look at but, alas, AMG does have a lot of parameters. > >> > >> Thanks, > >> Mark > >> > >> On Mon, Aug 14, 2023 at 4:26?PM Mark Adams wrote: > >> > >>> > >>> On Mon, Aug 14, 2023 at 11:03?AM Stephan Kramer < > s.kramer at imperial.ac.uk> > >>> wrote: > >>> > >>>> Many thanks for looking into this, Mark > >>>>> My 3D tests were not that different and I see you lowered the > >>>> threshold. > >>>>> Note, you can set the threshold to zero, but your test is running so > >>>> much > >>>>> differently than mine there is something else going on. > >>>>> Note, the new, bad, coarsening rate of 30:1 is what we tend to shoot > >>>> for > >>>>> in 3D. > >>>>> > >>>>> So it is not clear what the problem is. Some questions: > >>>>> > >>>>> * do you have a picture of this mesh to show me? > >>>> It's just a standard hexahedral cubed sphere mesh with the refinement > >>>> level giving the number of times each of the six sides have been > >>>> subdivided: so Level_5 mean 2^5 x 2^5 squares which is extruded to 16 > >>>> layers. So the total number of elements at Level_5 is 6 x 32 x 32 x > 16 = > >>>> 98304 hexes. And everything doubles in all 3 dimensions (so 2^3) > going > >>>> to the next Level > >>>> > >>> I see, and I assume these are pretty stretched elements. > >>> > >>> > >>>>> * what do you mean by Q1-Q2 elements? > >>>> Q2-Q1, basically Taylor hood on hexes, so (tri)quadratic for velocity > >>>> and (tri)linear for pressure > >>>> > >>>> I guess you could argue we could/should just do good old geometric > >>>> multigrid instead. More generally we do use this solver configuration > a > >>>> lot for tetrahedral Taylor Hood (P2-P1) in particular also for our > >>>> adaptive mesh runs - would it be worth to see if we have the same > >>>> performance issues with tetrahedral P2-P1? > >>>> > >>> No, you have a clear reproducer, if not minimal. > >>> The first coarsening is very different. > >>> > >>> I am working on this and I see that I added a heuristic for thin bodies > >>> where you order the vertices in greedy algorithms with minimum degree > first. > >>> This will tend to pick corners first, edges then faces, etc. > >>> That may be the problem. I would like to understand it better (see > below). > >>> > >>> > >>> > >>>>> It would be nice to see if the new and old codes are similar without > >>>>> aggressive coarsening. > >>>>> This was the intended change of the major change in this time frame > as > >>>> you > >>>>> noticed. > >>>>> If these jobs are easy to run, could you check that the old and new > >>>>> versions are similar with "-pc_gamg_square_graph 0 ", ( and you > only > >>>> need > >>>>> one time step). > >>>>> All you need to do is check that the first coarse grid has about the > >>>> same > >>>>> number of equations (large). > >>>> Unfortunately we're seeing some memory errors when we use this option, > >>>> and I'm not entirely clear whether we're just running out of memory > and > >>>> need to put it on a special queue. > >>>> > >>>> The run with square_graph 0 using new PETSc managed to get through one > >>>> solve at level 5, and is giving the following mg levels: > >>>> > >>>> rows=174, cols=174, bs=6 > >>>> total: nonzeros=30276, allocated nonzeros=30276 > >>>> -- > >>>> rows=2106, cols=2106, bs=6 > >>>> total: nonzeros=4238532, allocated nonzeros=4238532 > >>>> -- > >>>> rows=21828, cols=21828, bs=6 > >>>> total: nonzeros=62588232, allocated nonzeros=62588232 > >>>> -- > >>>> rows=589824, cols=589824, bs=6 > >>>> total: nonzeros=1082528928, allocated nonzeros=1082528928 > >>>> -- > >>>> rows=2433222, cols=2433222, bs=3 > >>>> total: nonzeros=456526098, allocated nonzeros=456526098 > >>>> > >>>> comparing with square_graph 100 with new PETSc > >>>> > >>>> rows=96, cols=96, bs=6 > >>>> total: nonzeros=9216, allocated nonzeros=9216 > >>>> -- > >>>> rows=1440, cols=1440, bs=6 > >>>> total: nonzeros=647856, allocated nonzeros=647856 > >>>> -- > >>>> rows=97242, cols=97242, bs=6 > >>>> total: nonzeros=65656836, allocated nonzeros=65656836 > >>>> -- > >>>> rows=2433222, cols=2433222, bs=3 > >>>> total: nonzeros=456526098, allocated nonzeros=456526098 > >>>> > >>>> and old PETSc with square_graph 100 > >>>> > >>>> rows=90, cols=90, bs=6 > >>>> total: nonzeros=8100, allocated nonzeros=8100 > >>>> -- > >>>> rows=1872, cols=1872, bs=6 > >>>> total: nonzeros=1234080, allocated nonzeros=1234080 > >>>> -- > >>>> rows=47652, cols=47652, bs=6 > >>>> total: nonzeros=23343264, allocated nonzeros=23343264 > >>>> -- > >>>> rows=2433222, cols=2433222, bs=3 > >>>> total: nonzeros=456526098, allocated nonzeros=456526098 > >>>> -- > >>>> > >>>> Unfortunately old PETSc with square_graph 0 did not complete a single > >>>> solve before giving the memory error > >>>> > >>> OK, thanks for trying. > >>> > >>> I am working on this and I will give you a branch to test, but if you > can > >>> rebuild PETSc here is a quick test that might fix your problem. > >>> In src/ksp/pc/impls/gamg/agg.c you will see: > >>> > >>> PetscCall(PetscSortIntWithArray(nloc, degree, permute)); > >>> > >>> If you can comment this out in the new code and compare with the old, > >>> that might fix the problem. > >>> > >>> Thanks, > >>> Mark > >>> > >>> > >>>>> BTW, I am starting to think I should add the old method back as an > >>>> option. > >>>>> I did not think this change would cause large differences. > >>>> Yes, I think that would be much appreciated. Let us know if we can do > >>>> any testing > >>>> > >>>> Best wishes > >>>> Stephan > >>>> > >>>> > >>>>> Thanks, > >>>>> Mark > >>>>> > >>>>> > >>>>> > >>>>> > >>>>>> Note that we are providing the rigid body near nullspace, > >>>>>> hence the bs=3 to bs=6. > >>>>>> We have tried different values for the gamg_threshold but it doesn't > >>>>>> really seem to significantly alter the coarsening amount in that > first > >>>>>> step. > >>>>>> > >>>>>> Do you have any suggestions for further things we should try/look > at? > >>>>>> Any feedback would be much appreciated > >>>>>> > >>>>>> Best wishes > >>>>>> Stephan Kramer > >>>>>> > >>>>>> Full logs including log_view timings available from > >>>>>> https://github.com/stephankramer/petsc-scaling/ > >>>>>> > >>>>>> In particular: > >>>>>> > >>>>>> > >>>>>> > >>>> > https://github.com/stephankramer/petsc-scaling/blob/main/before/Level_5/output_2.dat > >>>>>> > >>>> > https://github.com/stephankramer/petsc-scaling/blob/main/after/Level_5/output_2.dat > >>>>>> > >>>> > https://github.com/stephankramer/petsc-scaling/blob/main/before/Level_6/output_2.dat > >>>>>> > >>>> > https://github.com/stephankramer/petsc-scaling/blob/main/after/Level_6/output_2.dat > >>>>>> > >>>> > https://github.com/stephankramer/petsc-scaling/blob/main/before/Level_7/output_2.dat > >>>>>> > >>>> > https://github.com/stephankramer/petsc-scaling/blob/main/after/Level_7/output_2.dat > >>>>>> > >>>> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Fri Sep 1 12:09:31 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Fri, 1 Sep 2023 22:39:31 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Message-ID: Hi Satish, -with-blaslapack-dir=/path/to/matlab_dir --known-64-bit-blas-indices=1 Is this what you are suggesting? On Fri, Sep 1, 2023, 20:42 Satish Balay wrote: > Also: > > '-known-64-bit-blas-indices=1', > > Note: most externalpackages might not work in this mode. > > [we can't really over come such dependency/conflicts across packages] > > Satish > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > > Here is the matlab test that runs in CI > > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > > # Note: regular BLAS [with 32-bit integers] conflict with > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > > > Ah - so you need to use the ilp64 blas/lapack with matlab - to have a > compatible build > > > > '--with-blaslapack-dir='+matlab_dir, > > > > Satish > > > > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > > > Hi Amneet, > > > > > > Without libmesh, even for PETSc with MATLAB is not working. It is > showing > > > error for both 3.13.4 and 3.17.5 versions. > > > > > > I am trying to install IBAMR in HPC cluster with libmesh and this is > for > > > general usage not only for WEC. This I tried without linking Matlab > with > > > PETSc. Here also I got the error while configuring libmesh 1.6.2 that > PETSc > > > was not found but --enable-petsc-required is specified. > > > > > > The reason for specifically asking for libmesh with PETSc and Matlab > is in > > > the cfd-mpc-wecs application for complicated geometries it is > mentioned to > > > build cfd-mpc-wecs with libmesh construct. > > > > > > For the past 10 days I am trying these various things and ended up with > > > errors. > > > I want to solve this and proceed further to do my research work. > > > > > > Please help me to solve this as soon as possible. > > > > > > > > > Thanks and Regards > > > Srinivas > > > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla > wrote: > > > > > > > Hi Srinivas, > > > > > > > > As discussed earlier you don?t need libMesh for the WEC application. > You > > > > can just work with PETSc 3.17.5 that builds with Matlab. > > > > > > > > Do you have a specific reason for wanting to build libMesh? > > > > > > > > Thanks, > > > > ?Amneet > > > > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via > petsc-users > > > > wrote: > > > > > > > >> Hi, > > > >> > > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences of > "-lut > > > >> -licudata -licui18n -licuuc". When I ran "make test" got the > following > > > >> errors > > > >> in petsc/3.13.4/linux-debug: > > > >> TEST > > > >> > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > code: 124 > > > >> # Running problem 5 > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > >> -------------------------------------------------------------- > > > >> # [0]PETSC ERROR: Error in external library > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >> # [0]PETSC ERROR: See > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > >> shooting. > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named > MB108SMEC028 > > > >> by vit Fri Sep 1 10:01:11 2023 > > > >> # [0]PETSC ERROR: Configure options > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > > > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > >> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > >> # [0]PETSC ERROR: -prob_id 5 > > > >> # [0]PETSC ERROR: -tao_smonitor > > > >> # [0]PETSC ERROR: ----------------End of Error Message -------send > entire > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > >> # > > > >> > -------------------------------------------------------------------------- > > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > >> # with errorcode 126076. > > > >> # > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > > >> # You may or may not see output from other processes, depending on > > > >> # exactly when Open MPI kills them. > > > >> # > > > >> > -------------------------------------------------------------------------- > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > > >> failed so no diff > > > >> > > > >> in petsc/3.13.4/linux-opt > > > >> TEST > > > >> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > code: 124 > > > >> # Running problem 5 > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > >> -------------------------------------------------------------- > > > >> # [0]PETSC ERROR: Error in external library > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >> # [0]PETSC ERROR: See > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > >> shooting. > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > MB108SMEC028 by > > > >> vit Fri Sep 1 10:34:12 2023 > > > >> # [0]PETSC ERROR: Configure options > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > --with-debugging=0 > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > > > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > >> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > >> # [0]PETSC ERROR: -prob_id 5 > > > >> # [0]PETSC ERROR: -tao_smonitor > > > >> # [0]PETSC ERROR: ----------------End of Error Message -------send > entire > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > >> # > > > >> > -------------------------------------------------------------------------- > > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > >> # with errorcode 126076. > > > >> # > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > > >> # You may or may not see output from other processes, depending on > > > >> # exactly when Open MPI kills them. > > > >> # > > > >> > -------------------------------------------------------------------------- > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > > >> failed so no diff. > > > >> > > > >> The same errors occurred for petsc 3.17.5 version. I am sharing the > > > >> config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. > Please find > > > >> the attachment and do the needful. > > > >> > > > >> Thanks and regards > > > >> Srinivas > > > >> > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay > wrote: > > > >> > > > >>> Well - you sent in libmesh log not petsc's configure.log/make.log > for > > > >>> petsc-3.17 > > > >>> > > > >>> Anyway - with petsc-3.13 - you have: > > > >>> > > > >>> >>>> > > > >>> > > > >>> Matlab: > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > >>> /usr/local/MATLAB/R2020b > > > >>> MatlabEngine: > > > >>> Library: > > > >>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx > -lmat -lut > > > >>> -licudata -licui18n -licuuc > > > >>> Language used to compile PETSc: C > > > >>> <<<<< > > > >>> > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > > >>> > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > >>> > > > >>> >>> > > > >>> Matlab: > > > >>> Includes: > > > >>> > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > >>> Libraries: > > > >>> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > >>> > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > >>> -leng -lmex -lmx -lmat > > > >>> Executable: > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > >>> mex: > > > >>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > >>> matlab: > > > >>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > >>> -glnxa64 > > > >>> <<< > > > >>> > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. This > might > > > >>> be a change wrt newer matlab versions. > > > >>> > > > >>> You can: > > > >>> > > > >>> - edit > > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > and > > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > > >>> > > > >>> And see if the build works now. > > > >>> > > > >>> Satish > > > >>> > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > > > >>> > > > >>> > I am sharing the log files while building petsc3.13.4 with > matlab and > > > >>> also > > > >>> > the log file while building libmesh with petsc3.17.5 and matlab. > > > >>> Building > > > >>> > petsc 3.17.5 with matlab was done successfully. But libmesh is > not > > > >>> able to > > > >>> > find the petsc > > > >>> > Please find the attachments. > > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay > > > >>> wrote: > > > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or > 3.19]. > > > >>> > > > > > >>> > > [you can gzip them to make the logs friendly to mailing list - > or > > > >>> send > > > >>> > > them to petsc-maint] > > > >>> > > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > > >>> > > > > > >>> > > Satish > > > >>> > > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > > > >>> > > > > > >>> > > > I am sharing the make.log file while building petsc-3.13.4 > with > > > >>> Matlab. > > > >>> > > > Please find the attachment and do the needful. > > > >>> > > > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > >>> > > > > > > >>> > > > > I tried with petsc-3.17.5. During building of libmesh, the > error > > > >>> shows > > > >>> > > > > petsc was not found > > > >>> > > > > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > balay at mcs.anl.gov> > > > >>> > > wrote: > > > >>> > > > > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > > >>> > > > >> > > > >>> > > > >> Here you are using 3.13 > > > >>> > > > >> > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > >>> > > > >> > > > >>> > > > >> Satish > > > >>> > > > >> > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via > petsc-users > > > >>> wrote: > > > >>> > > > >> > > > >>> > > > >> > Hello, > > > >>> > > > >> > > > > >>> > > > >> > I want to build PETSc with MATLAB for working on the > > > >>> simulation > > > >>> > > using > > > >>> > > > >> IBAMR > > > >>> > > > >> > open software. While building the PETSc, using the > following > > > >>> > > > >> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > >>> > > > >> > ./configure \ > > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > >>> > > > >> > --with-debugging=1 \ > > > >>> > > > >> > --download-hypre=1 \ > > > >>> > > > >> > --download-fblaslapack=1 \ > > > >>> > > > >> > --with-x=0 \ > > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>> > > > >> > --with-matlab-engine=1 > > > >>> > > > >> > > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>> > > > >> > > > > >>> > > > >> > make -j4 > > > >>> > > > >> > make -j4 test > > > >>> > > > >> > > > > >>> > > > >> > I got the following error > > > >>> > > > >> > CLINKER > > > >>> > > > >> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > >> > function `EvaluateResidual': > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > >> > function `EvaluateJacobian': > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > >> > function `TaoPounders': > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > >> > function `main': > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > > > >>> > > > >> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > >>> > > > >> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > >>> > > > >> Error 1 > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > > >>> > > > >> > > > > >>> > > > >> > Please help me to solve this issue > > > >>> > > > >> > > > > >>> > > > >> > Thank you > > > >>> > > > >> > Srinivas > > > >>> > > > >> > > > > >>> > > > >> > > > > >>> > > > >> > > > >>> > > > >> > > > >>> > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > >>> > > > > >>> > > > >> > > > >> > > > >> *Disclaimer:This message was sent from Vellore Institute of > Technology. > > > >> The contents of this email may contain legally protected > confidential or > > > >> privileged information of ?Vellore Institute of Technology?. If > you are > > > >> not the intended recipient, you should not disseminate, distribute > or copy > > > >> this e-mail. Please notify the sender immediately and destroy all > copies of > > > >> this message and any attachments. If you have received this email > in error, > > > >> please promptly notify the sender by reply email and delete the > original > > > >> email and any backup copies without reading them.* > > > >> > > > > > > > > > > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. 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URL: From balay at mcs.anl.gov Fri Sep 1 12:23:51 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 1 Sep 2023 12:23:51 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Message-ID: yes [and remove fblaslapack. don't know if hypre will work here]. i.e: ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 \ --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 Satish On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > Hi Satish, > > -with-blaslapack-dir=/path/to/matlab_dir > --known-64-bit-blas-indices=1 > > Is this what you are suggesting? > > On Fri, Sep 1, 2023, 20:42 Satish Balay wrote: > > > Also: > > > > '-known-64-bit-blas-indices=1', > > > > Note: most externalpackages might not work in this mode. > > > > [we can't really over come such dependency/conflicts across packages] > > > > Satish > > > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > > > > Here is the matlab test that runs in CI > > > > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > > > > # Note: regular BLAS [with 32-bit integers] conflict with > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > > > > > Ah - so you need to use the ilp64 blas/lapack with matlab - to have a > > compatible build > > > > > > '--with-blaslapack-dir='+matlab_dir, > > > > > > Satish > > > > > > > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > > > > > Hi Amneet, > > > > > > > > Without libmesh, even for PETSc with MATLAB is not working. It is > > showing > > > > error for both 3.13.4 and 3.17.5 versions. > > > > > > > > I am trying to install IBAMR in HPC cluster with libmesh and this is > > for > > > > general usage not only for WEC. This I tried without linking Matlab > > with > > > > PETSc. Here also I got the error while configuring libmesh 1.6.2 that > > PETSc > > > > was not found but --enable-petsc-required is specified. > > > > > > > > The reason for specifically asking for libmesh with PETSc and Matlab > > is in > > > > the cfd-mpc-wecs application for complicated geometries it is > > mentioned to > > > > build cfd-mpc-wecs with libmesh construct. > > > > > > > > For the past 10 days I am trying these various things and ended up with > > > > errors. > > > > I want to solve this and proceed further to do my research work. > > > > > > > > Please help me to solve this as soon as possible. > > > > > > > > > > > > Thanks and Regards > > > > Srinivas > > > > > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla > > wrote: > > > > > > > > > Hi Srinivas, > > > > > > > > > > As discussed earlier you don?t need libMesh for the WEC application. > > You > > > > > can just work with PETSc 3.17.5 that builds with Matlab. > > > > > > > > > > Do you have a specific reason for wanting to build libMesh? > > > > > > > > > > Thanks, > > > > > ?Amneet > > > > > > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via > > petsc-users > > > > > wrote: > > > > > > > > > >> Hi, > > > > >> > > > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences of > > "-lut > > > > >> -licudata -licui18n -licuuc". When I ran "make test" got the > > following > > > > >> errors > > > > >> in petsc/3.13.4/linux-debug: > > > > >> TEST > > > > >> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > code: 124 > > > > >> # Running problem 5 > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > > >> -------------------------------------------------------------- > > > > >> # [0]PETSC ERROR: Error in external library > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > >> # [0]PETSC ERROR: See > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > > >> shooting. > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named > > MB108SMEC028 > > > > >> by vit Fri Sep 1 10:01:11 2023 > > > > >> # [0]PETSC ERROR: Configure options > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --with-debugging=1 > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > > > > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > >> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > >> # [0]PETSC ERROR: ----------------End of Error Message -------send > > entire > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > > >> # > > > > >> > > -------------------------------------------------------------------------- > > > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > >> # with errorcode 126076. > > > > >> # > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > > >> # You may or may not see output from other processes, depending on > > > > >> # exactly when Open MPI kills them. > > > > >> # > > > > >> > > -------------------------------------------------------------------------- > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > > > >> failed so no diff > > > > >> > > > > >> in petsc/3.13.4/linux-opt > > > > >> TEST > > > > >> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > code: 124 > > > > >> # Running problem 5 > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > > >> -------------------------------------------------------------- > > > > >> # [0]PETSC ERROR: Error in external library > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > >> # [0]PETSC ERROR: See > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > > >> shooting. > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > MB108SMEC028 by > > > > >> vit Fri Sep 1 10:34:12 2023 > > > > >> # [0]PETSC ERROR: Configure options > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 --COPTFLAGS=-O3 > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > > --with-debugging=0 > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ --with-matlab-engine=1 > > > > >> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > >> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > >> # [0]PETSC ERROR: ----------------End of Error Message -------send > > entire > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > > >> # > > > > >> > > -------------------------------------------------------------------------- > > > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > >> # with errorcode 126076. > > > > >> # > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > > >> # You may or may not see output from other processes, depending on > > > > >> # exactly when Open MPI kills them. > > > > >> # > > > > >> > > -------------------------------------------------------------------------- > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > > > >> failed so no diff. > > > > >> > > > > >> The same errors occurred for petsc 3.17.5 version. I am sharing the > > > > >> config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. > > Please find > > > > >> the attachment and do the needful. > > > > >> > > > > >> Thanks and regards > > > > >> Srinivas > > > > >> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay > > wrote: > > > > >> > > > > >>> Well - you sent in libmesh log not petsc's configure.log/make.log > > for > > > > >>> petsc-3.17 > > > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > > > >>> > > > > >>> >>>> > > > > >>> > > > > >>> Matlab: > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > > >>> /usr/local/MATLAB/R2020b > > > > >>> MatlabEngine: > > > > >>> Library: > > > > >>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx > > -lmat -lut > > > > >>> -licudata -licui18n -licuuc > > > > >>> Language used to compile PETSc: C > > > > >>> <<<<< > > > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > >>> > > > > >>> >>> > > > > >>> Matlab: > > > > >>> Includes: > > > > >>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > > >>> Libraries: > > > > >>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > >>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > >>> -leng -lmex -lmx -lmat > > > > >>> Executable: > > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > > >>> mex: > > > > >>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > > >>> matlab: > > > > >>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > > >>> -glnxa64 > > > > >>> <<< > > > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. This > > might > > > > >>> be a change wrt newer matlab versions. > > > > >>> > > > > >>> You can: > > > > >>> > > > > >>> - edit > > > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > and > > > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > > > >>> > > > > >>> And see if the build works now. > > > > >>> > > > > >>> Satish > > > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > wrote: > > > > >>> > > > > >>> > I am sharing the log files while building petsc3.13.4 with > > matlab and > > > > >>> also > > > > >>> > the log file while building libmesh with petsc3.17.5 and matlab. > > > > >>> Building > > > > >>> > petsc 3.17.5 with matlab was done successfully. But libmesh is > > not > > > > >>> able to > > > > >>> > find the petsc > > > > >>> > Please find the attachments. > > > > >>> > > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay > > > > >>> wrote: > > > > >>> > > > > > >>> > > Send configure.log, make.log from both petsc-3.13 and 3.17 [or > > 3.19]. > > > > >>> > > > > > > >>> > > [you can gzip them to make the logs friendly to mailing list - > > or > > > > >>> send > > > > >>> > > them to petsc-maint] > > > > >>> > > > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > > > >>> > > > > > > >>> > > Satish > > > > >>> > > > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > wrote: > > > > >>> > > > > > > >>> > > > I am sharing the make.log file while building petsc-3.13.4 > > with > > > > >>> Matlab. > > > > >>> > > > Please find the attachment and do the needful. > > > > >>> > > > > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS 20PHD0548 < > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > >>> > > > > > > > >>> > > > > I tried with petsc-3.17.5. During building of libmesh, the > > error > > > > >>> shows > > > > >>> > > > > petsc was not found > > > > >>> > > > > > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > > balay at mcs.anl.gov> > > > > >>> > > wrote: > > > > >>> > > > > > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > > > >>> > > > >> > > > > >>> > > > >> Here you are using 3.13 > > > > >>> > > > >> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > > >>> > > > >> > > > > >>> > > > >> Satish > > > > >>> > > > >> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > petsc-users > > > > >>> wrote: > > > > >>> > > > >> > > > > >>> > > > >> > Hello, > > > > >>> > > > >> > > > > > >>> > > > >> > I want to build PETSc with MATLAB for working on the > > > > >>> simulation > > > > >>> > > using > > > > >>> > > > >> IBAMR > > > > >>> > > > >> > open software. While building the PETSc, using the > > following > > > > >>> > > > >> > > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > > >>> > > > >> > ./configure \ > > > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > > >>> > > > >> > --with-debugging=1 \ > > > > >>> > > > >> > --download-hypre=1 \ > > > > >>> > > > >> > --download-fblaslapack=1 \ > > > > >>> > > > >> > --with-x=0 \ > > > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>> > > > >> > --with-matlab-engine=1 > > > > >>> > > > >> > > > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>> > > > >> > > > > > >>> > > > >> > make -j4 > > > > >>> > > > >> > make -j4 test > > > > >>> > > > >> > > > > > >>> > > > >> > I got the following error > > > > >>> > > > >> > CLINKER > > > > >>> > > > >> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > >> > function `EvaluateResidual': > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > >> > function `EvaluateJacobian': > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > >> > function `TaoPounders': > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > >> > function `main': > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > > > > >>> > > > >> > > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > > >>> > > > >> > > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > > >>> > > > >> Error 1 > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > > > >>> > > > >> > > > > > >>> > > > >> > Please help me to solve this issue > > > > >>> > > > >> > > > > > >>> > > > >> > Thank you > > > > >>> > > > >> > Srinivas > > > > >>> > > > >> > > > > > >>> > > > >> > > > > > >>> > > > >> > > > > >>> > > > >> > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > > >>> > > > > >> > > > > >> > > > > >> *Disclaimer:This message was sent from Vellore Institute of > > Technology. > > > > >> The contents of this email may contain legally protected > > confidential or > > > > >> privileged information of ?Vellore Institute of Technology?. If > > you are > > > > >> not the intended recipient, you should not disseminate, distribute > > or copy > > > > >> this e-mail. Please notify the sender immediately and destroy all > > copies of > > > > >> this message and any attachments. If you have received this email > > in error, > > > > >> please promptly notify the sender by reply email and delete the > > original > > > > >> email and any backup copies without reading them.* > > > > >> > > > > > > > > > > > > > > > > > > > > From inturu.srinivas2020 at vitstudent.ac.in Fri Sep 1 12:25:10 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Fri, 1 Sep 2023 22:55:10 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Message-ID: Thank you Sathish.I will try this On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: > yes [and remove fblaslapack. don't know if hypre will work here]. > > i.e: > > ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 \ > --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 > -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 > > Satish > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > Hi Satish, > > > > -with-blaslapack-dir=/path/to/matlab_dir > > --known-64-bit-blas-indices=1 > > > > Is this what you are suggesting? > > > > On Fri, Sep 1, 2023, 20:42 Satish Balay wrote: > > > > > Also: > > > > > > '-known-64-bit-blas-indices=1', > > > > > > Note: most externalpackages might not work in this mode. > > > > > > [we can't really over come such dependency/conflicts across packages] > > > > > > Satish > > > > > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > > > > > > Here is the matlab test that runs in CI > > > > > > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > > > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > > > > > > # Note: regular BLAS [with 32-bit integers] conflict with > > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > > > > > > > Ah - so you need to use the ilp64 blas/lapack with matlab - to have > a > > > compatible build > > > > > > > > '--with-blaslapack-dir='+matlab_dir, > > > > > > > > Satish > > > > > > > > > > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > > > > > > > Hi Amneet, > > > > > > > > > > Without libmesh, even for PETSc with MATLAB is not working. It is > > > showing > > > > > error for both 3.13.4 and 3.17.5 versions. > > > > > > > > > > I am trying to install IBAMR in HPC cluster with libmesh and this > is > > > for > > > > > general usage not only for WEC. This I tried without linking Matlab > > > with > > > > > PETSc. Here also I got the error while configuring libmesh 1.6.2 > that > > > PETSc > > > > > was not found but --enable-petsc-required is specified. > > > > > > > > > > The reason for specifically asking for libmesh with PETSc and > Matlab > > > is in > > > > > the cfd-mpc-wecs application for complicated geometries it is > > > mentioned to > > > > > build cfd-mpc-wecs with libmesh construct. > > > > > > > > > > For the past 10 days I am trying these various things and ended up > with > > > > > errors. > > > > > I want to solve this and proceed further to do my research work. > > > > > > > > > > Please help me to solve this as soon as possible. > > > > > > > > > > > > > > > Thanks and Regards > > > > > Srinivas > > > > > > > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla > > > wrote: > > > > > > > > > > > Hi Srinivas, > > > > > > > > > > > > As discussed earlier you don?t need libMesh for the WEC > application. > > > You > > > > > > can just work with PETSc 3.17.5 that builds with Matlab. > > > > > > > > > > > > Do you have a specific reason for wanting to build libMesh? > > > > > > > > > > > > Thanks, > > > > > > ?Amneet > > > > > > > > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via > > > petsc-users > > > > > > wrote: > > > > > > > > > > > >> Hi, > > > > > >> > > > > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences of > > > "-lut > > > > > >> -licudata -licui18n -licuuc". When I ran "make test" got the > > > following > > > > > >> errors > > > > > >> in petsc/3.13.4/linux-debug: > > > > > >> TEST > > > > > >> > > > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > > code: 124 > > > > > >> # Running problem 5 > > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > > > >> -------------------------------------------------------------- > > > > > >> # [0]PETSC ERROR: Error in external library > > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > > >> # [0]PETSC ERROR: See > > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble > > > > > >> shooting. > > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named > > > MB108SMEC028 > > > > > >> by vit Fri Sep 1 10:01:11 2023 > > > > > >> # [0]PETSC ERROR: Configure options > > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > --with-debugging=1 > > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > --with-matlab-engine=1 > > > > > >> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > -------send > > > entire > > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > > > >> # > > > > > >> > > > > -------------------------------------------------------------------------- > > > > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > > >> # with errorcode 126076. > > > > > >> # > > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > > processes. > > > > > >> # You may or may not see output from other processes, depending > on > > > > > >> # exactly when Open MPI kills them. > > > > > >> # > > > > > >> > > > > -------------------------------------------------------------------------- > > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > Command > > > > > >> failed so no diff > > > > > >> > > > > > >> in petsc/3.13.4/linux-opt > > > > > >> TEST > > > > > >> > > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > > code: 124 > > > > > >> # Running problem 5 > > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > > > >> -------------------------------------------------------------- > > > > > >> # [0]PETSC ERROR: Error in external library > > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > > >> # [0]PETSC ERROR: See > > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble > > > > > >> shooting. > > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > > MB108SMEC028 by > > > > > >> vit Fri Sep 1 10:34:12 2023 > > > > > >> # [0]PETSC ERROR: Configure options > > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > --COPTFLAGS=-O3 > > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > > > --with-debugging=0 > > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > --with-matlab-engine=1 > > > > > >> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > > >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > > >> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > -------send > > > entire > > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > > > >> # > > > > > >> > > > > -------------------------------------------------------------------------- > > > > > >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > > >> # with errorcode 126076. > > > > > >> # > > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > > processes. > > > > > >> # You may or may not see output from other processes, depending > on > > > > > >> # exactly when Open MPI kills them. > > > > > >> # > > > > > >> > > > > -------------------------------------------------------------------------- > > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > Command > > > > > >> failed so no diff. > > > > > >> > > > > > >> The same errors occurred for petsc 3.17.5 version. I am sharing > the > > > > > >> config.log and make.log for both petsc 3.13.4 and petsc 3.17.5. > > > Please find > > > > > >> the attachment and do the needful. > > > > > >> > > > > > >> Thanks and regards > > > > > >> Srinivas > > > > > >> > > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > balay at mcs.anl.gov> > > > wrote: > > > > > >> > > > > > >>> Well - you sent in libmesh log not petsc's > configure.log/make.log > > > for > > > > > >>> petsc-3.17 > > > > > >>> > > > > > >>> Anyway - with petsc-3.13 - you have: > > > > > >>> > > > > > >>> >>>> > > > > > >>> > > > > > >>> Matlab: > > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > > > >>> /usr/local/MATLAB/R2020b > > > > > >>> MatlabEngine: > > > > > >>> Library: > > > > > >>> > > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx > > > -lmat -lut > > > > > >>> -licudata -licui18n -licuuc > > > > > >>> Language used to compile PETSc: C > > > > > >>> <<<<< > > > > > >>> > > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > > > > >>> > > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > > >>> > > > > > >>> >>> > > > > > >>> Matlab: > > > > > >>> Includes: > > > > > >>> > > > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > > > >>> Libraries: > > > > > >>> > > > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > > >>> > > > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > > >>> -leng -lmex -lmx -lmat > > > > > >>> Executable: > > > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > > > >>> mex: > > > > > >>> > > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > > > >>> matlab: > > > > > >>> > > > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > > > >>> -glnxa64 > > > > > >>> <<< > > > > > >>> > > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. > This > > > might > > > > > >>> be a change wrt newer matlab versions. > > > > > >>> > > > > > >>> You can: > > > > > >>> > > > > > >>> - edit > > > > > >>> > /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > > and > > > > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > > > > >>> > > > > > >>> And see if the build works now. > > > > > >>> > > > > > >>> Satish > > > > > >>> > > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > > wrote: > > > > > >>> > > > > > >>> > I am sharing the log files while building petsc3.13.4 with > > > matlab and > > > > > >>> also > > > > > >>> > the log file while building libmesh with petsc3.17.5 and > matlab. > > > > > >>> Building > > > > > >>> > petsc 3.17.5 with matlab was done successfully. But libmesh > is > > > not > > > > > >>> able to > > > > > >>> > find the petsc > > > > > >>> > Please find the attachments. > > > > > >>> > > > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > balay at mcs.anl.gov> > > > > > >>> wrote: > > > > > >>> > > > > > > >>> > > Send configure.log, make.log from both petsc-3.13 and 3.17 > [or > > > 3.19]. > > > > > >>> > > > > > > > >>> > > [you can gzip them to make the logs friendly to mailing > list - > > > or > > > > > >>> send > > > > > >>> > > them to petsc-maint] > > > > > >>> > > > > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > > > > >>> > > > > > > > >>> > > Satish > > > > > >>> > > > > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > petsc-users > > > wrote: > > > > > >>> > > > > > > > >>> > > > I am sharing the make.log file while building > petsc-3.13.4 > > > with > > > > > >>> Matlab. > > > > > >>> > > > Please find the attachment and do the needful. > > > > > >>> > > > > > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS > 20PHD0548 < > > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > >>> > > > > > > > > >>> > > > > I tried with petsc-3.17.5. During building of libmesh, > the > > > error > > > > > >>> shows > > > > > >>> > > > > petsc was not found > > > > > >>> > > > > > > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > > > balay at mcs.anl.gov> > > > > > >>> > > wrote: > > > > > >>> > > > > > > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > > > > >>> > > > >> > > > > > >>> > > > >> Here you are using 3.13 > > > > > >>> > > > >> > > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > > > >>> > > > >> > > > > > >>> > > > >> Satish > > > > > >>> > > > >> > > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > > petsc-users > > > > > >>> wrote: > > > > > >>> > > > >> > > > > > >>> > > > >> > Hello, > > > > > >>> > > > >> > > > > > > >>> > > > >> > I want to build PETSc with MATLAB for working on the > > > > > >>> simulation > > > > > >>> > > using > > > > > >>> > > > >> IBAMR > > > > > >>> > > > >> > open software. While building the PETSc, using the > > > following > > > > > >>> > > > >> > > > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > > > >>> > > > >> > ./configure \ > > > > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > > > >>> > > > >> > --with-debugging=1 \ > > > > > >>> > > > >> > --download-hypre=1 \ > > > > > >>> > > > >> > --download-fblaslapack=1 \ > > > > > >>> > > > >> > --with-x=0 \ > > > > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > > >>> > > > >> > --with-matlab-engine=1 > > > > > >>> > > > >> > > > > > > >>> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > > >>> > > > >> > > > > > > >>> > > > >> > make -j4 > > > > > >>> > > > >> > make -j4 test > > > > > >>> > > > >> > > > > > > >>> > > > >> > I got the following error > > > > > >>> > > > >> > CLINKER > > > > > >>> > > > >> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > > > > > >>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > > >>> > > > >> > function `EvaluateResidual': > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > > > > > >>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > > >>> > > > >> > function `EvaluateJacobian': > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > > > > > >>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > > >>> > > > >> > function `TaoPounders': > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > > > > > >>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > > >>> > > > >> > function `main': > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > > > > >>> > > > >> > /usr/bin/ld: > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > > > > > >>> > > > >> > > > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > > > >>> > > > >> > > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > > > >>> > > > >> Error 1 > > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > > > > >>> > > > >> > > > > > > >>> > > > >> > Please help me to solve this issue > > > > > >>> > > > >> > > > > > > >>> > > > >> > Thank you > > > > > >>> > > > >> > Srinivas > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > > >>> > > > >> > > > > > >>> > > > >> > > > > > >>> > > > > > > > > >>> > > > > > > > > >>> > > > > > > > >>> > > > > > > >>> > > > > > > >>> > > > > > >> > > > > > >> > > > > > >> *Disclaimer:This message was sent from Vellore Institute of > > > Technology. > > > > > >> The contents of this email may contain legally protected > > > confidential or > > > > > >> privileged information of ?Vellore Institute of Technology?. If > > > you are > > > > > >> not the intended recipient, you should not disseminate, > distribute > > > or copy > > > > > >> this e-mail. Please notify the sender immediately and destroy > all > > > copies of > > > > > >> this message and any attachments. If you have received this > email > > > in error, > > > > > >> please promptly notify the sender by reply email and delete the > > > original > > > > > >> email and any backup copies without reading them.* > > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Sat Sep 2 02:05:57 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Sat, 2 Sep 2023 12:35:57 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <47c457d8-6b74-dee2-f061-9962e50b133f@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Message-ID: Based on the suggestions given by Sathish, I have tried to configure petsc 3.13.4 with Matlab-R2020b. But, it was not successful. After running make -j 10 test command I have got the following error message. not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 # Running problem 5 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine on # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by vit Sat Sep 2 12:27:22 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -prob_id 5 # [0]PETSC ERROR: -tao_smonitor # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF # with errorcode 126076. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- I request you to help me to sort out this error. Thanks Srinivas On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla wrote: > I think there should be two hyphens in > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > i.e.: > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via petsc-users < > petsc-users at mcs.anl.gov> wrote: > >> Thank you Sathish.I will try this >> >> On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: >> >>> yes [and remove fblaslapack. don't know if hypre will work here]. >>> >>> i.e: >>> >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> --with-debugging=0 --with-x=0 \ >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 >>> >>> Satish >>> >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>> >>> > Hi Satish, >>> > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>> > --known-64-bit-blas-indices=1 >>> > >>> > Is this what you are suggesting? >>> > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay wrote: >>> > >>> > > Also: >>> > > >>> > > '-known-64-bit-blas-indices=1', >>> > > >>> > > Note: most externalpackages might not work in this mode. >>> > > >>> > > [we can't really over come such dependency/conflicts across packages] >>> > > >>> > > Satish >>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>> > > >>> > > > Here is the matlab test that runs in CI >>> > > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> > > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>> > > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with >>> > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 >>> > > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab - to >>> have a >>> > > compatible build >>> > > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>> > > > >>> > > > Satish >>> > > > >>> > > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>> wrote: >>> > > > >>> > > > > Hi Amneet, >>> > > > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not working. It is >>> > > showing >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>> > > > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh and >>> this is >>> > > for >>> > > > > general usage not only for WEC. This I tried without linking >>> Matlab >>> > > with >>> > > > > PETSc. Here also I got the error while configuring libmesh 1.6.2 >>> that >>> > > PETSc >>> > > > > was not found but --enable-petsc-required is specified. >>> > > > > >>> > > > > The reason for specifically asking for libmesh with PETSc and >>> Matlab >>> > > is in >>> > > > > the cfd-mpc-wecs application for complicated geometries it is >>> > > mentioned to >>> > > > > build cfd-mpc-wecs with libmesh construct. >>> > > > > >>> > > > > For the past 10 days I am trying these various things and ended >>> up with >>> > > > > errors. >>> > > > > I want to solve this and proceed further to do my research work. >>> > > > > >>> > > > > Please help me to solve this as soon as possible. >>> > > > > >>> > > > > >>> > > > > Thanks and Regards >>> > > > > Srinivas >>> > > > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla >>> > > wrote: >>> > > > > >>> > > > > > Hi Srinivas, >>> > > > > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC >>> application. >>> > > You >>> > > > > > can just work with PETSc 3.17.5 that builds with Matlab. >>> > > > > > >>> > > > > > Do you have a specific reason for wanting to build libMesh? >>> > > > > > >>> > > > > > Thanks, >>> > > > > > ?Amneet >>> > > > > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via >>> > > petsc-users >>> > > > > > wrote: >>> > > > > > >>> > > > > >> Hi, >>> > > > > >> >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences >>> of >>> > > "-lut >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" got the >>> > > following >>> > > > > >> errors >>> > > > > >> in petsc/3.13.4/linux-debug: >>> > > > > >> TEST >>> > > > > >> >>> > > >>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> Error >>> > > code: 124 >>> > > > > >> # Running problem 5 >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >>> > > > > >> -------------------------------------------------------------- >>> > > > > >> # [0]PETSC ERROR: Error in external library >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > > > >> # [0]PETSC ERROR: See >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>> trouble >>> > > > > >> shooting. >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named >>> > > MB108SMEC028 >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>> > > > > >> # [0]PETSC ERROR: Configure options >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> --with-debugging=1 >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> --with-matlab-engine=1 >>> > > > > >> >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > > > > >> >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>> > > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message >>> -------send >>> > > entire >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >>> > > > > >> # >>> > > > > >> >>> > > >>> -------------------------------------------------------------------------- >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>> MPI_COMM_SELF >>> > > > > >> # with errorcode 126076. >>> > > > > >> # >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>> > > processes. >>> > > > > >> # You may or may not see output from other processes, >>> depending on >>> > > > > >> # exactly when Open MPI kills them. >>> > > > > >> # >>> > > > > >> >>> > > >>> -------------------------------------------------------------------------- >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>> Command >>> > > > > >> failed so no diff >>> > > > > >> >>> > > > > >> in petsc/3.13.4/linux-opt >>> > > > > >> TEST >>> > > > > >> >>> > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> Error >>> > > code: 124 >>> > > > > >> # Running problem 5 >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >>> > > > > >> -------------------------------------------------------------- >>> > > > > >> # [0]PETSC ERROR: Error in external library >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > > > >> # [0]PETSC ERROR: See >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>> trouble >>> > > > > >> shooting. >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>> > > MB108SMEC028 by >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>> > > > > >> # [0]PETSC ERROR: Configure options >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> --COPTFLAGS=-O3 >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt >>> > > --with-debugging=0 >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> --with-matlab-engine=1 >>> > > > > >> >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > > > > >> >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>> > > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message >>> -------send >>> > > entire >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >>> > > > > >> # >>> > > > > >> >>> > > >>> -------------------------------------------------------------------------- >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>> MPI_COMM_SELF >>> > > > > >> # with errorcode 126076. >>> > > > > >> # >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>> > > processes. >>> > > > > >> # You may or may not see output from other processes, >>> depending on >>> > > > > >> # exactly when Open MPI kills them. >>> > > > > >> # >>> > > > > >> >>> > > >>> -------------------------------------------------------------------------- >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>> Command >>> > > > > >> failed so no diff. >>> > > > > >> >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I am >>> sharing the >>> > > > > >> config.log and make.log for both petsc 3.13.4 and petsc >>> 3.17.5. >>> > > Please find >>> > > > > >> the attachment and do the needful. >>> > > > > >> >>> > > > > >> Thanks and regards >>> > > > > >> Srinivas >>> > > > > >> >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>> balay at mcs.anl.gov> >>> > > wrote: >>> > > > > >> >>> > > > > >>> Well - you sent in libmesh log not petsc's >>> configure.log/make.log >>> > > for >>> > > > > >>> petsc-3.17 >>> > > > > >>> >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>> > > > > >>> >>> > > > > >>> >>>> >>> > > > > >>> >>> > > > > >>> Matlab: >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> > > > > >>> /usr/local/MATLAB/R2020b >>> > > > > >>> MatlabEngine: >>> > > > > >>> Library: >>> > > > > >>> >>> > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>> -lmx >>> > > -lmat -lut >>> > > > > >>> -licudata -licui18n -licuuc >>> > > > > >>> Language used to compile PETSc: C >>> > > > > >>> <<<<< >>> > > > > >>> >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: >>> > > > > >>> >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> > > > > >>> >>> > > > > >>> >>> >>> > > > > >>> Matlab: >>> > > > > >>> Includes: >>> > > > > >>> >>> > > >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>> > > > > >>> Libraries: >>> > > > > >>> >>> > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> > > > > >>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> > > > > >>> -leng -lmex -lmx -lmat >>> > > > > >>> Executable: >>> > > > > >>> >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>> > > > > >>> mex: >>> > > > > >>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>> > > > > >>> matlab: >>> > > > > >>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>> > > > > >>> -glnxa64 >>> > > > > >>> <<< >>> > > > > >>> >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. >>> This >>> > > might >>> > > > > >>> be a change wrt newer matlab versions. >>> > > > > >>> >>> > > > > >>> You can: >>> > > > > >>> >>> > > > > >>> - edit >>> > > > > >>> >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>> > > and >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' >>> > > > > >>> >>> > > > > >>> And see if the build works now. >>> > > > > >>> >>> > > > > >>> Satish >>> > > > > >>> >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via >>> petsc-users >>> > > wrote: >>> > > > > >>> >>> > > > > >>> > I am sharing the log files while building petsc3.13.4 with >>> > > matlab and >>> > > > > >>> also >>> > > > > >>> > the log file while building libmesh with petsc3.17.5 and >>> matlab. >>> > > > > >>> Building >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But >>> libmesh is >>> > > not >>> > > > > >>> able to >>> > > > > >>> > find the petsc >>> > > > > >>> > Please find the attachments. >>> > > > > >>> > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>> balay at mcs.anl.gov> >>> > > > > >>> wrote: >>> > > > > >>> > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 and >>> 3.17 [or >>> > > 3.19]. >>> > > > > >>> > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to mailing >>> list - >>> > > or >>> > > > > >>> send >>> > > > > >>> > > them to petsc-maint] >>> > > > > >>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] >>> > > > > >>> > > >>> > > > > >>> > > Satish >>> > > > > >>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via >>> petsc-users >>> > > wrote: >>> > > > > >>> > > >>> > > > > >>> > > > I am sharing the make.log file while building >>> petsc-3.13.4 >>> > > with >>> > > > > >>> Matlab. >>> > > > > >>> > > > Please find the attachment and do the needful. >>> > > > > >>> > > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS >>> 20PHD0548 < >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> > > > > >>> > > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of >>> libmesh, the >>> > > error >>> > > > > >>> shows >>> > > > > >>> > > > > petsc was not found >>> > > > > >>> > > > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < >>> > > balay at mcs.anl.gov> >>> > > > > >>> > > wrote: >>> > > > > >>> > > > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 >>> > > > > >>> > > > >> >>> > > > > >>> > > > >> Here you are using 3.13 >>> > > > > >>> > > > >> >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>> > > > > >>> > > > >> >>> > > > > >>> > > > >> Satish >>> > > > > >>> > > > >> >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via >>> > > petsc-users >>> > > > > >>> wrote: >>> > > > > >>> > > > >> >>> > > > > >>> > > > >> > Hello, >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for working on >>> the >>> > > > > >>> simulation >>> > > > > >>> > > using >>> > > > > >>> > > > >> IBAMR >>> > > > > >>> > > > >> > open software. While building the PETSc, using the >>> > > following >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>> > > > > >>> > > > >> > ./configure \ >>> > > > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>> > > > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>> > > > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>> > > > > >>> > > > >> > --with-debugging=1 \ >>> > > > > >>> > > > >> > --download-hypre=1 \ >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>> > > > > >>> > > > >> > --with-x=0 \ >>> > > > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>> > > > > >>> > > > >> > >>> > > > > >>> >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > make -j4 >>> > > > > >>> > > > >> > make -j4 test >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > I got the following error >>> > > > > >>> > > > >> > CLINKER >>> > > > > >>> > > > >> >>> > > > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > > >>> > > > >> > function `EvaluateResidual': >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > > >>> > > > >> > function `TaoPounders': >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > > >>> > > > >> > function `main': >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>> > > > > >>> > > > >> > >>> > > > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>> > > > > >>> > > > >> Error 1 >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > Please help me to solve this issue >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > Thank you >>> > > > > >>> > > > >> > Srinivas >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> >>> > > > > >>> > > > >> >>> > > > > >>> > > > >>> > > > > >>> > > > >>> > > > > >>> > > >>> > > > > >>> > >>> > > > > >>> > >>> > > > > >>> >>> > > > > >> >>> > > > > >> >>> > > > > >> *Disclaimer:This message was sent from Vellore Institute of >>> > > Technology. >>> > > > > >> The contents of this email may contain legally protected >>> > > confidential or >>> > > > > >> privileged information of ?Vellore Institute of Technology?. >>> If >>> > > you are >>> > > > > >> not the intended recipient, you should not disseminate, >>> distribute >>> > > or copy >>> > > > > >> this e-mail. Please notify the sender immediately and destroy >>> all >>> > > copies of >>> > > > > >> this message and any attachments. If you have received this >>> email >>> > > in error, >>> > > > > >> please promptly notify the sender by reply email and delete >>> the >>> > > original >>> > > > > >> email and any backup copies without reading them.* >>> > > > > >> >>> > > > > > >>> > > > > >>> > > > > >>> > > > >>> > > >>> > >>> > >>> >> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> > > > -- > --Amneet > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Sat Sep 2 11:42:08 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Sat, 2 Sep 2023 11:42:08 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> Message-ID: <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Please don't cc: both petsc-users and petsc-maint [reverting thread to petsc-users only] I'm not sure what is happening here. Can you send the corresponding configure.log, make.log [compressed]? Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, with Matlab-R2021a - and that works: balay at compute-386-07:/scratch/balay/petsc$ git branch main release * release-3.13 balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a balay at compute-386-07:/scratch/balay/petsc$ which matlab /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab balay at compute-386-07:/scratch/balay/petsc$ ./configure --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a --known-64-bit-blas-indices=1 --with-matlab-engine=1 Compilers: C Compiler: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 C++ Compiler: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 Fortran Compiler: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 Linkers: Shared linker: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Dynamic linker: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Libraries linked against: -lquadmath -lstdc++ -ldl make: Version: 4.2 /usr/bin/make BlasLapack: Library: /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 -liomp5 -lpthread uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads uses 8 byte integers MPI: Version: 4 Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec MPICH_NUMVERSION: 40002300 pthread: Library: -lpthread cmake: Version: 3.16.3 /usr/bin/cmake regex: Matlab: Includes: -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a MatlabEngine: Library: -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc sowing: Version: 1.1.25 /scratch/balay/petsc/linux-opt/bin/bfort valgrind: Language used to compile PETSc: C PETSc: PETSC_ARCH: linux-opt PETSC_DIR: /scratch/balay/petsc Scalar type: real Precision: double Support for __float128 Integer size: 4 bytes shared libraries: enabled Memory alignment from malloc(): 16 bytes xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with: make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all xxx=========================================================================xxx balay at compute-386-07:/scratch/balay/petsc$ make FC linux-opt/obj/tao/f90-mod/petsctaomod.o CLINKER linux-opt/lib/libpetsc.so.3.13.6 BEGINNING TO COMPILE MATLAB INTERFACE Building with 'gcc'. /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. ========================================= Now to check if the libraries are working do: make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check ========================================= balay at compute-386-07:/scratch/balay/petsc$ make test query=requires queryval=matlab Using MAKEFLAGS: -- queryval=matlab query=requires CC linux-opt/tests/ksp/ksp/tutorials/ex72.o CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 # ../ex72: /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: version `GFORTRAN_9' not found (required by /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff CC linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o CLINKER linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 1 # ../matlab_ls_test: /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: version `GFORTRAN_9' not found (required by /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff balay at compute-386-07:/scratch/balay/petsc$ LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires queryval=matlab Using MAKEFLAGS: -- queryval=matlab query=requires TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts ok ksp_ksp_tutorials-ex72_12 ok diff-ksp_ksp_tutorials-ex72_12 TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts ok tao_leastsquares_tutorials_matlab-matlab_ls_test ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test # ------------- # Summary # ------------- # success 4/4 tests (100.0%) # failed 0/4 tests (0.0%) # todo 0/4 tests (0.0%) # skip 0/4 tests (0.0%) # # Wall clock time for tests: 27 sec # Approximate CPU time (not incl. build time): 15.190000000000001 sec # # Timing summary (actual test time / total CPU time): # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 sec # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec balay at compute-386-07:/scratch/balay/petsc$ On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > Based on the suggestions given by Sathish, I have tried to configure petsc > 3.13.4 with Matlab-R2020b. But, it was not successful. After running make > -j 10 test command I have got the following error message. > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > vit Sat Sep 2 12:27:22 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 126076. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > > I request you to help me to sort out this error. > > Thanks > Srinivas > > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla wrote: > > > I think there should be two hyphens in > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > i.e.: > > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via petsc-users < > > petsc-users at mcs.anl.gov> wrote: > > > >> Thank you Sathish.I will try this > >> > >> On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: > >> > >>> yes [and remove fblaslapack. don't know if hypre will work here]. > >>> > >>> i.e: > >>> > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>> --with-debugging=0 --with-x=0 \ > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 > >>> > >>> Satish > >>> > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > >>> > >>> > Hi Satish, > >>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > >>> > --known-64-bit-blas-indices=1 > >>> > > >>> > Is this what you are suggesting? > >>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay wrote: > >>> > > >>> > > Also: > >>> > > > >>> > > '-known-64-bit-blas-indices=1', > >>> > > > >>> > > Note: most externalpackages might not work in this mode. > >>> > > > >>> > > [we can't really over come such dependency/conflicts across packages] > >>> > > > >>> > > Satish > >>> > > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > >>> > > > >>> > > > Here is the matlab test that runs in CI > >>> > > > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>> > > > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > >>> > > > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with > >>> > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > >>> > > > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab - to > >>> have a > >>> > > compatible build > >>> > > > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > >>> > > > > >>> > > > Satish > >>> > > > > >>> > > > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > >>> wrote: > >>> > > > > >>> > > > > Hi Amneet, > >>> > > > > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not working. It is > >>> > > showing > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > >>> > > > > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh and > >>> this is > >>> > > for > >>> > > > > general usage not only for WEC. This I tried without linking > >>> Matlab > >>> > > with > >>> > > > > PETSc. Here also I got the error while configuring libmesh 1.6.2 > >>> that > >>> > > PETSc > >>> > > > > was not found but --enable-petsc-required is specified. > >>> > > > > > >>> > > > > The reason for specifically asking for libmesh with PETSc and > >>> Matlab > >>> > > is in > >>> > > > > the cfd-mpc-wecs application for complicated geometries it is > >>> > > mentioned to > >>> > > > > build cfd-mpc-wecs with libmesh construct. > >>> > > > > > >>> > > > > For the past 10 days I am trying these various things and ended > >>> up with > >>> > > > > errors. > >>> > > > > I want to solve this and proceed further to do my research work. > >>> > > > > > >>> > > > > Please help me to solve this as soon as possible. > >>> > > > > > >>> > > > > > >>> > > > > Thanks and Regards > >>> > > > > Srinivas > >>> > > > > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla > >>> > > wrote: > >>> > > > > > >>> > > > > > Hi Srinivas, > >>> > > > > > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC > >>> application. > >>> > > You > >>> > > > > > can just work with PETSc 3.17.5 that builds with Matlab. > >>> > > > > > > >>> > > > > > Do you have a specific reason for wanting to build libMesh? > >>> > > > > > > >>> > > > > > Thanks, > >>> > > > > > ?Amneet > >>> > > > > > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via > >>> > > petsc-users > >>> > > > > > wrote: > >>> > > > > > > >>> > > > > >> Hi, > >>> > > > > >> > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences > >>> of > >>> > > "-lut > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" got the > >>> > > following > >>> > > > > >> errors > >>> > > > > >> in petsc/3.13.4/linux-debug: > >>> > > > > >> TEST > >>> > > > > >> > >>> > > > >>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > >>> Error > >>> > > code: 124 > >>> > > > > >> # Running problem 5 > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > >>> > > > > >> -------------------------------------------------------------- > >>> > > > > >> # [0]PETSC ERROR: Error in external library > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > >>> > > > > >> # [0]PETSC ERROR: See > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for > >>> trouble > >>> > > > > >> shooting. > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named > >>> > > MB108SMEC028 > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > >>> > > > > >> # [0]PETSC ERROR: Configure options > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>> --with-debugging=1 > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>> --with-matlab-engine=1 > >>> > > > > >> > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>> > > > > >> > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > >>> > > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > >>> -------send > >>> > > entire > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > >>> > > > > >> # > >>> > > > > >> > >>> > > > >>> -------------------------------------------------------------------------- > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > >>> MPI_COMM_SELF > >>> > > > > >> # with errorcode 126076. > >>> > > > > >> # > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > >>> > > processes. > >>> > > > > >> # You may or may not see output from other processes, > >>> depending on > >>> > > > > >> # exactly when Open MPI kills them. > >>> > > > > >> # > >>> > > > > >> > >>> > > > >>> -------------------------------------------------------------------------- > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > >>> Command > >>> > > > > >> failed so no diff > >>> > > > > >> > >>> > > > > >> in petsc/3.13.4/linux-opt > >>> > > > > >> TEST > >>> > > > > >> > >>> > > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > >>> Error > >>> > > code: 124 > >>> > > > > >> # Running problem 5 > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > >>> > > > > >> -------------------------------------------------------------- > >>> > > > > >> # [0]PETSC ERROR: Error in external library > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > >>> > > > > >> # [0]PETSC ERROR: See > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for > >>> trouble > >>> > > > > >> shooting. > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > >>> > > MB108SMEC028 by > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > >>> > > > > >> # [0]PETSC ERROR: Configure options > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>> --COPTFLAGS=-O3 > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > >>> > > --with-debugging=0 > >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>> --with-matlab-engine=1 > >>> > > > > >> > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>> > > > > >> > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > >>> > > > > >> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > >>> -------send > >>> > > entire > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > >>> > > > > >> # > >>> > > > > >> > >>> > > > >>> -------------------------------------------------------------------------- > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > >>> MPI_COMM_SELF > >>> > > > > >> # with errorcode 126076. > >>> > > > > >> # > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > >>> > > processes. > >>> > > > > >> # You may or may not see output from other processes, > >>> depending on > >>> > > > > >> # exactly when Open MPI kills them. > >>> > > > > >> # > >>> > > > > >> > >>> > > > >>> -------------------------------------------------------------------------- > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > >>> Command > >>> > > > > >> failed so no diff. > >>> > > > > >> > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I am > >>> sharing the > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and petsc > >>> 3.17.5. > >>> > > Please find > >>> > > > > >> the attachment and do the needful. > >>> > > > > >> > >>> > > > > >> Thanks and regards > >>> > > > > >> Srinivas > >>> > > > > >> > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > >>> balay at mcs.anl.gov> > >>> > > wrote: > >>> > > > > >> > >>> > > > > >>> Well - you sent in libmesh log not petsc's > >>> configure.log/make.log > >>> > > for > >>> > > > > >>> petsc-3.17 > >>> > > > > >>> > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > >>> > > > > >>> > >>> > > > > >>> >>>> > >>> > > > > >>> > >>> > > > > >>> Matlab: > >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > >>> > > > > >>> /usr/local/MATLAB/R2020b > >>> > > > > >>> MatlabEngine: > >>> > > > > >>> Library: > >>> > > > > >>> > >>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex > >>> -lmx > >>> > > -lmat -lut > >>> > > > > >>> -licudata -licui18n -licuuc > >>> > > > > >>> Language used to compile PETSc: C > >>> > > > > >>> <<<<< > >>> > > > > >>> > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > >>> > > > > >>> > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>> > > > > >>> > >>> > > > > >>> >>> > >>> > > > > >>> Matlab: > >>> > > > > >>> Includes: > >>> > > > > >>> > >>> > > > >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > >>> > > > > >>> Libraries: > >>> > > > > >>> > >>> > > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>> > > > > >>> > >>> > > > >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>> > > > > >>> -leng -lmex -lmx -lmat > >>> > > > > >>> Executable: > >>> > > > > >>> > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > >>> > > > > >>> mex: > >>> > > > > >>> > >>> > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > >>> > > > > >>> matlab: > >>> > > > > >>> > >>> > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > >>> > > > > >>> -glnxa64 > >>> > > > > >>> <<< > >>> > > > > >>> > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. > >>> This > >>> > > might > >>> > > > > >>> be a change wrt newer matlab versions. > >>> > > > > >>> > >>> > > > > >>> You can: > >>> > > > > >>> > >>> > > > > >>> - edit > >>> > > > > >>> > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > >>> > > and > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > >>> > > > > >>> > >>> > > > > >>> And see if the build works now. > >>> > > > > >>> > >>> > > > > >>> Satish > >>> > > > > >>> > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > >>> petsc-users > >>> > > wrote: > >>> > > > > >>> > >>> > > > > >>> > I am sharing the log files while building petsc3.13.4 with > >>> > > matlab and > >>> > > > > >>> also > >>> > > > > >>> > the log file while building libmesh with petsc3.17.5 and > >>> matlab. > >>> > > > > >>> Building > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But > >>> libmesh is > >>> > > not > >>> > > > > >>> able to > >>> > > > > >>> > find the petsc > >>> > > > > >>> > Please find the attachments. > >>> > > > > >>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > >>> balay at mcs.anl.gov> > >>> > > > > >>> wrote: > >>> > > > > >>> > > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 and > >>> 3.17 [or > >>> > > 3.19]. > >>> > > > > >>> > > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to mailing > >>> list - > >>> > > or > >>> > > > > >>> send > >>> > > > > >>> > > them to petsc-maint] > >>> > > > > >>> > > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > >>> > > > > >>> > > > >>> > > > > >>> > > Satish > >>> > > > > >>> > > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > >>> petsc-users > >>> > > wrote: > >>> > > > > >>> > > > >>> > > > > >>> > > > I am sharing the make.log file while building > >>> petsc-3.13.4 > >>> > > with > >>> > > > > >>> Matlab. > >>> > > > > >>> > > > Please find the attachment and do the needful. > >>> > > > > >>> > > > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS > >>> 20PHD0548 < > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > >>> > > > > >>> > > > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of > >>> libmesh, the > >>> > > error > >>> > > > > >>> shows > >>> > > > > >>> > > > > petsc was not found > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > >>> > > balay at mcs.anl.gov> > >>> > > > > >>> > > wrote: > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> Here you are using 3.13 > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> Satish > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via > >>> > > petsc-users > >>> > > > > >>> wrote: > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > Hello, > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for working on > >>> the > >>> > > > > >>> simulation > >>> > > > > >>> > > using > >>> > > > > >>> > > > >> IBAMR > >>> > > > > >>> > > > >> > open software. While building the PETSc, using the > >>> > > following > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > >>> > > > > >>> > > > >> > ./configure \ > >>> > > > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > >>> > > > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > >>> > > > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > >>> > > > > >>> > > > >> > --with-debugging=1 \ > >>> > > > > >>> > > > >> > --download-hypre=1 \ > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > >>> > > > > >>> > > > >> > --with-x=0 \ > >>> > > > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > >>> > > > > >>> > > > >> > > >>> > > > > >>> > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > make -j4 > >>> > > > > >>> > > > >> > make -j4 test > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > I got the following error > >>> > > > > >>> > > > >> > CLINKER > >>> > > > > >>> > > > >> > >>> > > > > >>> > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > > >>> > > > >> > function `EvaluateResidual': > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > > >>> > > > >> > function `TaoPounders': > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>> > > > > >>> > > > >> > function `main': > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >>> > > > > >>> > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > >>> > > > > >>> > > > >> > > >>> > > > > >>> > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > >>> > > > > >>> > > > >> Error 1 > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > Please help me to solve this issue > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > Thank you > >>> > > > > >>> > > > >> > Srinivas > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > >> > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > >>> > > > > >>> > > >>> > > > > >>> > > >>> > > > > >>> > >>> > > > > >> > >>> > > > > >> > >>> > > > > >> *Disclaimer:This message was sent from Vellore Institute of > >>> > > Technology. > >>> > > > > >> The contents of this email may contain legally protected > >>> > > confidential or > >>> > > > > >> privileged information of ?Vellore Institute of Technology?. > >>> If > >>> > > you are > >>> > > > > >> not the intended recipient, you should not disseminate, > >>> distribute > >>> > > or copy > >>> > > > > >> this e-mail. Please notify the sender immediately and destroy > >>> all > >>> > > copies of > >>> > > > > >> this message and any attachments. If you have received this > >>> email > >>> > > in error, > >>> > > > > >> please promptly notify the sender by reply email and delete > >>> the > >>> > > original > >>> > > > > >> email and any backup copies without reading them.* > >>> > > > > >> > >>> > > > > > > >>> > > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > >>> > > >>> > >> > >> > >> *Disclaimer:This message was sent from Vellore Institute of Technology. > >> The contents of this email may contain legally protected confidential or > >> privileged information of ?Vellore Institute of Technology?. If you are > >> not the intended recipient, you should not disseminate, distribute or copy > >> this e-mail. Please notify the sender immediately and destroy all copies of > >> this message and any attachments. If you have received this email in error, > >> please promptly notify the sender by reply email and delete the original > >> email and any backup copies without reading them.* > >> > > > > > > -- > > --Amneet > > > > > > > > > > From balay at mcs.anl.gov Sat Sep 2 12:45:36 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Sat, 2 Sep 2023 12:45:36 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: Perhaps you can try the following to get additional info - and debug Satish ---------- balay at compute-386-07:/scratch/balay/petsc$ cd src/tao/leastsquares/tutorials/matlab/ balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ make matlab_ls_test /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib -L/scratch/balay/petsc/linux-opt/lib -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R202 1a/exter n/lib/glnxa64 -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o matlab_ls_test balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test -tao_smonitor -prob_id 5 -info [0] PetscInitialize(): PETSc successfully started: number of processors = 1 [0] PetscGetHostName(): Rejecting domainname, likely is NIS compute-386-07.(none) [0] PetscInitialize(): Running on machine: compute-386-07 Running problem 5 [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 -2080374784 max tags = 268435455 [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab -glnxa64 -nodisplay -nosplash [0] PetscMatlabEngineCreate(): Started MATLAB engine [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: TestingInitialize [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: TestingInitialize 5 <<<< Now verify if the above matlab command actually works for you - on this machine..>>>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab -glnxa64 -nodisplay -nosplash < M A T L A B (R) > Copyright 1984-2021 The MathWorks, Inc. R2021a (9.10.0.1602886) 64-bit (glnxa64) February 17, 2021 To get started, type doc. For product information, visit www.mathworks.com. >> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > Please don't cc: both petsc-users and petsc-maint [reverting thread to petsc-users only] > > I'm not sure what is happening here. Can you send the corresponding configure.log, make.log [compressed]? > > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, with Matlab-R2021a - and that works: > > balay at compute-386-07:/scratch/balay/petsc$ git branch > main > release > * release-3.13 > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a > balay at compute-386-07:/scratch/balay/petsc$ which matlab > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > balay at compute-386-07:/scratch/balay/petsc$ ./configure --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > Compilers: > C Compiler: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > C++ Compiler: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > Fortran Compiler: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > Linkers: > Shared linker: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > Dynamic linker: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > Libraries linked against: -lquadmath -lstdc++ -ldl > make: > Version: 4.2 > /usr/bin/make > BlasLapack: > Library: /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 -liomp5 -lpthread > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads > uses 8 byte integers > MPI: > Version: 4 > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > MPICH_NUMVERSION: 40002300 > pthread: > Library: -lpthread > cmake: > Version: 3.16.3 > /usr/bin/cmake > regex: > Matlab: > Includes: -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > MatlabEngine: > Library: -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > sowing: > Version: 1.1.25 > /scratch/balay/petsc/linux-opt/bin/bfort > valgrind: > Language used to compile PETSc: C > PETSc: > PETSC_ARCH: linux-opt > PETSC_DIR: /scratch/balay/petsc > Scalar type: real > Precision: double > Support for __float128 > Integer size: 4 bytes > shared libraries: enabled > Memory alignment from malloc(): 16 bytes > xxx=========================================================================xxx > Configure stage complete. Now build PETSc libraries with: > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > xxx=========================================================================xxx > balay at compute-386-07:/scratch/balay/petsc$ make > > > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > ========================================= > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires queryval=matlab > Using MAKEFLAGS: -- queryval=matlab query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > # ../ex72: /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: version `GFORTRAN_9' not found (required by /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > CC linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > CLINKER linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 1 > # ../matlab_ls_test: /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: version `GFORTRAN_9' not found (required by /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff > > balay at compute-386-07:/scratch/balay/petsc$ LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires queryval=matlab > Using MAKEFLAGS: -- queryval=matlab query=requires > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > ok ksp_ksp_tutorials-ex72_12 > ok diff-ksp_ksp_tutorials-ex72_12 > TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > > # ------------- > # Summary > # ------------- > # success 4/4 tests (100.0%) > # failed 0/4 tests (0.0%) > # todo 0/4 tests (0.0%) > # skip 0/4 tests (0.0%) > # > # Wall clock time for tests: 27 sec > # Approximate CPU time (not incl. build time): 15.190000000000001 sec > # > # Timing summary (actual test time / total CPU time): > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 sec > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > balay at compute-386-07:/scratch/balay/petsc$ > > > > > > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > > > Based on the suggestions given by Sathish, I have tried to configure petsc > > 3.13.4 with Matlab-R2020b. But, it was not successful. After running make > > -j 10 test command I have got the following error message. > > > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > > # Running problem 5 > > # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > # [0]PETSC ERROR: Error in external library > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > > vit Sat Sep 2 12:27:22 2023 > > # [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > # [0]PETSC ERROR: #2 main() line 126 in > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > # [0]PETSC ERROR: PETSc Option Table entries: > > # [0]PETSC ERROR: -prob_id 5 > > # [0]PETSC ERROR: -tao_smonitor > > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > > error message to petsc-maint at mcs.anl.gov---------- > > # -------------------------------------------------------------------------- > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > # with errorcode 126076. > > # > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > # You may or may not see output from other processes, depending on > > # exactly when Open MPI kills them. > > # -------------------------------------------------------------------------- > > > > I request you to help me to sort out this error. > > > > Thanks > > Srinivas > > > > > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla wrote: > > > > > I think there should be two hyphens in > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > > > i.e.: > > > > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via petsc-users < > > > petsc-users at mcs.anl.gov> wrote: > > > > > >> Thank you Sathish.I will try this > > >> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: > > >> > > >>> yes [and remove fblaslapack. don't know if hypre will work here]. > > >>> > > >>> i.e: > > >>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > >>> --with-debugging=0 --with-x=0 \ > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 > > >>> > > >>> Satish > > >>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > >>> > > >>> > Hi Satish, > > >>> > > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > > >>> > --known-64-bit-blas-indices=1 > > >>> > > > >>> > Is this what you are suggesting? > > >>> > > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay wrote: > > >>> > > > >>> > > Also: > > >>> > > > > >>> > > '-known-64-bit-blas-indices=1', > > >>> > > > > >>> > > Note: most externalpackages might not work in this mode. > > >>> > > > > >>> > > [we can't really over come such dependency/conflicts across packages] > > >>> > > > > >>> > > Satish > > >>> > > > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > >>> > > > > >>> > > > Here is the matlab test that runs in CI > > >>> > > > > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > >>> > > > > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > > >>> > > > > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with > > >>> > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > >>> > > > > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab - to > > >>> have a > > >>> > > compatible build > > >>> > > > > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > > >>> > > > > > >>> > > > Satish > > >>> > > > > > >>> > > > > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > >>> wrote: > > >>> > > > > > >>> > > > > Hi Amneet, > > >>> > > > > > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not working. It is > > >>> > > showing > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > > >>> > > > > > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh and > > >>> this is > > >>> > > for > > >>> > > > > general usage not only for WEC. This I tried without linking > > >>> Matlab > > >>> > > with > > >>> > > > > PETSc. Here also I got the error while configuring libmesh 1.6.2 > > >>> that > > >>> > > PETSc > > >>> > > > > was not found but --enable-petsc-required is specified. > > >>> > > > > > > >>> > > > > The reason for specifically asking for libmesh with PETSc and > > >>> Matlab > > >>> > > is in > > >>> > > > > the cfd-mpc-wecs application for complicated geometries it is > > >>> > > mentioned to > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > > >>> > > > > > > >>> > > > > For the past 10 days I am trying these various things and ended > > >>> up with > > >>> > > > > errors. > > >>> > > > > I want to solve this and proceed further to do my research work. > > >>> > > > > > > >>> > > > > Please help me to solve this as soon as possible. > > >>> > > > > > > >>> > > > > > > >>> > > > > Thanks and Regards > > >>> > > > > Srinivas > > >>> > > > > > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla > > >>> > > wrote: > > >>> > > > > > > >>> > > > > > Hi Srinivas, > > >>> > > > > > > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC > > >>> application. > > >>> > > You > > >>> > > > > > can just work with PETSc 3.17.5 that builds with Matlab. > > >>> > > > > > > > >>> > > > > > Do you have a specific reason for wanting to build libMesh? > > >>> > > > > > > > >>> > > > > > Thanks, > > >>> > > > > > ?Amneet > > >>> > > > > > > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS 20PHD0548 via > > >>> > > petsc-users > > >>> > > > > > wrote: > > >>> > > > > > > > >>> > > > > >> Hi, > > >>> > > > > >> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all occurrences > > >>> of > > >>> > > "-lut > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" got the > > >>> > > following > > >>> > > > > >> errors > > >>> > > > > >> in petsc/3.13.4/linux-debug: > > >>> > > > > >> TEST > > >>> > > > > >> > > >>> > > > > >>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > > >>> Error > > >>> > > code: 124 > > >>> > > > > >> # Running problem 5 > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > >>> > > > > >> -------------------------------------------------------------- > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > >>> > > > > >> # [0]PETSC ERROR: See > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for > > >>> trouble > > >>> > > > > >> shooting. > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named > > >>> > > MB108SMEC028 > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > >>> --with-debugging=1 > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>> --with-matlab-engine=1 > > >>> > > > > >> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>> > > > > >> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > >>> > > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > > >>> -------send > > >>> > > entire > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > >>> > > > > >> # > > >>> > > > > >> > > >>> > > > > >>> -------------------------------------------------------------------------- > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > >>> MPI_COMM_SELF > > >>> > > > > >> # with errorcode 126076. > > >>> > > > > >> # > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > >>> > > processes. > > >>> > > > > >> # You may or may not see output from other processes, > > >>> depending on > > >>> > > > > >> # exactly when Open MPI kills them. > > >>> > > > > >> # > > >>> > > > > >> > > >>> > > > > >>> -------------------------------------------------------------------------- > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > > >>> Command > > >>> > > > > >> failed so no diff > > >>> > > > > >> > > >>> > > > > >> in petsc/3.13.4/linux-opt > > >>> > > > > >> TEST > > >>> > > > > >> > > >>> > > > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > > >>> Error > > >>> > > code: 124 > > >>> > > > > >> # Running problem 5 > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > >>> > > > > >> -------------------------------------------------------------- > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > >>> > > > > >> # [0]PETSC ERROR: See > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html for > > >>> trouble > > >>> > > > > >> shooting. > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > >>> > > MB108SMEC028 by > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > >>> --COPTFLAGS=-O3 > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > > >>> > > --with-debugging=0 > > >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>> --with-matlab-engine=1 > > >>> > > > > >> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>> > > > > >> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > >>> > > > > >> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > > >>> -------send > > >>> > > entire > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > >>> > > > > >> # > > >>> > > > > >> > > >>> > > > > >>> -------------------------------------------------------------------------- > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > >>> MPI_COMM_SELF > > >>> > > > > >> # with errorcode 126076. > > >>> > > > > >> # > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > >>> > > processes. > > >>> > > > > >> # You may or may not see output from other processes, > > >>> depending on > > >>> > > > > >> # exactly when Open MPI kills them. > > >>> > > > > >> # > > >>> > > > > >> > > >>> > > > > >>> -------------------------------------------------------------------------- > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > > >>> Command > > >>> > > > > >> failed so no diff. > > >>> > > > > >> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I am > > >>> sharing the > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and petsc > > >>> 3.17.5. > > >>> > > Please find > > >>> > > > > >> the attachment and do the needful. > > >>> > > > > >> > > >>> > > > > >> Thanks and regards > > >>> > > > > >> Srinivas > > >>> > > > > >> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > > >>> balay at mcs.anl.gov> > > >>> > > wrote: > > >>> > > > > >> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > > >>> configure.log/make.log > > >>> > > for > > >>> > > > > >>> petsc-3.17 > > >>> > > > > >>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > >>> > > > > >>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> > > >>> > > > > >>> Matlab: > > >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > >>> > > > > >>> /usr/local/MATLAB/R2020b > > >>> > > > > >>> MatlabEngine: > > >>> > > > > >>> Library: > > >>> > > > > >>> > > >>> > > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex > > >>> -lmx > > >>> > > -lmat -lut > > >>> > > > > >>> -licudata -licui18n -licuuc > > >>> > > > > >>> Language used to compile PETSc: C > > >>> > > > > >>> <<<<< > > >>> > > > > >>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > >>> > > > > >>> > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > >>> > > > > >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> Matlab: > > >>> > > > > >>> Includes: > > >>> > > > > >>> > > >>> > > > > >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > >>> > > > > >>> Libraries: > > >>> > > > > >>> > > >>> > > > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > >>> > > > > >>> > > >>> > > > > >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > >>> > > > > >>> -leng -lmex -lmx -lmat > > >>> > > > > >>> Executable: > > >>> > > > > >>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > >>> > > > > >>> mex: > > >>> > > > > >>> > > >>> > > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > >>> > > > > >>> matlab: > > >>> > > > > >>> > > >>> > > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > >>> > > > > >>> -glnxa64 > > >>> > > > > >>> <<< > > >>> > > > > >>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset here. > > >>> This > > >>> > > might > > >>> > > > > >>> be a change wrt newer matlab versions. > > >>> > > > > >>> > > >>> > > > > >>> You can: > > >>> > > > > >>> > > >>> > > > > >>> - edit > > >>> > > > > >>> > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > >>> > > and > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n -licuuc" > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > >>> > > > > >>> > > >>> > > > > >>> And see if the build works now. > > >>> > > > > >>> > > >>> > > > > >>> Satish > > >>> > > > > >>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > >>> petsc-users > > >>> > > wrote: > > >>> > > > > >>> > > >>> > > > > >>> > I am sharing the log files while building petsc3.13.4 with > > >>> > > matlab and > > >>> > > > > >>> also > > >>> > > > > >>> > the log file while building libmesh with petsc3.17.5 and > > >>> matlab. > > >>> > > > > >>> Building > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But > > >>> libmesh is > > >>> > > not > > >>> > > > > >>> able to > > >>> > > > > >>> > find the petsc > > >>> > > > > >>> > Please find the attachments. > > >>> > > > > >>> > > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > > >>> balay at mcs.anl.gov> > > >>> > > > > >>> wrote: > > >>> > > > > >>> > > > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 and > > >>> 3.17 [or > > >>> > > 3.19]. > > >>> > > > > >>> > > > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to mailing > > >>> list - > > >>> > > or > > >>> > > > > >>> send > > >>> > > > > >>> > > them to petsc-maint] > > >>> > > > > >>> > > > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > >>> > > > > >>> > > > > >>> > > > > >>> > > Satish > > >>> > > > > >>> > > > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > >>> petsc-users > > >>> > > wrote: > > >>> > > > > >>> > > > > >>> > > > > >>> > > > I am sharing the make.log file while building > > >>> petsc-3.13.4 > > >>> > > with > > >>> > > > > >>> Matlab. > > >>> > > > > >>> > > > Please find the attachment and do the needful. > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS > > >>> 20PHD0548 < > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of > > >>> libmesh, the > > >>> > > error > > >>> > > > > >>> shows > > >>> > > > > >>> > > > > petsc was not found > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > > >>> > > balay at mcs.anl.gov> > > >>> > > > > >>> > > wrote: > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> Here you are using 3.13 > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> Satish > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > >>> > > petsc-users > > >>> > > > > >>> wrote: > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > Hello, > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for working on > > >>> the > > >>> > > > > >>> simulation > > >>> > > > > >>> > > using > > >>> > > > > >>> > > > >> IBAMR > > >>> > > > > >>> > > > >> > open software. While building the PETSc, using the > > >>> > > following > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > >>> > > > > >>> > > > >> > ./configure \ > > >>> > > > > >>> > > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > >>> > > > > >>> > > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > >>> > > > > >>> > > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > > >>> > > > > >>> > > > >> > --with-x=0 \ > > >>> > > > > >>> > > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > make -j4 > > >>> > > > > >>> > > > >> > make -j4 test > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > I got the following error > > >>> > > > > >>> > > > >> > CLINKER > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEnginePut' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > > >>> > > > >> > function `TaoPounders': > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGet' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>> > > > > >>> > > > >> > function `main': > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineCreate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineGetArray' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineEvaluate' > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > >>> > > > > >>> > > > >> > undefined reference to `PetscMatlabEngineDestroy' > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > >>> > > > > >>> > > > >> Error 1 > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > Please help me to solve this issue > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > Thank you > > >>> > > > > >>> > > > >> > Srinivas > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > >>> > > > > >>> > > > >>> > > > > >>> > > >>> > > > > >> > > >>> > > > > >> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore Institute of > > >>> > > Technology. > > >>> > > > > >> The contents of this email may contain legally protected > > >>> > > confidential or > > >>> > > > > >> privileged information of ?Vellore Institute of Technology?. > > >>> If > > >>> > > you are > > >>> > > > > >> not the intended recipient, you should not disseminate, > > >>> distribute > > >>> > > or copy > > >>> > > > > >> this e-mail. Please notify the sender immediately and destroy > > >>> all > > >>> > > copies of > > >>> > > > > >> this message and any attachments. If you have received this > > >>> email > > >>> > > in error, > > >>> > > > > >> please promptly notify the sender by reply email and delete > > >>> the > > >>> > > original > > >>> > > > > >> email and any backup copies without reading them.* > > >>> > > > > >> > > >>> > > > > > > > >>> > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > >>> > > >> > > >> > > >> *Disclaimer:This message was sent from Vellore Institute of Technology. > > >> The contents of this email may contain legally protected confidential or > > >> privileged information of ?Vellore Institute of Technology?. If you are > > >> not the intended recipient, you should not disseminate, distribute or copy > > >> this e-mail. Please notify the sender immediately and destroy all copies of > > >> this message and any attachments. If you have received this email in error, > > >> please promptly notify the sender by reply email and delete the original > > >> email and any backup copies without reading them.* > > >> > > > > > > > > > -- > > > --Amneet > > > > > > > > > > > > > > > > From david.knezevic at akselos.com Sat Sep 2 14:04:14 2023 From: david.knezevic at akselos.com (David Knezevic) Date: Sat, 2 Sep 2023 15:04:14 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? Message-ID: Hi all, I'm using the SNES solver for a plasticity model, and the issue I've run into is that in some time steps the solver terminates after "NL step 0" since the initial residual (based on the solution from the previous time step) is below the specified tolerance. I gather that "NL step 0" only checks the residual and doesn't actually do a Newtown update, and hence it seems that this is leading to inaccurate results in some cases. I can of course specify a smaller convergence tolerance to avoid this issue, but I've found it difficult to find a smaller tolerance that works well in all cases (e.g. it leads to too many iterations or non-convergence). So instead what I would like to do is ensure that the solver does at least 1 Newton iteration instead of terminating at "NL step 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", or specifying a "minimum number of iterations"? I didn't see anything like this in the documentation, so I was wondering if there are any suggestions on how to proceed for this. Thanks, David -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Sep 2 14:23:35 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 2 Sep 2023 15:23:35 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: On Sat, Sep 2, 2023 at 3:05?PM David Knezevic via petsc-users < petsc-users at mcs.anl.gov> wrote: > Hi all, > > I'm using the SNES solver for a plasticity model, and the issue I've run > into is that in some time steps the solver terminates after "NL step 0" > since the initial residual (based on the solution from the previous time > step) is below the specified tolerance. > > I gather that "NL step 0" only checks the residual and doesn't actually do > a Newtown update, and hence it seems that this is leading to inaccurate > results in some cases. > I do not understand this comment. What do you mean by "inaccurate"? Since we do not have the true solution, we usually say "inaccurate" for large residual, but you already said that the residual is small. Why would you want to do another iterate? > I can of course specify a smaller convergence tolerance to avoid this > issue, but I've found it difficult to find a smaller tolerance that works > well in all cases (e.g. it leads to too many iterations or > non-convergence). So instead what I would like to do is ensure that the > solver does at least 1 Newton iteration instead of terminating at "NL step > 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", > or specifying a "minimum number of iterations"? I didn't see anything like > this in the documentation, so I was wondering if there are any suggestions > on how to proceed for this. > The easiest way to do this is to write a custom convergence test that looks like this PetscErrorCode SNESConvergedDefault(SNES snes, PetscInt it, PetscReal xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void *dummy) { PetscFunctionBeginUser; if (!it) { *reason = SNES_CONVERGED_ITERATING; PetscFunctionReturn(PETSC_SUCCESS); } PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, reason, dummy)); PetscFunctionReturn(PETSC_SUCCESS); } Thanks, Matt > Thanks, > David > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.knezevic at akselos.com Sat Sep 2 16:44:32 2023 From: david.knezevic at akselos.com (David Knezevic) Date: Sat, 2 Sep 2023 17:44:32 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: OK, thanks, I'll look into the custom convergence test. I do not understand this comment. What do you mean by "inaccurate"? Since > we do not have the true solution, we usually say "inaccurate" for large > residual, but you already said that the residual is small. Why would you > want to do another iterate? I agree with your comments, but the specific case I'm considering is very numerically sensitive since it includes creep (which unfortunately has large exponential terms in it) which is the root cause of the issues I'm facing. Based on test cases with a known reference solution we're finding that we get inaccurate results due to steps with "zero iterations". We can fix this by tightening the tolerance but then we do an excessive number of iterations in other steps. So it seems to me that ensuring that we do at least one iteration will help here, so that's what I wanted to try. Thanks again for your help. Best, David On Sat, Sep 2, 2023 at 3:23?PM Matthew Knepley wrote: > On Sat, Sep 2, 2023 at 3:05?PM David Knezevic via petsc-users < > petsc-users at mcs.anl.gov> wrote: > >> Hi all, >> >> I'm using the SNES solver for a plasticity model, and the issue I've run >> into is that in some time steps the solver terminates after "NL step 0" >> since the initial residual (based on the solution from the previous time >> step) is below the specified tolerance. >> >> I gather that "NL step 0" only checks the residual and doesn't actually >> do a Newtown update, and hence it seems that this is leading to inaccurate >> results in some cases. >> > > I do not understand this comment. What do you mean by "inaccurate"? Since > we do not have the true solution, we usually say "inaccurate" for large > residual, but you already said that the residual is small. > Why would you want to do another iterate? > > >> I can of course specify a smaller convergence tolerance to avoid this >> issue, but I've found it difficult to find a smaller tolerance that works >> well in all cases (e.g. it leads to too many iterations or >> non-convergence). So instead what I would like to do is ensure that the >> solver does at least 1 Newton iteration instead of terminating at "NL step >> 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", >> or specifying a "minimum number of iterations"? I didn't see anything like >> this in the documentation, so I was wondering if there are any suggestions >> on how to proceed for this. >> > > The easiest way to do this is to write a custom convergence test that > looks like this > > PetscErrorCode SNESConvergedDefault(SNES snes, PetscInt it, PetscReal > xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void > *dummy) > { > PetscFunctionBeginUser; > if (!it) { > *reason = SNES_CONVERGED_ITERATING; > PetscFunctionReturn(PETSC_SUCCESS); > } > PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, reason, > dummy)); > PetscFunctionReturn(PETSC_SUCCESS); > } > > Thanks, > > Matt > > >> Thanks, >> David >> > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Sep 2 16:54:16 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 2 Sep 2023 17:54:16 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: On Sat, Sep 2, 2023 at 5:45?PM David Knezevic wrote: > OK, thanks, I'll look into the custom convergence test. > > I do not understand this comment. What do you mean by "inaccurate"? Since >> we do not have the true solution, we usually say "inaccurate" for large >> residual, but you already said that the residual is small. Why would you >> want to do another iterate? > > > I agree with your comments, but the specific case I'm considering is very > numerically sensitive since it includes creep (which unfortunately has > large exponential terms in it) which is the root cause of the issues I'm > facing. Based on test cases with a known reference solution we're finding > that we get inaccurate results due to steps with "zero iterations". We can > fix this by tightening the tolerance but then we do an excessive number of > iterations in other steps. So it seems to me that ensuring that we do at > least one iteration will help here, so that's what I wanted to try. > Hmm, it sounds like the convergence measure is bad. Maybe using a weighted norm would be better? Thanks, Matt > Thanks again for your help. > > Best, > David > > On Sat, Sep 2, 2023 at 3:23?PM Matthew Knepley wrote: > >> On Sat, Sep 2, 2023 at 3:05?PM David Knezevic via petsc-users < >> petsc-users at mcs.anl.gov> wrote: >> >>> Hi all, >>> >>> I'm using the SNES solver for a plasticity model, and the issue I've run >>> into is that in some time steps the solver terminates after "NL step 0" >>> since the initial residual (based on the solution from the previous time >>> step) is below the specified tolerance. >>> >>> I gather that "NL step 0" only checks the residual and doesn't actually >>> do a Newtown update, and hence it seems that this is leading to inaccurate >>> results in some cases. >>> >> >> I do not understand this comment. What do you mean by "inaccurate"? Since >> we do not have the true solution, we usually say "inaccurate" for large >> residual, but you already said that the residual is small. >> Why would you want to do another iterate? >> >> >>> I can of course specify a smaller convergence tolerance to avoid this >>> issue, but I've found it difficult to find a smaller tolerance that works >>> well in all cases (e.g. it leads to too many iterations or >>> non-convergence). So instead what I would like to do is ensure that the >>> solver does at least 1 Newton iteration instead of terminating at "NL step >>> 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", >>> or specifying a "minimum number of iterations"? I didn't see anything like >>> this in the documentation, so I was wondering if there are any suggestions >>> on how to proceed for this. >>> >> >> The easiest way to do this is to write a custom convergence test that >> looks like this >> >> PetscErrorCode SNESConvergedDefault(SNES snes, PetscInt it, PetscReal >> xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void >> *dummy) >> { >> PetscFunctionBeginUser; >> if (!it) { >> *reason = SNES_CONVERGED_ITERATING; >> PetscFunctionReturn(PETSC_SUCCESS); >> } >> PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, reason, >> dummy)); >> PetscFunctionReturn(PETSC_SUCCESS); >> } >> >> Thanks, >> >> Matt >> >> >>> Thanks, >>> David >>> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.knezevic at akselos.com Sat Sep 2 17:58:01 2023 From: david.knezevic at akselos.com (David Knezevic) Date: Sat, 2 Sep 2023 18:58:01 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: > > Hmm, it sounds like the convergence measure is bad. Maybe using a weighted > norm would be better? That's a good thought, I'd like to look into that idea too. Could you please give me some guidance on how to use a weighted norm in the convergence test? (Or are there any examples of doing that in the example suite?) Thanks, David On Sat, Sep 2, 2023 at 5:54?PM Matthew Knepley wrote: > On Sat, Sep 2, 2023 at 5:45?PM David Knezevic > wrote: > >> OK, thanks, I'll look into the custom convergence test. >> >> I do not understand this comment. What do you mean by "inaccurate"? Since >>> we do not have the true solution, we usually say "inaccurate" for large >>> residual, but you already said that the residual is small. Why would you >>> want to do another iterate? >> >> >> I agree with your comments, but the specific case I'm considering is very >> numerically sensitive since it includes creep (which unfortunately has >> large exponential terms in it) which is the root cause of the issues I'm >> facing. Based on test cases with a known reference solution we're finding >> that we get inaccurate results due to steps with "zero iterations". We can >> fix this by tightening the tolerance but then we do an excessive number of >> iterations in other steps. So it seems to me that ensuring that we do at >> least one iteration will help here, so that's what I wanted to try. >> > > Hmm, it sounds like the convergence measure is bad. Maybe using a weighted > norm would be better? > > Thanks, > > Matt > > >> Thanks again for your help. >> >> Best, >> David >> >> On Sat, Sep 2, 2023 at 3:23?PM Matthew Knepley wrote: >> >>> On Sat, Sep 2, 2023 at 3:05?PM David Knezevic via petsc-users < >>> petsc-users at mcs.anl.gov> wrote: >>> >>>> Hi all, >>>> >>>> I'm using the SNES solver for a plasticity model, and the issue I've >>>> run into is that in some time steps the solver terminates after "NL step 0" >>>> since the initial residual (based on the solution from the previous time >>>> step) is below the specified tolerance. >>>> >>>> I gather that "NL step 0" only checks the residual and doesn't actually >>>> do a Newtown update, and hence it seems that this is leading to inaccurate >>>> results in some cases. >>>> >>> >>> I do not understand this comment. What do you mean by "inaccurate"? >>> Since we do not have the true solution, we usually say "inaccurate" for >>> large residual, but you already said that the residual is small. >>> Why would you want to do another iterate? >>> >>> >>>> I can of course specify a smaller convergence tolerance to avoid this >>>> issue, but I've found it difficult to find a smaller tolerance that works >>>> well in all cases (e.g. it leads to too many iterations or >>>> non-convergence). So instead what I would like to do is ensure that the >>>> solver does at least 1 Newton iteration instead of terminating at "NL step >>>> 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", >>>> or specifying a "minimum number of iterations"? I didn't see anything like >>>> this in the documentation, so I was wondering if there are any suggestions >>>> on how to proceed for this. >>>> >>> >>> The easiest way to do this is to write a custom convergence test that >>> looks like this >>> >>> PetscErrorCode SNESConvergedDefault(SNES snes, PetscInt it, PetscReal >>> xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void >>> *dummy) >>> { >>> PetscFunctionBeginUser; >>> if (!it) { >>> *reason = SNES_CONVERGED_ITERATING; >>> PetscFunctionReturn(PETSC_SUCCESS); >>> } >>> PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, reason, >>> dummy)); >>> PetscFunctionReturn(PETSC_SUCCESS); >>> } >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> Thanks, >>>> David >>>> >>> >>> >>> -- >>> What most experimenters take for granted before they begin their >>> experiments is infinitely more interesting than any results to which their >>> experiments lead. >>> -- Norbert Wiener >>> >>> https://www.cse.buffalo.edu/~knepley/ >>> >>> >> > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Sat Sep 2 18:15:19 2023 From: bsmith at petsc.dev (Barry Smith) Date: Sat, 2 Sep 2023 19:15:19 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: https://petsc.org/release/manualpages/SNES/SNESSetForceIteration/#snessetforceiteration > On Sep 2, 2023, at 3:04 PM, David Knezevic via petsc-users wrote: > > Hi all, > > I'm using the SNES solver for a plasticity model, and the issue I've run into is that in some time steps the solver terminates after "NL step 0" since the initial residual (based on the solution from the previous time step) is below the specified tolerance. > > I gather that "NL step 0" only checks the residual and doesn't actually do a Newtown update, and hence it seems that this is leading to inaccurate results in some cases. I can of course specify a smaller convergence tolerance to avoid this issue, but I've found it difficult to find a smaller tolerance that works well in all cases (e.g. it leads to too many iterations or non-convergence). So instead what I would like to do is ensure that the solver does at least 1 Newton iteration instead of terminating at "NL step 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", or specifying a "minimum number of iterations"? I didn't see anything like this in the documentation, so I was wondering if there are any suggestions on how to proceed for this. > > Thanks, > David -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Sun Sep 3 02:16:44 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Sun, 3 Sep 2023 12:46:44 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: Hi Sathish, Thank you so much for your efforts and the support you are giving me to sort this out. I tried to follow the same procedure which you followed to build Petsc 3.13.4 with Matlab-R2020b on Ubuntu20.04. *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1* Using python3 for Python =============================================================================== Configuring PETSc to compile on your system =============================================================================== =============================================================================== It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure =============================================================================== Compilers: C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 Linkers: Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 Libraries linked against: -lquadmath -lstdc++ -ldl make: Version: 4.2 /usr/bin/make BlasLapack: Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads uses 8 byte integers MPI: Version: 3 Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe OMPI_VERSION: 4.1.4 pthread: cmake: Version: 3.16.3 /usr/bin/cmake regex: Matlab: Includes: -I/usr/local/MATLAB/R2020b/extern/include /usr/local/MATLAB/R2020b MatlabEngine: Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc Language used to compile PETSc: C PETSc: PETSC_ARCH: linux-opt PETSC_DIR: /home/vit/sfw/petsc/3.13.4 Scalar type: real Precision: double Support for __float128 Integer size: 4 bytes shared libraries: enabled Memory alignment from malloc(): 16 bytes xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with: make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all xxx=========================================================================xxx Then I removed all occurrences of -lut -licudata -licui18n -licuuc as you suggested earlier. *$make* FC linux-opt/obj/tao/f90-mod/petsctaomod.o CLINKER linux-opt/lib/libpetsc.so.3.13.4 BEGINNING TO COMPILE MATLAB INTERFACE Building with 'gcc'. /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. ========================================= Now to check if the libraries are working do: make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check =============================================== *$make test query=requires queryval=matlab* Using MAKEFLAGS: -- queryval=matlab query=requires CC linux-opt/tests/ksp/ksp/tutorials/ex72.o CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Unable to open file # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun Sep 3 11:51:03 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c # [0]PETSC ERROR: #5 MatLoad() line 1225 in /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c # [0]PETSC ERROR: #6 main() line 113 in /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -f0 /matrices/arco1 # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab # [0]PETSC ERROR: -pc_type lu # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF # with errorcode 113065. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff CC linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o CLINKER linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 # Running problem 5 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine on # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by vit Sun Sep 3 11:51:05 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -prob_id 5 # [0]PETSC ERROR: -tao_smonitor # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF # with errorcode 126076. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff # ------------- # Summary # ------------- # FAILED ksp_ksp_tutorials-ex72_12 tao_leastsquares_tutorials_matlab-matlab_ls_test # success 0/2 tests (0.0%) # failed 2/2 tests (100.0%) # todo 0/2 tests (0.0%) # skip 0/2 tests (0.0%) # # Wall clock time for tests: 3 sec # Approximate CPU time (not incl. build time): 0.05 sec # # To rerun failed tests: # /usr/bin/make -f gmakefile test test-fail=1 # # Timing summary (actual test time / total CPU time): # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec *How to sort out this error?* *$cd src/tao/leastsquares/tutorials/matlab/* *$make matlab_ls_test* /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -I/home/vit/sfw/petsc/3.13.4/include -I/home/vit/sfw/petsc/3.13.4/linux-opt/include -I/usr/local/MATLAB/R2020b/extern/include -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib -L/home/vit/sfw/linux/openmpi/4.1.4/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o matlab_ls_test I think there is a problem with the Matlab-R2020b version. I am sharing the configure.log and make.log files. Please find the attachment and do the needful. Thanks and regards Srinivas On Sat, Sep 2, 2023 at 11:15?PM Satish Balay wrote: > Perhaps you can try the following to get additional info - and debug > > Satish > ---------- > > balay at compute-386-07:/scratch/balay/petsc$ cd > src/tao/leastsquares/tutorials/matlab/ > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > make matlab_ls_test > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > -L/scratch/balay/petsc/linux-opt/lib > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex > -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi > -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o > matlab_ls_test > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > -tao_smonitor -prob_id 5 -info > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > compute-386-07.(none) > [0] PetscInitialize(): Running on machine: compute-386-07 > Running problem 5 > [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > -2080374784 max tags = 268435455 > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > -glnxa64 -nodisplay -nosplash > [0] PetscMatlabEngineCreate(): Started MATLAB engine > [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > TestingInitialize > [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > TestingInitialize > 5 > > > <<<< Now verify if the above matlab command actually works for you - on > this machine..>>>>> > > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > -glnxa64 -nodisplay -nosplash > > > < M A T L A B (R) > > > Copyright 1984-2021 The MathWorks, Inc. > > R2021a (9.10.0.1602886) 64-bit (glnxa64) > > February 17, 2021 > > > To get started, type doc. > For product information, visit www.mathworks.com. > > >> > > > On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > > > Please don't cc: both petsc-users and petsc-maint [reverting thread to > petsc-users only] > > > > I'm not sure what is happening here. Can you send the corresponding > configure.log, make.log [compressed]? > > > > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, with > Matlab-R2021a - and that works: > > > > balay at compute-386-07:/scratch/balay/petsc$ git branch > > main > > release > > * release-3.13 > > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a > > balay at compute-386-07:/scratch/balay/petsc$ which matlab > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > balay at compute-386-07:/scratch/balay/petsc$ ./configure > --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 --with-x=0 > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > > Compilers: > > > > > C Compiler: > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 > > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > C++ Compiler: > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC > > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > Fortran Compiler: > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall > -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > Linkers: > > Shared linker: > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC > -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > > Dynamic linker: > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC > -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > > Libraries linked against: -lquadmath -lstdc++ -ldl > > make: > > Version: 4.2 > > /usr/bin/make > > BlasLapack: > > Library: > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > -liomp5 -lpthread > > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to > control the number of threads > > uses 8 byte integers > > MPI: > > Version: 4 > > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > > MPICH_NUMVERSION: 40002300 > > pthread: > > Library: -lpthread > > cmake: > > Version: 3.16.3 > > /usr/bin/cmake > > regex: > > Matlab: > > Includes: > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > MatlabEngine: > > Library: > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > > sowing: > > Version: 1.1.25 > > /scratch/balay/petsc/linux-opt/bin/bfort > > valgrind: > > Language used to compile PETSc: C > > PETSc: > > PETSC_ARCH: linux-opt > > PETSC_DIR: /scratch/balay/petsc > > Scalar type: real > > Precision: double > > Support for __float128 > > Integer size: 4 bytes > > shared libraries: enabled > > Memory alignment from malloc(): 16 bytes > > > xxx=========================================================================xxx > > Configure stage complete. Now build PETSc libraries with: > > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > > > xxx=========================================================================xxx > > balay at compute-386-07:/scratch/balay/petsc$ make > > > > > > > > > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > > BEGINNING TO COMPILE MATLAB INTERFACE > > Building with 'gcc'. > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > | ^ > > > > MEX completed successfully. > > Building with 'gcc'. > > MEX completed successfully. > > Building with 'gcc'. > > MEX completed successfully. > > Building with 'gcc'. > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > | ^ > > > > MEX completed successfully. > > ========================================= > > Now to check if the libraries are working do: > > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > > ========================================= > > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires > queryval=matlab > > Using MAKEFLAGS: -- queryval=matlab query=requires > > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > > # ../ex72: > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > version `GFORTRAN_9' not found (required by > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > CC > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > CLINKER > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 1 > > # ../matlab_ls_test: > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > version `GFORTRAN_9' not found (required by > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > failed so no diff > > > > balay at compute-386-07:/scratch/balay/petsc$ > LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires > queryval=matlab > > Using MAKEFLAGS: -- queryval=matlab query=requires > > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > ok ksp_ksp_tutorials-ex72_12 > > ok diff-ksp_ksp_tutorials-ex72_12 > > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > # ------------- > > # Summary > > # ------------- > > # success 4/4 tests (100.0%) > > # failed 0/4 tests (0.0%) > > # todo 0/4 tests (0.0%) > > # skip 0/4 tests (0.0%) > > # > > # Wall clock time for tests: 27 sec > > # Approximate CPU time (not incl. build time): 15.190000000000001 sec > > # > > # Timing summary (actual test time / total CPU time): > > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 sec > > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > > balay at compute-386-07:/scratch/balay/petsc$ > > > > > > > > > > > > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > > > > > Based on the suggestions given by Sathish, I have tried to configure > petsc > > > 3.13.4 with Matlab-R2020b. But, it was not successful. After running > make > > > -j 10 test command I have got the following error message. > > > > > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: > 124 > > > # Running problem 5 > > > # [0]PETSC ERROR: --------------------- Error Message > > > -------------------------------------------------------------- > > > # [0]PETSC ERROR: Error in external library > > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > for trouble shooting. > > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 > by > > > vit Sat Sep 2 12:27:22 2023 > > > # [0]PETSC ERROR: Configure options > > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > --known-64-bit-blas-indices=1 > > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > # [0]PETSC ERROR: #2 main() line 126 in > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > # [0]PETSC ERROR: PETSc Option Table entries: > > > # [0]PETSC ERROR: -prob_id 5 > > > # [0]PETSC ERROR: -tao_smonitor > > > # [0]PETSC ERROR: ----------------End of Error Message -------send > entire > > > error message to petsc-maint at mcs.anl.gov---------- > > > # > -------------------------------------------------------------------------- > > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > # with errorcode 126076. > > > # > > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > > # You may or may not see output from other processes, depending on > > > # exactly when Open MPI kills them. > > > # > -------------------------------------------------------------------------- > > > > > > I request you to help me to sort out this error. > > > > > > Thanks > > > Srinivas > > > > > > > > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla > wrote: > > > > > > > I think there should be two hyphens in > > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > > > > > i.e.: > > > > > > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > > > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via > petsc-users < > > > > petsc-users at mcs.anl.gov> wrote: > > > > > > > >> Thank you Sathish.I will try this > > > >> > > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: > > > >> > > > >>> yes [and remove fblaslapack. don't know if hypre will work here]. > > > >>> > > > >>> i.e: > > > >>> > > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > >>> --with-debugging=0 --with-x=0 \ > > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 > > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 > > > >>> > > > >>> Satish > > > >>> > > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > > > >>> > > > >>> > Hi Satish, > > > >>> > > > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > > > >>> > --known-64-bit-blas-indices=1 > > > >>> > > > > >>> > Is this what you are suggesting? > > > >>> > > > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay > wrote: > > > >>> > > > > >>> > > Also: > > > >>> > > > > > >>> > > '-known-64-bit-blas-indices=1', > > > >>> > > > > > >>> > > Note: most externalpackages might not work in this mode. > > > >>> > > > > > >>> > > [we can't really over come such dependency/conflicts across > packages] > > > >>> > > > > > >>> > > Satish > > > >>> > > > > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > > >>> > > > > > >>> > > > Here is the matlab test that runs in CI > > > >>> > > > > > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > >>> > > > > > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > >>> > > > > > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with > > > >>> > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > > >>> > > > > > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab - > to > > > >>> have a > > > >>> > > compatible build > > > >>> > > > > > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > > > >>> > > > > > > >>> > > > Satish > > > >>> > > > > > > >>> > > > > > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > > >>> wrote: > > > >>> > > > > > > >>> > > > > Hi Amneet, > > > >>> > > > > > > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not > working. It is > > > >>> > > showing > > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > > > >>> > > > > > > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh > and > > > >>> this is > > > >>> > > for > > > >>> > > > > general usage not only for WEC. This I tried without > linking > > > >>> Matlab > > > >>> > > with > > > >>> > > > > PETSc. Here also I got the error while configuring libmesh > 1.6.2 > > > >>> that > > > >>> > > PETSc > > > >>> > > > > was not found but --enable-petsc-required is specified. > > > >>> > > > > > > > >>> > > > > The reason for specifically asking for libmesh with PETSc > and > > > >>> Matlab > > > >>> > > is in > > > >>> > > > > the cfd-mpc-wecs application for complicated geometries it > is > > > >>> > > mentioned to > > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > > > >>> > > > > > > > >>> > > > > For the past 10 days I am trying these various things and > ended > > > >>> up with > > > >>> > > > > errors. > > > >>> > > > > I want to solve this and proceed further to do my research > work. > > > >>> > > > > > > > >>> > > > > Please help me to solve this as soon as possible. > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > Thanks and Regards > > > >>> > > > > Srinivas > > > >>> > > > > > > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > mail2amneet at gmail.com> > > > >>> > > wrote: > > > >>> > > > > > > > >>> > > > > > Hi Srinivas, > > > >>> > > > > > > > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC > > > >>> application. > > > >>> > > You > > > >>> > > > > > can just work with PETSc 3.17.5 that builds with Matlab. > > > >>> > > > > > > > > >>> > > > > > Do you have a specific reason for wanting to build > libMesh? > > > >>> > > > > > > > > >>> > > > > > Thanks, > > > >>> > > > > > ?Amneet > > > >>> > > > > > > > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS > 20PHD0548 via > > > >>> > > petsc-users > > > >>> > > > > > wrote: > > > >>> > > > > > > > > >>> > > > > >> Hi, > > > >>> > > > > >> > > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all > occurrences > > > >>> of > > > >>> > > "-lut > > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" > got the > > > >>> > > following > > > >>> > > > > >> errors > > > >>> > > > > >> in petsc/3.13.4/linux-debug: > > > >>> > > > > >> TEST > > > >>> > > > > >> > > > >>> > > > > > >>> > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test > # > > > >>> Error > > > >>> > > code: 124 > > > >>> > > > > >> # Running problem 5 > > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > >>> > > > > >> > -------------------------------------------------------------- > > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>> > > > > >> # [0]PETSC ERROR: See > > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html > for > > > >>> trouble > > > >>> > > > > >> shooting. > > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > 2020 > > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug > named > > > >>> > > MB108SMEC028 > > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > >>> --with-debugging=1 > > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>> --with-matlab-engine=1 > > > >>> > > > > >> > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 > in > > > >>> > > > > >> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > >>> > > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > > > >>> -------send > > > >>> > > entire > > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > >>> > > > > >> # > > > >>> > > > > >> > > > >>> > > > > > >>> > -------------------------------------------------------------------------- > > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > > >>> MPI_COMM_SELF > > > >>> > > > > >> # with errorcode 126076. > > > >>> > > > > >> # > > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all > MPI > > > >>> > > processes. > > > >>> > > > > >> # You may or may not see output from other processes, > > > >>> depending on > > > >>> > > > > >> # exactly when Open MPI kills them. > > > >>> > > > > >> # > > > >>> > > > > >> > > > >>> > > > > > >>> > -------------------------------------------------------------------------- > > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > SKIP > > > >>> Command > > > >>> > > > > >> failed so no diff > > > >>> > > > > >> > > > >>> > > > > >> in petsc/3.13.4/linux-opt > > > >>> > > > > >> TEST > > > >>> > > > > >> > > > >>> > > > > > >>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test > # > > > >>> Error > > > >>> > > code: 124 > > > >>> > > > > >> # Running problem 5 > > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > >>> > > > > >> > -------------------------------------------------------------- > > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>> > > > > >> # [0]PETSC ERROR: See > > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html > for > > > >>> trouble > > > >>> > > > > >> shooting. > > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > 2020 > > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > > >>> > > MB108SMEC028 by > > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > >>> --COPTFLAGS=-O3 > > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > > > >>> > > --with-debugging=0 > > > >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>> --with-matlab-engine=1 > > > >>> > > > > >> > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 > in > > > >>> > > > > >> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > >>> > > > > >> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > > > >>> -------send > > > >>> > > entire > > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > >>> > > > > >> # > > > >>> > > > > >> > > > >>> > > > > > >>> > -------------------------------------------------------------------------- > > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > > >>> MPI_COMM_SELF > > > >>> > > > > >> # with errorcode 126076. > > > >>> > > > > >> # > > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all > MPI > > > >>> > > processes. > > > >>> > > > > >> # You may or may not see output from other processes, > > > >>> depending on > > > >>> > > > > >> # exactly when Open MPI kills them. > > > >>> > > > > >> # > > > >>> > > > > >> > > > >>> > > > > > >>> > -------------------------------------------------------------------------- > > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > SKIP > > > >>> Command > > > >>> > > > > >> failed so no diff. > > > >>> > > > > >> > > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I am > > > >>> sharing the > > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and petsc > > > >>> 3.17.5. > > > >>> > > Please find > > > >>> > > > > >> the attachment and do the needful. > > > >>> > > > > >> > > > >>> > > > > >> Thanks and regards > > > >>> > > > > >> Srinivas > > > >>> > > > > >> > > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > > > >>> balay at mcs.anl.gov> > > > >>> > > wrote: > > > >>> > > > > >> > > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > > > >>> configure.log/make.log > > > >>> > > for > > > >>> > > > > >>> petsc-3.17 > > > >>> > > > > >>> > > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > > >>> > > > > >>> > > > >>> > > > > >>> >>>> > > > >>> > > > > >>> > > > >>> > > > > >>> Matlab: > > > >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > >>> > > > > >>> /usr/local/MATLAB/R2020b > > > >>> > > > > >>> MatlabEngine: > > > >>> > > > > >>> Library: > > > >>> > > > > >>> > > > >>> > > > > > >>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng > -lmex > > > >>> -lmx > > > >>> > > -lmat -lut > > > >>> > > > > >>> -licudata -licui18n -licuuc > > > >>> > > > > >>> Language used to compile PETSc: C > > > >>> > > > > >>> <<<<< > > > >>> > > > > >>> > > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > > >>> > > > > >>> > > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > >>> > > > > >>> > > > >>> > > > > >>> >>> > > > >>> > > > > >>> Matlab: > > > >>> > > > > >>> Includes: > > > >>> > > > > >>> > > > >>> > > > > > >>> > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > >>> > > > > >>> Libraries: > > > >>> > > > > >>> > > > >>> > > > > > >>> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > >>> > > > > >>> > > > >>> > > > > > >>> > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > >>> > > > > >>> -leng -lmex -lmx -lmat > > > >>> > > > > >>> Executable: > > > >>> > > > > >>> > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > >>> > > > > >>> mex: > > > >>> > > > > >>> > > > >>> > > > > > >>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > >>> > > > > >>> matlab: > > > >>> > > > > >>> > > > >>> > > > > > >>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > >>> > > > > >>> -glnxa64 > > > >>> > > > > >>> <<< > > > >>> > > > > >>> > > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset > here. > > > >>> This > > > >>> > > might > > > >>> > > > > >>> be a change wrt newer matlab versions. > > > >>> > > > > >>> > > > >>> > > > > >>> You can: > > > >>> > > > > >>> > > > >>> > > > > >>> - edit > > > >>> > > > > >>> > > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > > >>> > > and > > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n > -licuuc" > > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > > >>> > > > > >>> > > > >>> > > > > >>> And see if the build works now. > > > >>> > > > > >>> > > > >>> > > > > >>> Satish > > > >>> > > > > >>> > > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > > >>> petsc-users > > > >>> > > wrote: > > > >>> > > > > >>> > > > >>> > > > > >>> > I am sharing the log files while building > petsc3.13.4 with > > > >>> > > matlab and > > > >>> > > > > >>> also > > > >>> > > > > >>> > the log file while building libmesh with petsc3.17.5 > and > > > >>> matlab. > > > >>> > > > > >>> Building > > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But > > > >>> libmesh is > > > >>> > > not > > > >>> > > > > >>> able to > > > >>> > > > > >>> > find the petsc > > > >>> > > > > >>> > Please find the attachments. > > > >>> > > > > >>> > > > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > > > >>> balay at mcs.anl.gov> > > > >>> > > > > >>> wrote: > > > >>> > > > > >>> > > > > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 > and > > > >>> 3.17 [or > > > >>> > > 3.19]. > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to > mailing > > > >>> list - > > > >>> > > or > > > >>> > > > > >>> send > > > >>> > > > > >>> > > them to petsc-maint] > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > Satish > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > > >>> petsc-users > > > >>> > > wrote: > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > I am sharing the make.log file while building > > > >>> petsc-3.13.4 > > > >>> > > with > > > >>> > > > > >>> Matlab. > > > >>> > > > > >>> > > > Please find the attachment and do the needful. > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS > > > >>> 20PHD0548 < > > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of > > > >>> libmesh, the > > > >>> > > error > > > >>> > > > > >>> shows > > > >>> > > > > >>> > > > > petsc was not found > > > >>> > > > > >>> > > > > > > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > > > >>> > > balay at mcs.anl.gov> > > > >>> > > > > >>> > > wrote: > > > >>> > > > > >>> > > > > > > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> Here you are using 3.13 > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> Satish > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS > 20PHD0548 via > > > >>> > > petsc-users > > > >>> > > > > >>> wrote: > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > Hello, > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for > working on > > > >>> the > > > >>> > > > > >>> simulation > > > >>> > > > > >>> > > using > > > >>> > > > > >>> > > > >> IBAMR > > > >>> > > > > >>> > > > >> > open software. While building the PETSc, > using the > > > >>> > > following > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > >>> > > > > >>> > > > >> > ./configure \ > > > >>> > > > > >>> > > > >> > > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > >>> > > > > >>> > > > >> > > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > >>> > > > > >>> > > > >> > > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > > > >>> > > > > >>> > > > >> > --with-x=0 \ > > > >>> > > > > >>> > > > >> > > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > make -j4 > > > >>> > > > > >>> > > > >> > make -j4 test > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > I got the following error > > > >>> > > > > >>> > > > >> > CLINKER > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEnginePut' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineEvaluate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGet' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEnginePut' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineEvaluate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGet' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > > >>> > > > >> > function `TaoPounders': > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGet' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>> > > > > >>> > > > >> > function `main': > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineCreate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineEvaluate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineEvaluate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGetArray' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGetArray' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGetArray' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGetArray' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineGetArray' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineEvaluate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineEvaluate' > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > >>> > > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > >>> > > > > >>> > > > >> > undefined reference to > `PetscMatlabEngineDestroy' > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > >>> > > > > >>> > > > >> Error 1 > > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > Please help me to solve this issue > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > Thank you > > > >>> > > > > >>> > > > >> > Srinivas > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > >> > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> > > > >>> > > > > >> > > > >>> > > > > >> > > > >>> > > > > >> *Disclaimer:This message was sent from Vellore > Institute of > > > >>> > > Technology. > > > >>> > > > > >> The contents of this email may contain legally protected > > > >>> > > confidential or > > > >>> > > > > >> privileged information of ?Vellore Institute of > Technology?. > > > >>> If > > > >>> > > you are > > > >>> > > > > >> not the intended recipient, you should not disseminate, > > > >>> distribute > > > >>> > > or copy > > > >>> > > > > >> this e-mail. Please notify the sender immediately and > destroy > > > >>> all > > > >>> > > copies of > > > >>> > > > > >> this message and any attachments. If you have received > this > > > >>> email > > > >>> > > in error, > > > >>> > > > > >> please promptly notify the sender by reply email and > delete > > > >>> the > > > >>> > > original > > > >>> > > > > >> email and any backup copies without reading them.* > > > >>> > > > > >> > > > >>> > > > > > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > >>> > > > > >>> > > > >> > > > >> > > > >> *Disclaimer:This message was sent from Vellore Institute of > Technology. > > > >> The contents of this email may contain legally protected > confidential or > > > >> privileged information of ?Vellore Institute of Technology?. If > you are > > > >> not the intended recipient, you should not disseminate, distribute > or copy > > > >> this e-mail. Please notify the sender immediately and destroy all > copies of > > > >> this message and any attachments. If you have received this email > in error, > > > >> please promptly notify the sender by reply email and delete the > original > > > >> email and any backup copies without reading them.* > > > >> > > > > > > > > > > > > -- > > > > --Amneet > > > > > > > > > > > > > > > > > > > > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: make.log.gz Type: application/gzip Size: 12780 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log.gz Type: application/gzip Size: 105735 bytes Desc: not available URL: From knepley at gmail.com Sun Sep 3 07:33:39 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 3 Sep 2023 08:33:39 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: On Sat, Sep 2, 2023 at 6:58?PM David Knezevic wrote: > Hmm, it sounds like the convergence measure is bad. Maybe using a weighted >> norm would be better? > > > That's a good thought, I'd like to look into that idea too. Could you > please give me some guidance on how to use a weighted norm in the > convergence test? (Or are there any examples of doing that in the example > suite?) > I guess the idea would be the following: You have exponential terms in your equation. You get a relatively small residual, but unacceptable error. This leads me to believe that some part of the residual is swamping other parts you care about. This should be confirmed by plotting the residual for one of these 0-iterate cases. To prevent this imbalance, you would scale the residual to give more weight to the underrepresented parts, probably with an inverse of the exponential. This is just a more complicated form of the diagonal scaling commonly used to give all fields the same scale. Thanks, Matt > Thanks, > David > > On Sat, Sep 2, 2023 at 5:54?PM Matthew Knepley wrote: > >> On Sat, Sep 2, 2023 at 5:45?PM David Knezevic >> wrote: >> >>> OK, thanks, I'll look into the custom convergence test. >>> >>> I do not understand this comment. What do you mean by "inaccurate"? >>>> Since we do not have the true solution, we usually say "inaccurate" for >>>> large residual, but you already said that the residual is small. Why would >>>> you want to do another iterate? >>> >>> >>> I agree with your comments, but the specific case I'm considering is >>> very numerically sensitive since it includes creep (which unfortunately has >>> large exponential terms in it) which is the root cause of the issues I'm >>> facing. Based on test cases with a known reference solution we're finding >>> that we get inaccurate results due to steps with "zero iterations". We can >>> fix this by tightening the tolerance but then we do an excessive number of >>> iterations in other steps. So it seems to me that ensuring that we do at >>> least one iteration will help here, so that's what I wanted to try. >>> >> >> Hmm, it sounds like the convergence measure is bad. Maybe using a >> weighted norm would be better? >> >> Thanks, >> >> Matt >> >> >>> Thanks again for your help. >>> >>> Best, >>> David >>> >>> On Sat, Sep 2, 2023 at 3:23?PM Matthew Knepley >>> wrote: >>> >>>> On Sat, Sep 2, 2023 at 3:05?PM David Knezevic via petsc-users < >>>> petsc-users at mcs.anl.gov> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I'm using the SNES solver for a plasticity model, and the issue I've >>>>> run into is that in some time steps the solver terminates after "NL step 0" >>>>> since the initial residual (based on the solution from the previous time >>>>> step) is below the specified tolerance. >>>>> >>>>> I gather that "NL step 0" only checks the residual and doesn't >>>>> actually do a Newtown update, and hence it seems that this is leading to >>>>> inaccurate results in some cases. >>>>> >>>> >>>> I do not understand this comment. What do you mean by "inaccurate"? >>>> Since we do not have the true solution, we usually say "inaccurate" for >>>> large residual, but you already said that the residual is small. >>>> Why would you want to do another iterate? >>>> >>>> >>>>> I can of course specify a smaller convergence tolerance to avoid this >>>>> issue, but I've found it difficult to find a smaller tolerance that works >>>>> well in all cases (e.g. it leads to too many iterations or >>>>> non-convergence). So instead what I would like to do is ensure that the >>>>> solver does at least 1 Newton iteration instead of terminating at "NL step >>>>> 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", >>>>> or specifying a "minimum number of iterations"? I didn't see anything like >>>>> this in the documentation, so I was wondering if there are any suggestions >>>>> on how to proceed for this. >>>>> >>>> >>>> The easiest way to do this is to write a custom convergence test that >>>> looks like this >>>> >>>> PetscErrorCode SNESConvergedDefault(SNES snes, PetscInt it, PetscReal >>>> xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void >>>> *dummy) >>>> { >>>> PetscFunctionBeginUser; >>>> if (!it) { >>>> *reason = SNES_CONVERGED_ITERATING; >>>> PetscFunctionReturn(PETSC_SUCCESS); >>>> } >>>> PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, reason, >>>> dummy)); >>>> PetscFunctionReturn(PETSC_SUCCESS); >>>> } >>>> >>>> Thanks, >>>> >>>> Matt >>>> >>>> >>>>> Thanks, >>>>> David >>>>> >>>> >>>> >>>> -- >>>> What most experimenters take for granted before they begin their >>>> experiments is infinitely more interesting than any results to which their >>>> experiments lead. >>>> -- Norbert Wiener >>>> >>>> https://www.cse.buffalo.edu/~knepley/ >>>> >>>> >>> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> >> > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sun Sep 3 07:36:36 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 3 Sep 2023 08:36:36 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via petsc-users < petsc-users at mcs.anl.gov> wrote: > Hi Sathish, > > Thank you so much for your efforts and the support you are giving me to > sort this out. > > I tried to follow the same procedure which you followed to build Petsc > 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1* > Using python3 for Python > > =============================================================================== > Configuring PETSc to compile on your system > > > =============================================================================== > =============================================================================== > It appears you do not have valgrind > installed on your system. > We HIGHLY recommend you install it from www.valgrind.org > Or install valgrind-devel or > equivalent using your package manager. > Then rerun ./configure > > =============================================================================== > Compilers: > > C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC > -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx -Wall > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC > Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 -fPIC > -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > Linkers: > Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared > -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared > -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > Libraries linked against: -lquadmath -lstdc++ -ldl > make: > Version: 4.2 > /usr/bin/make > BlasLapack: > Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to > control the number of threads > uses 8 byte integers > MPI: > Version: 3 > Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe > OMPI_VERSION: 4.1.4 > pthread: > cmake: > Version: 3.16.3 > /usr/bin/cmake > regex: > Matlab: > Includes: -I/usr/local/MATLAB/R2020b/extern/include > /usr/local/MATLAB/R2020b > MatlabEngine: > Library: > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut > -licudata -licui18n -licuuc > Language used to compile PETSc: C > PETSc: > PETSC_ARCH: linux-opt > PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > Scalar type: real > Precision: double > Support for __float128 > Integer size: 4 bytes > shared libraries: enabled > Memory alignment from malloc(): 16 bytes > > xxx=========================================================================xxx > Configure stage complete. Now build PETSc libraries with: > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all > > xxx=========================================================================xxx > > Then I removed all occurrences of -lut -licudata -licui18n -licuuc as you > suggested earlier. > > *$make* > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > =============================================== > > *$make test query=requires queryval=matlab* > Using MAKEFLAGS: -- queryval=matlab query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Unable to open file > # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > No, the problem is that you do not have DATAFILESPATH defined, so it cannot find the matrix to test. Try running some test of yours. Thanks, Matt > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun Sep > 3 11:51:03 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > # [0]PETSC ERROR: #5 MatLoad() line 1225 in > /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > # [0]PETSC ERROR: #6 main() line 113 in > /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -f0 /matrices/arco1 > # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > # [0]PETSC ERROR: -pc_type lu > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # > -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 113065. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # > -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > CC > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > CLINKER > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > vit Sun Sep 3 11:51:05 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # > -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 126076. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # > -------------------------------------------------------------------------- > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed > so no diff > > # ------------- > # Summary > # ------------- > # FAILED ksp_ksp_tutorials-ex72_12 > tao_leastsquares_tutorials_matlab-matlab_ls_test > # success 0/2 tests (0.0%) > # failed 2/2 tests (100.0%) > # todo 0/2 tests (0.0%) > # skip 0/2 tests (0.0%) > # > # Wall clock time for tests: 3 sec > # Approximate CPU time (not incl. build time): 0.05 sec > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > # > # Timing summary (actual test time / total CPU time): > # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec > > *How to sort out this error?* > > *$cd src/tao/leastsquares/tutorials/matlab/* > *$make matlab_ls_test* > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > -I/home/vit/sfw/petsc/3.13.4/include > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > -I/usr/local/MATLAB/R2020b/extern/include > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath > -lstdc++ -ldl -o matlab_ls_test > > I think there is a problem with the Matlab-R2020b version. > I am sharing the configure.log and make.log files. Please find the > attachment and do the needful. > > > Thanks and regards > Srinivas > > > On Sat, Sep 2, 2023 at 11:15?PM Satish Balay wrote: > >> Perhaps you can try the following to get additional info - and debug >> >> Satish >> ---------- >> >> balay at compute-386-07:/scratch/balay/petsc$ cd >> src/tao/leastsquares/tutorials/matlab/ >> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >> make matlab_ls_test >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >> -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include >> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >> -L/scratch/balay/petsc/linux-opt/lib >> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex >> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi >> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >> matlab_ls_test >> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >> -tao_smonitor -prob_id 5 -info >> [0] PetscInitialize(): PETSc successfully started: number of processors = >> 1 >> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >> compute-386-07.(none) >> [0] PetscInitialize(): Running on machine: compute-386-07 >> Running problem 5 >> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >> -2080374784 max tags = 268435455 >> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >> -glnxa64 -nodisplay -nosplash >> [0] PetscMatlabEngineCreate(): Started MATLAB engine >> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >> TestingInitialize >> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >> TestingInitialize >> 5 >> >> >> <<<< Now verify if the above matlab command actually works for you - on >> this machine..>>>>> >> >> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >> -glnxa64 -nodisplay -nosplash >> >> >> < M A T L A B (R) > >> >> Copyright 1984-2021 The MathWorks, Inc. >> >> R2021a (9.10.0.1602886) 64-bit (glnxa64) >> >> February 17, 2021 >> >> >> To get started, type doc. >> For product information, visit www.mathworks.com. >> >> >> >> >> >> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >> >> > Please don't cc: both petsc-users and petsc-maint [reverting thread to >> petsc-users only] >> > >> > I'm not sure what is happening here. Can you send the corresponding >> configure.log, make.log [compressed]? >> > >> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, with >> Matlab-R2021a - and that works: >> > >> > balay at compute-386-07:/scratch/balay/petsc$ git branch >> > main >> > release >> > * release-3.13 >> > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a >> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >> > >> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >> --with-debugging=0 --with-x=0 >> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >> > >> > Compilers: >> >> >> >> > C Compiler: >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >> -fvisibility=hidden -O3 >> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> > C++ Compiler: >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >> -fvisibility=hidden -O3 -fPIC >> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> > Fortran Compiler: >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall >> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> > Linkers: >> > Shared linker: >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC >> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -fvisibility=hidden -O3 >> > Dynamic linker: >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC >> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -fvisibility=hidden -O3 >> > Libraries linked against: -lquadmath -lstdc++ -ldl >> > make: >> > Version: 4.2 >> > /usr/bin/make >> > BlasLapack: >> > Library: >> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >> -liomp5 -lpthread >> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>> to control the number of threads >> > uses 8 byte integers >> > MPI: >> > Version: 4 >> > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >> > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >> > MPICH_NUMVERSION: 40002300 >> > pthread: >> > Library: -lpthread >> > cmake: >> > Version: 3.16.3 >> > /usr/bin/cmake >> > regex: >> > Matlab: >> > Includes: >> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >> > MatlabEngine: >> > Library: >> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >> > sowing: >> > Version: 1.1.25 >> > /scratch/balay/petsc/linux-opt/bin/bfort >> > valgrind: >> > Language used to compile PETSc: C >> > PETSc: >> > PETSC_ARCH: linux-opt >> > PETSC_DIR: /scratch/balay/petsc >> > Scalar type: real >> > Precision: double >> > Support for __float128 >> > Integer size: 4 bytes >> > shared libraries: enabled >> > Memory alignment from malloc(): 16 bytes >> > >> xxx=========================================================================xxx >> > Configure stage complete. Now build PETSc libraries with: >> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >> > >> xxx=========================================================================xxx >> > balay at compute-386-07:/scratch/balay/petsc$ make >> >> >> >> > >> > >> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >> > BEGINNING TO COMPILE MATLAB INTERFACE >> > Building with 'gcc'. >> > >> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >> function ?PetscBinaryWrite?: >> > >> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> > | ^ >> > >> > MEX completed successfully. >> > Building with 'gcc'. >> > MEX completed successfully. >> > Building with 'gcc'. >> > MEX completed successfully. >> > Building with 'gcc'. >> > >> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >> function ?PetscBinaryWrite?: >> > >> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> > | ^ >> > >> > MEX completed successfully. >> > ========================================= >> > Now to check if the libraries are working do: >> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >> > ========================================= >> > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires >> queryval=matlab >> > Using MAKEFLAGS: -- queryval=matlab query=requires >> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >> > # ../ex72: >> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >> version `GFORTRAN_9' not found (required by >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >> > CC >> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >> > CLINKER >> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >> > TEST >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 1 >> > # ../matlab_ls_test: >> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >> version `GFORTRAN_9' not found (required by >> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >> failed so no diff >> > >> > balay at compute-386-07:/scratch/balay/petsc$ >> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires >> queryval=matlab >> > Using MAKEFLAGS: -- queryval=matlab query=requires >> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >> > ok ksp_ksp_tutorials-ex72_12 >> > ok diff-ksp_ksp_tutorials-ex72_12 >> > TEST >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >> > >> > # ------------- >> > # Summary >> > # ------------- >> > # success 4/4 tests (100.0%) >> > # failed 0/4 tests (0.0%) >> > # todo 0/4 tests (0.0%) >> > # skip 0/4 tests (0.0%) >> > # >> > # Wall clock time for tests: 27 sec >> > # Approximate CPU time (not incl. build time): 15.190000000000001 sec >> > # >> > # Timing summary (actual test time / total CPU time): >> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 >> sec >> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >> > balay at compute-386-07:/scratch/balay/petsc$ >> > >> > >> > >> > >> > >> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >> > >> > > Based on the suggestions given by Sathish, I have tried to configure >> petsc >> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After running >> make >> > > -j 10 test command I have got the following error message. >> > > >> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: >> 124 >> > > # Running problem 5 >> > > # [0]PETSC ERROR: --------------------- Error Message >> > > -------------------------------------------------------------- >> > > # [0]PETSC ERROR: Error in external library >> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >> > > # [0]PETSC ERROR: See >> https://www.mcs.anl.gov/petsc/documentation/faq.html >> > > for trouble shooting. >> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 >> by >> > > vit Sat Sep 2 12:27:22 2023 >> > > # [0]PETSC ERROR: Configure options >> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >> > > --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> > > --known-64-bit-blas-indices=1 >> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >> > > # [0]PETSC ERROR: #2 main() line 126 in >> > > >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >> > > # [0]PETSC ERROR: PETSc Option Table entries: >> > > # [0]PETSC ERROR: -prob_id 5 >> > > # [0]PETSC ERROR: -tao_smonitor >> > > # [0]PETSC ERROR: ----------------End of Error Message -------send >> entire >> > > error message to petsc-maint at mcs.anl.gov---------- >> > > # >> -------------------------------------------------------------------------- >> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >> > > # with errorcode 126076. >> > > # >> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> > > # You may or may not see output from other processes, depending on >> > > # exactly when Open MPI kills them. >> > > # >> -------------------------------------------------------------------------- >> > > >> > > I request you to help me to sort out this error. >> > > >> > > Thanks >> > > Srinivas >> > > >> > > >> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla >> wrote: >> > > >> > > > I think there should be two hyphens in >> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >> > > > >> > > > i.e.: >> > > > >> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> > > > >> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >> petsc-users < >> > > > petsc-users at mcs.anl.gov> wrote: >> > > > >> > > >> Thank you Sathish.I will try this >> > > >> >> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: >> > > >> >> > > >>> yes [and remove fblaslapack. don't know if hypre will work here]. >> > > >>> >> > > >>> i.e: >> > > >>> >> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >> > > >>> --with-debugging=0 --with-x=0 \ >> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 >> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 >> > > >>> >> > > >>> Satish >> > > >>> >> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >> wrote: >> > > >>> >> > > >>> > Hi Satish, >> > > >>> > >> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >> > > >>> > --known-64-bit-blas-indices=1 >> > > >>> > >> > > >>> > Is this what you are suggesting? >> > > >>> > >> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay >> wrote: >> > > >>> > >> > > >>> > > Also: >> > > >>> > > >> > > >>> > > '-known-64-bit-blas-indices=1', >> > > >>> > > >> > > >>> > > Note: most externalpackages might not work in this mode. >> > > >>> > > >> > > >>> > > [we can't really over come such dependency/conflicts across >> packages] >> > > >>> > > >> > > >>> > > Satish >> > > >>> > > >> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >> > > >>> > > >> > > >>> > > > Here is the matlab test that runs in CI >> > > >>> > > > >> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >> > > >>> > > > >> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >> > > >>> > > > >> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with >> > > >>> > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 >> > > >>> > > > >> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab >> - to >> > > >>> have a >> > > >>> > > compatible build >> > > >>> > > > >> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >> > > >>> > > > >> > > >>> > > > Satish >> > > >>> > > > >> > > >>> > > > >> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >> petsc-users >> > > >>> wrote: >> > > >>> > > > >> > > >>> > > > > Hi Amneet, >> > > >>> > > > > >> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >> working. It is >> > > >>> > > showing >> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >> > > >>> > > > > >> > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh >> and >> > > >>> this is >> > > >>> > > for >> > > >>> > > > > general usage not only for WEC. This I tried without >> linking >> > > >>> Matlab >> > > >>> > > with >> > > >>> > > > > PETSc. Here also I got the error while configuring >> libmesh 1.6.2 >> > > >>> that >> > > >>> > > PETSc >> > > >>> > > > > was not found but --enable-petsc-required is specified. >> > > >>> > > > > >> > > >>> > > > > The reason for specifically asking for libmesh with PETSc >> and >> > > >>> Matlab >> > > >>> > > is in >> > > >>> > > > > the cfd-mpc-wecs application for complicated geometries >> it is >> > > >>> > > mentioned to >> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >> > > >>> > > > > >> > > >>> > > > > For the past 10 days I am trying these various things and >> ended >> > > >>> up with >> > > >>> > > > > errors. >> > > >>> > > > > I want to solve this and proceed further to do my >> research work. >> > > >>> > > > > >> > > >>> > > > > Please help me to solve this as soon as possible. >> > > >>> > > > > >> > > >>> > > > > >> > > >>> > > > > Thanks and Regards >> > > >>> > > > > Srinivas >> > > >>> > > > > >> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >> mail2amneet at gmail.com> >> > > >>> > > wrote: >> > > >>> > > > > >> > > >>> > > > > > Hi Srinivas, >> > > >>> > > > > > >> > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC >> > > >>> application. >> > > >>> > > You >> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with Matlab. >> > > >>> > > > > > >> > > >>> > > > > > Do you have a specific reason for wanting to build >> libMesh? >> > > >>> > > > > > >> > > >>> > > > > > Thanks, >> > > >>> > > > > > ?Amneet >> > > >>> > > > > > >> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >> 20PHD0548 via >> > > >>> > > petsc-users >> > > >>> > > > > > wrote: >> > > >>> > > > > > >> > > >>> > > > > >> Hi, >> > > >>> > > > > >> >> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >> occurrences >> > > >>> of >> > > >>> > > "-lut >> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" >> got the >> > > >>> > > following >> > > >>> > > > > >> errors >> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >> > > >>> > > > > >> TEST >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> > > >>> > > > > >> not ok >> tao_leastsquares_tutorials_matlab-matlab_ls_test # >> > > >>> Error >> > > >>> > > code: 124 >> > > >>> > > > > >> # Running problem 5 >> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >> > > >>> > > > > >> >> -------------------------------------------------------------- >> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >> > > >>> > > > > >> # [0]PETSC ERROR: See >> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html >> for >> > > >>> trouble >> > > >>> > > > > >> shooting. >> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >> 01, 2020 >> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug >> named >> > > >>> > > MB108SMEC028 >> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >> > > >>> --with-debugging=1 >> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 >> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >> > > >>> --with-matlab-engine=1 >> > > >>> > > > > >> >> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >> in >> > > >>> > > > > >> >> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message >> > > >>> -------send >> > > >>> > > entire >> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >> > > >>> > > > > >> # >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> -------------------------------------------------------------------------- >> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >> > > >>> MPI_COMM_SELF >> > > >>> > > > > >> # with errorcode 126076. >> > > >>> > > > > >> # >> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >> MPI >> > > >>> > > processes. >> > > >>> > > > > >> # You may or may not see output from other processes, >> > > >>> depending on >> > > >>> > > > > >> # exactly when Open MPI kills them. >> > > >>> > > > > >> # >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> -------------------------------------------------------------------------- >> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >> SKIP >> > > >>> Command >> > > >>> > > > > >> failed so no diff >> > > >>> > > > > >> >> > > >>> > > > > >> in petsc/3.13.4/linux-opt >> > > >>> > > > > >> TEST >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> > > >>> > > > > >> not ok >> tao_leastsquares_tutorials_matlab-matlab_ls_test # >> > > >>> Error >> > > >>> > > code: 124 >> > > >>> > > > > >> # Running problem 5 >> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >> > > >>> > > > > >> >> -------------------------------------------------------------- >> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >> > > >>> > > > > >> # [0]PETSC ERROR: See >> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html >> for >> > > >>> trouble >> > > >>> > > > > >> shooting. >> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >> 01, 2020 >> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >> named >> > > >>> > > MB108SMEC028 by >> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >> > > >>> --COPTFLAGS=-O3 >> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >> --PETSC_ARCH=linux-opt >> > > >>> > > --with-debugging=0 >> > > >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 >> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >> > > >>> --with-matlab-engine=1 >> > > >>> > > > > >> >> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >> in >> > > >>> > > > > >> >> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message >> > > >>> -------send >> > > >>> > > entire >> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >> > > >>> > > > > >> # >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> -------------------------------------------------------------------------- >> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >> > > >>> MPI_COMM_SELF >> > > >>> > > > > >> # with errorcode 126076. >> > > >>> > > > > >> # >> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >> MPI >> > > >>> > > processes. >> > > >>> > > > > >> # You may or may not see output from other processes, >> > > >>> depending on >> > > >>> > > > > >> # exactly when Open MPI kills them. >> > > >>> > > > > >> # >> > > >>> > > > > >> >> > > >>> > > >> > > >>> >> -------------------------------------------------------------------------- >> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >> SKIP >> > > >>> Command >> > > >>> > > > > >> failed so no diff. >> > > >>> > > > > >> >> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I am >> > > >>> sharing the >> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and petsc >> > > >>> 3.17.5. >> > > >>> > > Please find >> > > >>> > > > > >> the attachment and do the needful. >> > > >>> > > > > >> >> > > >>> > > > > >> Thanks and regards >> > > >>> > > > > >> Srinivas >> > > >>> > > > > >> >> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >> > > >>> balay at mcs.anl.gov> >> > > >>> > > wrote: >> > > >>> > > > > >> >> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >> > > >>> configure.log/make.log >> > > >>> > > for >> > > >>> > > > > >>> petsc-3.17 >> > > >>> > > > > >>> >> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >> > > >>> > > > > >>> >> > > >>> > > > > >>> >>>> >> > > >>> > > > > >>> >> > > >>> > > > > >>> Matlab: >> > > >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >> > > >>> > > > > >>> MatlabEngine: >> > > >>> > > > > >>> Library: >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >> -lmex >> > > >>> -lmx >> > > >>> > > -lmat -lut >> > > >>> > > > > >>> -licudata -licui18n -licuuc >> > > >>> > > > > >>> Language used to compile PETSc: C >> > > >>> > > > > >>> <<<<< >> > > >>> > > > > >>> >> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: >> > > >>> > > > > >>> >> > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >> > > >>> > > > > >>> >> > > >>> > > > > >>> >>> >> > > >>> > > > > >>> Matlab: >> > > >>> > > > > >>> Includes: >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >> > > >>> > > > > >>> Libraries: >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >> > > >>> > > > > >>> -leng -lmex -lmx -lmat >> > > >>> > > > > >>> Executable: >> > > >>> > > > > >>> >> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >> > > >>> > > > > >>> mex: >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >> > > >>> > > > > >>> matlab: >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >> > > >>> > > > > >>> -glnxa64 >> > > >>> > > > > >>> <<< >> > > >>> > > > > >>> >> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset >> here. >> > > >>> This >> > > >>> > > might >> > > >>> > > > > >>> be a change wrt newer matlab versions. >> > > >>> > > > > >>> >> > > >>> > > > > >>> You can: >> > > >>> > > > > >>> >> > > >>> > > > > >>> - edit >> > > >>> > > > > >>> >> > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >> > > >>> > > and >> > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n >> -licuuc" >> > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' >> > > >>> > > > > >>> >> > > >>> > > > > >>> And see if the build works now. >> > > >>> > > > > >>> >> > > >>> > > > > >>> Satish >> > > >>> > > > > >>> >> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via >> > > >>> petsc-users >> > > >>> > > wrote: >> > > >>> > > > > >>> >> > > >>> > > > > >>> > I am sharing the log files while building >> petsc3.13.4 with >> > > >>> > > matlab and >> > > >>> > > > > >>> also >> > > >>> > > > > >>> > the log file while building libmesh with >> petsc3.17.5 and >> > > >>> matlab. >> > > >>> > > > > >>> Building >> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But >> > > >>> libmesh is >> > > >>> > > not >> > > >>> > > > > >>> able to >> > > >>> > > > > >>> > find the petsc >> > > >>> > > > > >>> > Please find the attachments. >> > > >>> > > > > >>> > >> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >> > > >>> balay at mcs.anl.gov> >> > > >>> > > > > >>> wrote: >> > > >>> > > > > >>> > >> > > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 >> and >> > > >>> 3.17 [or >> > > >>> > > 3.19]. >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to >> mailing >> > > >>> list - >> > > >>> > > or >> > > >>> > > > > >>> send >> > > >>> > > > > >>> > > them to petsc-maint] >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> > > Satish >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via >> > > >>> petsc-users >> > > >>> > > wrote: >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> > > > I am sharing the make.log file while building >> > > >>> petsc-3.13.4 >> > > >>> > > with >> > > >>> > > > > >>> Matlab. >> > > >>> > > > > >>> > > > Please find the attachment and do the needful. >> > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS >> > > >>> 20PHD0548 < >> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >> > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of >> > > >>> libmesh, the >> > > >>> > > error >> > > >>> > > > > >>> shows >> > > >>> > > > > >>> > > > > petsc was not found >> > > >>> > > > > >>> > > > > >> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < >> > > >>> > > balay at mcs.anl.gov> >> > > >>> > > > > >>> > > wrote: >> > > >>> > > > > >>> > > > > >> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >> petsc-3.17 >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> Here you are using 3.13 >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> Satish >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >> 20PHD0548 via >> > > >>> > > petsc-users >> > > >>> > > > > >>> wrote: >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> > Hello, >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >> working on >> > > >>> the >> > > >>> > > > > >>> simulation >> > > >>> > > > > >>> > > using >> > > >>> > > > > >>> > > > >> IBAMR >> > > >>> > > > > >>> > > > >> > open software. While building the PETSc, >> using the >> > > >>> > > following >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >> > > >>> > > > > >>> > > > >> > ./configure \ >> > > >>> > > > > >>> > > > >> > >> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >> > > >>> > > > > >>> > > > >> > >> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >> > > >>> > > > > >>> > > > >> > >> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >> > > >>> > > > > >>> > > > >> > --with-x=0 \ >> > > >>> > > > > >>> > > > >> > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> >> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > make -j4 >> > > >>> > > > > >>> > > > >> > make -j4 test >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > I got the following error >> > > >>> > > > > >>> > > > >> > CLINKER >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> >> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEnginePut' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineEvaluate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGet' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEnginePut' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineEvaluate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGet' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >> > > >>> > > > > >>> > > > >> > function `TaoPounders': >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGet' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >> > > >>> > > > > >>> > > > >> > function `main': >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineCreate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineEvaluate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineEvaluate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGetArray' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGetArray' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGetArray' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGetArray' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineGetArray' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineEvaluate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineEvaluate' >> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> >> > > >>> > > >> > > >>> >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >> > > >>> > > > > >>> > > > >> > undefined reference to >> `PetscMatlabEngineDestroy' >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status >> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> >> > > >>> >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >> > > >>> > > > > >>> > > > >> Error 1 >> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > Thank you >> > > >>> > > > > >>> > > > >> > Srinivas >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> > >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> >> > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > > >> > > >>> > > > > >>> > > >> > > >>> > > > > >>> > >> > > >>> > > > > >>> > >> > > >>> > > > > >>> >> > > >>> > > > > >> >> > > >>> > > > > >> >> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >> Institute of >> > > >>> > > Technology. >> > > >>> > > > > >> The contents of this email may contain legally >> protected >> > > >>> > > confidential or >> > > >>> > > > > >> privileged information of ?Vellore Institute of >> Technology?. >> > > >>> If >> > > >>> > > you are >> > > >>> > > > > >> not the intended recipient, you should not disseminate, >> > > >>> distribute >> > > >>> > > or copy >> > > >>> > > > > >> this e-mail. Please notify the sender immediately and >> destroy >> > > >>> all >> > > >>> > > copies of >> > > >>> > > > > >> this message and any attachments. If you have received >> this >> > > >>> email >> > > >>> > > in error, >> > > >>> > > > > >> please promptly notify the sender by reply email and >> delete >> > > >>> the >> > > >>> > > original >> > > >>> > > > > >> email and any backup copies without reading them.* >> > > >>> > > > > >> >> > > >>> > > > > > >> > > >>> > > > > >> > > >>> > > > > >> > > >>> > > > >> > > >>> > > >> > > >>> > >> > > >>> > >> > > >>> >> > > >> >> > > >> >> > > >> *Disclaimer:This message was sent from Vellore Institute of >> Technology. >> > > >> The contents of this email may contain legally protected >> confidential or >> > > >> privileged information of ?Vellore Institute of Technology?. If >> you are >> > > >> not the intended recipient, you should not disseminate, distribute >> or copy >> > > >> this e-mail. Please notify the sender immediately and destroy all >> copies of >> > > >> this message and any attachments. If you have received this email >> in error, >> > > >> please promptly notify the sender by reply email and delete the >> original >> > > >> email and any backup copies without reading them.* >> > > >> >> > > > >> > > > >> > > > -- >> > > > --Amneet >> > > > >> > > > >> > > > >> > > > >> > > >> > > >> > > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Sun Sep 3 08:00:04 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Sun, 3 Sep 2023 18:30:04 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: Hi Matthew, I am using PETSc to simulate the problems using IBAMR. I do not have any separate test files to test PETSc alone. Can you please help me how to define this DATAFILESPATH? Thanks and regards Srinivas. On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley wrote: > On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via petsc-users < > petsc-users at mcs.anl.gov> wrote: > >> Hi Sathish, >> >> Thank you so much for your efforts and the support you are giving me to >> sort this out. >> >> I tried to follow the same procedure which you followed to build Petsc >> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >> >> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >> --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >> Using python3 for Python >> >> =============================================================================== >> Configuring PETSc to compile on your system >> >> >> =============================================================================== >> =============================================================================== >> It appears you do not have valgrind >> installed on your system. >> We HIGHLY recommend you install it from www.valgrind.org >> Or install valgrind-devel or >> equivalent using your package manager. >> Then rerun ./configure >> >> =============================================================================== >> Compilers: >> >> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC >> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -fvisibility=hidden -O3 >> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx -Wall >> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >> -fvisibility=hidden -O3 -fPIC >> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 -fPIC >> -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> Linkers: >> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared >> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -fvisibility=hidden -O3 >> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared >> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >> -fstack-protector -fvisibility=hidden -O3 >> Libraries linked against: -lquadmath -lstdc++ -ldl >> make: >> Version: 4.2 >> /usr/bin/make >> BlasLapack: >> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to >> control the number of threads >> uses 8 byte integers >> MPI: >> Version: 3 >> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe >> OMPI_VERSION: 4.1.4 >> pthread: >> cmake: >> Version: 3.16.3 >> /usr/bin/cmake >> regex: >> Matlab: >> Includes: -I/usr/local/MATLAB/R2020b/extern/include >> /usr/local/MATLAB/R2020b >> MatlabEngine: >> Library: >> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut >> -licudata -licui18n -licuuc >> Language used to compile PETSc: C >> PETSc: >> PETSC_ARCH: linux-opt >> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >> Scalar type: real >> Precision: double >> Support for __float128 >> Integer size: 4 bytes >> shared libraries: enabled >> Memory alignment from malloc(): 16 bytes >> >> xxx=========================================================================xxx >> Configure stage complete. Now build PETSc libraries with: >> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >> >> xxx=========================================================================xxx >> >> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as you >> suggested earlier. >> >> *$make* >> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >> BEGINNING TO COMPILE MATLAB INTERFACE >> Building with 'gcc'. >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> ========================================= >> Now to check if the libraries are working do: >> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >> =============================================== >> >> *$make test query=requires queryval=matlab* >> Using MAKEFLAGS: -- queryval=matlab query=requires >> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Unable to open file >> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >> > > No, the problem is that you do not have DATAFILESPATH defined, so it > cannot find the matrix to test. Try running some test of yours. > > Thanks, > > Matt > > >> # [0]PETSC ERROR: See >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun >> Sep 3 11:51:03 2023 >> # [0]PETSC ERROR: Configure options >> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >> # [0]PETSC ERROR: #6 main() line 113 in >> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -f0 /matrices/arco1 >> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >> # [0]PETSC ERROR: -pc_type lu >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >> # with errorcode 113065. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >> CC >> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >> CLINKER >> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >> TEST >> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >> # Running problem 5 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Error in external library >> # [0]PETSC ERROR: Unable to start MATLAB engine on >> # [0]PETSC ERROR: See >> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >> vit Sun Sep 3 11:51:05 2023 >> # [0]PETSC ERROR: Configure options >> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >> # [0]PETSC ERROR: #2 main() line 126 in >> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -prob_id 5 >> # [0]PETSC ERROR: -tao_smonitor >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >> # with errorcode 126076. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >> failed so no diff >> >> # ------------- >> # Summary >> # ------------- >> # FAILED ksp_ksp_tutorials-ex72_12 >> tao_leastsquares_tutorials_matlab-matlab_ls_test >> # success 0/2 tests (0.0%) >> # failed 2/2 tests (100.0%) >> # todo 0/2 tests (0.0%) >> # skip 0/2 tests (0.0%) >> # >> # Wall clock time for tests: 3 sec >> # Approximate CPU time (not incl. build time): 0.05 sec >> # >> # To rerun failed tests: >> # /usr/bin/make -f gmakefile test test-fail=1 >> # >> # Timing summary (actual test time / total CPU time): >> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec >> >> *How to sort out this error?* >> >> *$cd src/tao/leastsquares/tutorials/matlab/* >> *$make matlab_ls_test* >> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >> -I/home/vit/sfw/petsc/3.13.4/include >> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >> -I/usr/local/MATLAB/R2020b/extern/include >> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >> -lstdc++ -ldl -o matlab_ls_test >> >> I think there is a problem with the Matlab-R2020b version. >> I am sharing the configure.log and make.log files. Please find the >> attachment and do the needful. >> >> >> Thanks and regards >> Srinivas >> >> >> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay wrote: >> >>> Perhaps you can try the following to get additional info - and debug >>> >>> Satish >>> ---------- >>> >>> balay at compute-386-07:/scratch/balay/petsc$ cd >>> src/tao/leastsquares/tutorials/matlab/ >>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>> make matlab_ls_test >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall >>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>> -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include >>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>> -L/scratch/balay/petsc/linux-opt/lib >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex >>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi >>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>> matlab_ls_test >>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>> -tao_smonitor -prob_id 5 -info >>> [0] PetscInitialize(): PETSc successfully started: number of processors >>> = 1 >>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>> compute-386-07.(none) >>> [0] PetscInitialize(): Running on machine: compute-386-07 >>> Running problem 5 >>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>> -2080374784 max tags = 268435455 >>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>> -glnxa64 -nodisplay -nosplash >>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>> TestingInitialize >>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>> TestingInitialize >>> 5 >>> >>> >>> <<<< Now verify if the above matlab command actually works for you - on >>> this machine..>>>>> >>> >>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>> -glnxa64 -nodisplay -nosplash >>> >>> >>> < M A T L A B (R) > >>> >>> Copyright 1984-2021 The MathWorks, Inc. >>> >>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>> >>> February 17, 2021 >>> >>> >>> To get started, type doc. >>> For product information, visit www.mathworks.com. >>> >>> >> >>> >>> >>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>> >>> > Please don't cc: both petsc-users and petsc-maint [reverting thread to >>> petsc-users only] >>> > >>> > I'm not sure what is happening here. Can you send the corresponding >>> configure.log, make.log [compressed]? >>> > >>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>> with Matlab-R2021a - and that works: >>> > >>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>> > main >>> > release >>> > * release-3.13 >>> > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a >>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>> > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> --with-debugging=0 --with-x=0 >>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > >>> > Compilers: >>> >>> >>> >>> > C Compiler: >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall >>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>> -fvisibility=hidden -O3 >>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > C++ Compiler: >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>> -fvisibility=hidden -O3 -fPIC >>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > Fortran Compiler: >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall >>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > Linkers: >>> > Shared linker: >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> -fstack-protector -fvisibility=hidden -O3 >>> > Dynamic linker: >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> -fstack-protector -fvisibility=hidden -O3 >>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>> > make: >>> > Version: 4.2 >>> > /usr/bin/make >>> > BlasLapack: >>> > Library: >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>> -liomp5 -lpthread >>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>> to control the number of threads >>> > uses 8 byte integers >>> > MPI: >>> > Version: 4 >>> > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>> > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>> > MPICH_NUMVERSION: 40002300 >>> > pthread: >>> > Library: -lpthread >>> > cmake: >>> > Version: 3.16.3 >>> > /usr/bin/cmake >>> > regex: >>> > Matlab: >>> > Includes: >>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>> > MatlabEngine: >>> > Library: >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>> > sowing: >>> > Version: 1.1.25 >>> > /scratch/balay/petsc/linux-opt/bin/bfort >>> > valgrind: >>> > Language used to compile PETSc: C >>> > PETSc: >>> > PETSC_ARCH: linux-opt >>> > PETSC_DIR: /scratch/balay/petsc >>> > Scalar type: real >>> > Precision: double >>> > Support for __float128 >>> > Integer size: 4 bytes >>> > shared libraries: enabled >>> > Memory alignment from malloc(): 16 bytes >>> > >>> xxx=========================================================================xxx >>> > Configure stage complete. Now build PETSc libraries with: >>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>> > >>> xxx=========================================================================xxx >>> > balay at compute-386-07:/scratch/balay/petsc$ make >>> >>> >>> >>> > >>> > >>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>> > BEGINNING TO COMPILE MATLAB INTERFACE >>> > Building with 'gcc'. >>> > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>> function ?PetscBinaryWrite?: >>> > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> > | ^ >>> > >>> > MEX completed successfully. >>> > Building with 'gcc'. >>> > MEX completed successfully. >>> > Building with 'gcc'. >>> > MEX completed successfully. >>> > Building with 'gcc'. >>> > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>> function ?PetscBinaryWrite?: >>> > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> > | ^ >>> > >>> > MEX completed successfully. >>> > ========================================= >>> > Now to check if the libraries are working do: >>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>> > ========================================= >>> > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires >>> queryval=matlab >>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>> > # ../ex72: >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>> version `GFORTRAN_9' not found (required by >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> > CC >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>> > CLINKER >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > TEST >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 1 >>> > # ../matlab_ls_test: >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>> version `GFORTRAN_9' not found (required by >>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>> failed so no diff >>> > >>> > balay at compute-386-07:/scratch/balay/petsc$ >>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires >>> queryval=matlab >>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> > ok ksp_ksp_tutorials-ex72_12 >>> > ok diff-ksp_ksp_tutorials-ex72_12 >>> > TEST >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > >>> > # ------------- >>> > # Summary >>> > # ------------- >>> > # success 4/4 tests (100.0%) >>> > # failed 0/4 tests (0.0%) >>> > # todo 0/4 tests (0.0%) >>> > # skip 0/4 tests (0.0%) >>> > # >>> > # Wall clock time for tests: 27 sec >>> > # Approximate CPU time (not incl. build time): 15.190000000000001 sec >>> > # >>> > # Timing summary (actual test time / total CPU time): >>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 >>> sec >>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>> > balay at compute-386-07:/scratch/balay/petsc$ >>> > >>> > >>> > >>> > >>> > >>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>> > >>> > > Based on the suggestions given by Sathish, I have tried to configure >>> petsc >>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After running >>> make >>> > > -j 10 test command I have got the following error message. >>> > > >>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>> code: 124 >>> > > # Running problem 5 >>> > > # [0]PETSC ERROR: --------------------- Error Message >>> > > -------------------------------------------------------------- >>> > > # [0]PETSC ERROR: Error in external library >>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > > for trouble shooting. >>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>> MB108SMEC028 by >>> > > vit Sat Sep 2 12:27:22 2023 >>> > > # [0]PETSC ERROR: Configure options >>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > > --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > --known-64-bit-blas-indices=1 >>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > # [0]PETSC ERROR: #2 main() line 126 in >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>> > > # [0]PETSC ERROR: -prob_id 5 >>> > > # [0]PETSC ERROR: -tao_smonitor >>> > > # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire >>> > > error message to petsc-maint at mcs.anl.gov---------- >>> > > # >>> -------------------------------------------------------------------------- >>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> > > # with errorcode 126076. >>> > > # >>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> > > # You may or may not see output from other processes, depending on >>> > > # exactly when Open MPI kills them. >>> > > # >>> -------------------------------------------------------------------------- >>> > > >>> > > I request you to help me to sort out this error. >>> > > >>> > > Thanks >>> > > Srinivas >>> > > >>> > > >>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla >>> wrote: >>> > > >>> > > > I think there should be two hyphens in >>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>> > > > i.e.: >>> > > > >>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>> petsc-users < >>> > > > petsc-users at mcs.anl.gov> wrote: >>> > > > >>> > > >> Thank you Sathish.I will try this >>> > > >> >>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay >>> wrote: >>> > > >> >>> > > >>> yes [and remove fblaslapack. don't know if hypre will work here]. >>> > > >>> >>> > > >>> i.e: >>> > > >>> >>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> > > >>> --with-debugging=0 --with-x=0 \ >>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 >>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 >>> > > >>> >>> > > >>> Satish >>> > > >>> >>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>> wrote: >>> > > >>> >>> > > >>> > Hi Satish, >>> > > >>> > >>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>> > > >>> > --known-64-bit-blas-indices=1 >>> > > >>> > >>> > > >>> > Is this what you are suggesting? >>> > > >>> > >>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay >>> wrote: >>> > > >>> > >>> > > >>> > > Also: >>> > > >>> > > >>> > > >>> > > '-known-64-bit-blas-indices=1', >>> > > >>> > > >>> > > >>> > > Note: most externalpackages might not work in this mode. >>> > > >>> > > >>> > > >>> > > [we can't really over come such dependency/conflicts across >>> packages] >>> > > >>> > > >>> > > >>> > > Satish >>> > > >>> > > >>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>> > > >>> > > >>> > > >>> > > > Here is the matlab test that runs in CI >>> > > >>> > > > >>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> > > >>> > > > >>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>> > > >>> > > > >>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with >>> > > >>> > > > # MATLAB BLAS - hence requiring >>> -known-64-bit-blas-indices=1 >>> > > >>> > > > >>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab >>> - to >>> > > >>> have a >>> > > >>> > > compatible build >>> > > >>> > > > >>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>> > > >>> > > > >>> > > >>> > > > Satish >>> > > >>> > > > >>> > > >>> > > > >>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>> petsc-users >>> > > >>> wrote: >>> > > >>> > > > >>> > > >>> > > > > Hi Amneet, >>> > > >>> > > > > >>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>> working. It is >>> > > >>> > > showing >>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>> > > >>> > > > > >>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh >>> and >>> > > >>> this is >>> > > >>> > > for >>> > > >>> > > > > general usage not only for WEC. This I tried without >>> linking >>> > > >>> Matlab >>> > > >>> > > with >>> > > >>> > > > > PETSc. Here also I got the error while configuring >>> libmesh 1.6.2 >>> > > >>> that >>> > > >>> > > PETSc >>> > > >>> > > > > was not found but --enable-petsc-required is specified. >>> > > >>> > > > > >>> > > >>> > > > > The reason for specifically asking for libmesh with >>> PETSc and >>> > > >>> Matlab >>> > > >>> > > is in >>> > > >>> > > > > the cfd-mpc-wecs application for complicated geometries >>> it is >>> > > >>> > > mentioned to >>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>> > > >>> > > > > >>> > > >>> > > > > For the past 10 days I am trying these various things >>> and ended >>> > > >>> up with >>> > > >>> > > > > errors. >>> > > >>> > > > > I want to solve this and proceed further to do my >>> research work. >>> > > >>> > > > > >>> > > >>> > > > > Please help me to solve this as soon as possible. >>> > > >>> > > > > >>> > > >>> > > > > >>> > > >>> > > > > Thanks and Regards >>> > > >>> > > > > Srinivas >>> > > >>> > > > > >>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>> mail2amneet at gmail.com> >>> > > >>> > > wrote: >>> > > >>> > > > > >>> > > >>> > > > > > Hi Srinivas, >>> > > >>> > > > > > >>> > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC >>> > > >>> application. >>> > > >>> > > You >>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>> Matlab. >>> > > >>> > > > > > >>> > > >>> > > > > > Do you have a specific reason for wanting to build >>> libMesh? >>> > > >>> > > > > > >>> > > >>> > > > > > Thanks, >>> > > >>> > > > > > ?Amneet >>> > > >>> > > > > > >>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>> 20PHD0548 via >>> > > >>> > > petsc-users >>> > > >>> > > > > > wrote: >>> > > >>> > > > > > >>> > > >>> > > > > >> Hi, >>> > > >>> > > > > >> >>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>> occurrences >>> > > >>> of >>> > > >>> > > "-lut >>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" >>> got the >>> > > >>> > > following >>> > > >>> > > > > >> errors >>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>> > > >>> > > > > >> TEST >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > >>> > > > > >> not ok >>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> > > >>> Error >>> > > >>> > > code: 124 >>> > > >>> > > > > >> # Running problem 5 >>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >>> > > >>> > > > > >> >>> -------------------------------------------------------------- >>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > >>> > > > > >> # [0]PETSC ERROR: See >>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> for >>> > > >>> trouble >>> > > >>> > > > > >> shooting. >>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>> 01, 2020 >>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug >>> named >>> > > >>> > > MB108SMEC028 >>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> > > >>> --with-debugging=1 >>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 >>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > >>> --with-matlab-engine=1 >>> > > >>> > > > > >> >>> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>> 67 in >>> > > >>> > > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message >>> > > >>> -------send >>> > > >>> > > entire >>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >>> > > >>> > > > > >> # >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> -------------------------------------------------------------------------- >>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>> > > >>> MPI_COMM_SELF >>> > > >>> > > > > >> # with errorcode 126076. >>> > > >>> > > > > >> # >>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill >>> all MPI >>> > > >>> > > processes. >>> > > >>> > > > > >> # You may or may not see output from other processes, >>> > > >>> depending on >>> > > >>> > > > > >> # exactly when Open MPI kills them. >>> > > >>> > > > > >> # >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> -------------------------------------------------------------------------- >>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>> # SKIP >>> > > >>> Command >>> > > >>> > > > > >> failed so no diff >>> > > >>> > > > > >> >>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>> > > >>> > > > > >> TEST >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > >>> > > > > >> not ok >>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> > > >>> Error >>> > > >>> > > code: 124 >>> > > >>> > > > > >> # Running problem 5 >>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >>> > > >>> > > > > >> >>> -------------------------------------------------------------- >>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > >>> > > > > >> # [0]PETSC ERROR: See >>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> for >>> > > >>> trouble >>> > > >>> > > > > >> shooting. >>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>> 01, 2020 >>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>> named >>> > > >>> > > MB108SMEC028 by >>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> > > >>> --COPTFLAGS=-O3 >>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>> --PETSC_ARCH=linux-opt >>> > > >>> > > --with-debugging=0 >>> > > >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 >>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > >>> --with-matlab-engine=1 >>> > > >>> > > > > >> >>> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>> 67 in >>> > > >>> > > > > >> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message >>> > > >>> -------send >>> > > >>> > > entire >>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >>> > > >>> > > > > >> # >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> -------------------------------------------------------------------------- >>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>> > > >>> MPI_COMM_SELF >>> > > >>> > > > > >> # with errorcode 126076. >>> > > >>> > > > > >> # >>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill >>> all MPI >>> > > >>> > > processes. >>> > > >>> > > > > >> # You may or may not see output from other processes, >>> > > >>> depending on >>> > > >>> > > > > >> # exactly when Open MPI kills them. >>> > > >>> > > > > >> # >>> > > >>> > > > > >> >>> > > >>> > > >>> > > >>> >>> -------------------------------------------------------------------------- >>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>> # SKIP >>> > > >>> Command >>> > > >>> > > > > >> failed so no diff. >>> > > >>> > > > > >> >>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I >>> am >>> > > >>> sharing the >>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>> petsc >>> > > >>> 3.17.5. >>> > > >>> > > Please find >>> > > >>> > > > > >> the attachment and do the needful. >>> > > >>> > > > > >> >>> > > >>> > > > > >> Thanks and regards >>> > > >>> > > > > >> Srinivas >>> > > >>> > > > > >> >>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>> > > >>> balay at mcs.anl.gov> >>> > > >>> > > wrote: >>> > > >>> > > > > >> >>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>> > > >>> configure.log/make.log >>> > > >>> > > for >>> > > >>> > > > > >>> petsc-3.17 >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> >>>> >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> Matlab: >>> > > >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>> > > >>> > > > > >>> MatlabEngine: >>> > > >>> > > > > >>> Library: >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>> -lmex >>> > > >>> -lmx >>> > > >>> > > -lmat -lut >>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>> > > >>> > > > > >>> Language used to compile PETSc: C >>> > > >>> > > > > >>> <<<<< >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> >>> >>> > > >>> > > > > >>> Matlab: >>> > > >>> > > > > >>> Includes: >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>> > > >>> > > > > >>> Libraries: >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>> > > >>> > > > > >>> Executable: >>> > > >>> > > > > >>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>> > > >>> > > > > >>> mex: >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>> > > >>> > > > > >>> matlab: >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>> > > >>> > > > > >>> -glnxa64 >>> > > >>> > > > > >>> <<< >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>> preset here. >>> > > >>> This >>> > > >>> > > might >>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> You can: >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> - edit >>> > > >>> > > > > >>> >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>> > > >>> > > and >>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n >>> -licuuc" >>> > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> And see if the build works now. >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> Satish >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via >>> > > >>> petsc-users >>> > > >>> > > wrote: >>> > > >>> > > > > >>> >>> > > >>> > > > > >>> > I am sharing the log files while building >>> petsc3.13.4 with >>> > > >>> > > matlab and >>> > > >>> > > > > >>> also >>> > > >>> > > > > >>> > the log file while building libmesh with >>> petsc3.17.5 and >>> > > >>> matlab. >>> > > >>> > > > > >>> Building >>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But >>> > > >>> libmesh is >>> > > >>> > > not >>> > > >>> > > > > >>> able to >>> > > >>> > > > > >>> > find the petsc >>> > > >>> > > > > >>> > Please find the attachments. >>> > > >>> > > > > >>> > >>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>> > > >>> balay at mcs.anl.gov> >>> > > >>> > > > > >>> wrote: >>> > > >>> > > > > >>> > >>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>> petsc-3.13 and >>> > > >>> 3.17 [or >>> > > >>> > > 3.19]. >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to >>> mailing >>> > > >>> list - >>> > > >>> > > or >>> > > >>> > > > > >>> send >>> > > >>> > > > > >>> > > them to petsc-maint] >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> > > Satish >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>> via >>> > > >>> petsc-users >>> > > >>> > > wrote: >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> > > > I am sharing the make.log file while building >>> > > >>> petsc-3.13.4 >>> > > >>> > > with >>> > > >>> > > > > >>> Matlab. >>> > > >>> > > > > >>> > > > Please find the attachment and do the needful. >>> > > >>> > > > > >>> > > > >>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>> SRINIVAS >>> > > >>> 20PHD0548 < >>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> > > >>> > > > > >>> > > > >>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of >>> > > >>> libmesh, the >>> > > >>> > > error >>> > > >>> > > > > >>> shows >>> > > >>> > > > > >>> > > > > petsc was not found >>> > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay >>> < >>> > > >>> > > balay at mcs.anl.gov> >>> > > >>> > > > > >>> > > wrote: >>> > > >>> > > > > >>> > > > > >>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>> petsc-3.17 >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >> Satish >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>> 20PHD0548 via >>> > > >>> > > petsc-users >>> > > >>> > > > > >>> wrote: >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >> > Hello, >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>> working on >>> > > >>> the >>> > > >>> > > > > >>> simulation >>> > > >>> > > > > >>> > > using >>> > > >>> > > > > >>> > > > >> IBAMR >>> > > >>> > > > > >>> > > > >> > open software. While building the PETSc, >>> using the >>> > > >>> > > following >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>> > > >>> > > > > >>> > > > >> > ./configure \ >>> > > >>> > > > > >>> > > > >> > >>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>> > > >>> > > > > >>> > > > >> > >>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>> > > >>> > > > > >>> > > > >> > >>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>> > > >>> > > > > >>> > > > >> > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> >>> > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > make -j4 >>> > > >>> > > > > >>> > > > >> > make -j4 test >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > I got the following error >>> > > >>> > > > > >>> > > > >> > CLINKER >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> >>> > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEnginePut' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineEvaluate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGet' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEnginePut' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineEvaluate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGet' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGet' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > >>> > > > > >>> > > > >> > function `main': >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineCreate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineEvaluate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineEvaluate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGetArray' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGetArray' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGetArray' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGetArray' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineGetArray' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineEvaluate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineEvaluate' >>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> >>> > > >>> > > >>> > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>> > > >>> > > > > >>> > > > >> > undefined reference to >>> `PetscMatlabEngineDestroy' >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status >>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> >>> > > >>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>> > > >>> > > > > >>> > > > >> Error 1 >>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > Thank you >>> > > >>> > > > > >>> > > > >> > Srinivas >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> > >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >> >>> > > >>> > > > > >>> > > > >>> > > >>> > > > > >>> > > > >>> > > >>> > > > > >>> > > >>> > > >>> > > > > >>> > >>> > > >>> > > > > >>> > >>> > > >>> > > > > >>> >>> > > >>> > > > > >> >>> > > >>> > > > > >> >>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>> Institute of >>> > > >>> > > Technology. >>> > > >>> > > > > >> The contents of this email may contain legally >>> protected >>> > > >>> > > confidential or >>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>> Technology?. >>> > > >>> If >>> > > >>> > > you are >>> > > >>> > > > > >> not the intended recipient, you should not >>> disseminate, >>> > > >>> distribute >>> > > >>> > > or copy >>> > > >>> > > > > >> this e-mail. Please notify the sender immediately and >>> destroy >>> > > >>> all >>> > > >>> > > copies of >>> > > >>> > > > > >> this message and any attachments. If you have >>> received this >>> > > >>> email >>> > > >>> > > in error, >>> > > >>> > > > > >> please promptly notify the sender by reply email and >>> delete >>> > > >>> the >>> > > >>> > > original >>> > > >>> > > > > >> email and any backup copies without reading them.* >>> > > >>> > > > > >> >>> > > >>> > > > > > >>> > > >>> > > > > >>> > > >>> > > > > >>> > > >>> > > > >>> > > >>> > > >>> > > >>> > >>> > > >>> > >>> > > >>> >>> > > >> >>> > > >> >>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>> Technology. >>> > > >> The contents of this email may contain legally protected >>> confidential or >>> > > >> privileged information of ?Vellore Institute of Technology?. If >>> you are >>> > > >> not the intended recipient, you should not disseminate, >>> distribute or copy >>> > > >> this e-mail. Please notify the sender immediately and destroy all >>> copies of >>> > > >> this message and any attachments. If you have received this email >>> in error, >>> > > >> please promptly notify the sender by reply email and delete the >>> original >>> > > >> email and any backup copies without reading them.* >>> > > >> >>> > > > >>> > > > >>> > > > -- >>> > > > --Amneet >>> > > > >>> > > > >>> > > > >>> > > > >>> > > >>> > > >>> >> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sun Sep 3 07:55:22 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 3 Sep 2023 08:55:22 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < inturu.srinivas2020 at vitstudent.ac.in> wrote: > Hi Matthew, > > I am using PETSc to simulate the problems using IBAMR. I do not have any > separate test files to test PETSc alone. Can you please help me how to > define this DATAFILESPATH? > That test you tried uses a certain matrix. On our machine, we point to this matrix using an environment variable, DATAFILESPATH. You don't have those matrices, since they are just for testing here. That is why I suggested just using a different matrix, or running a problem you care about in IBAMR. Thanks, Matt > Thanks and regards > Srinivas. > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley wrote: > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via petsc-users < >> petsc-users at mcs.anl.gov> wrote: >> >>> Hi Sathish, >>> >>> Thank you so much for your efforts and the support you are giving me to >>> sort this out. >>> >>> I tried to follow the same procedure which you followed to build Petsc >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>> >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>> Using python3 for Python >>> >>> =============================================================================== >>> Configuring PETSc to compile on your system >>> >>> >>> =============================================================================== >>> =============================================================================== >>> It appears you do not have valgrind >>> installed on your system. >>> We HIGHLY recommend you install it from www.valgrind.org >>> Or install valgrind-devel or >>> equivalent using your package manager. >>> Then rerun ./configure >>> >>> =============================================================================== >>> Compilers: >>> >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> -fstack-protector -fvisibility=hidden -O3 >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> Linkers: >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> -fstack-protector -fvisibility=hidden -O3 >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> -fstack-protector -fvisibility=hidden -O3 >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>> make: >>> Version: 4.2 >>> /usr/bin/make >>> BlasLapack: >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to >>> control the number of threads >>> uses 8 byte integers >>> MPI: >>> Version: 3 >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe >>> OMPI_VERSION: 4.1.4 >>> pthread: >>> cmake: >>> Version: 3.16.3 >>> /usr/bin/cmake >>> regex: >>> Matlab: >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> /usr/local/MATLAB/R2020b >>> MatlabEngine: >>> Library: >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut >>> -licudata -licui18n -licuuc >>> Language used to compile PETSc: C >>> PETSc: >>> PETSC_ARCH: linux-opt >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>> Scalar type: real >>> Precision: double >>> Support for __float128 >>> Integer size: 4 bytes >>> shared libraries: enabled >>> Memory alignment from malloc(): 16 bytes >>> >>> xxx=========================================================================xxx >>> Configure stage complete. Now build PETSc libraries with: >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>> >>> xxx=========================================================================xxx >>> >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>> you suggested earlier. >>> >>> *$make* >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> Building with 'gcc'. >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> ========================================= >>> Now to check if the libraries are working do: >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>> =============================================== >>> >>> *$make test query=requires queryval=matlab* >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>> # [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> # [0]PETSC ERROR: Unable to open file >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>> >> >> No, the problem is that you do not have DATAFILESPATH defined, so it >> cannot find the matrix to test. Try running some test of yours. >> >> Thanks, >> >> Matt >> >> >>> # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>> shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun >>> Sep 3 11:51:03 2023 >>> # [0]PETSC ERROR: Configure options >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>> # [0]PETSC ERROR: #6 main() line 113 in >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> # [0]PETSC ERROR: -pc_type lu >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> # >>> -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> # with errorcode 113065. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # >>> -------------------------------------------------------------------------- >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> CC >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>> CLINKER >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> TEST >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>> # Running problem 5 >>> # [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> # [0]PETSC ERROR: Error in external library >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>> # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>> shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>> vit Sun Sep 3 11:51:05 2023 >>> # [0]PETSC ERROR: Configure options >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> # [0]PETSC ERROR: #2 main() line 126 in >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -prob_id 5 >>> # [0]PETSC ERROR: -tao_smonitor >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> # >>> -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> # with errorcode 126076. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # >>> -------------------------------------------------------------------------- >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>> failed so no diff >>> >>> # ------------- >>> # Summary >>> # ------------- >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>> # success 0/2 tests (0.0%) >>> # failed 2/2 tests (100.0%) >>> # todo 0/2 tests (0.0%) >>> # skip 0/2 tests (0.0%) >>> # >>> # Wall clock time for tests: 3 sec >>> # Approximate CPU time (not incl. build time): 0.05 sec >>> # >>> # To rerun failed tests: >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> # >>> # Timing summary (actual test time / total CPU time): >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec >>> >>> *How to sort out this error?* >>> >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>> *$make matlab_ls_test* >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>> -I/home/vit/sfw/petsc/3.13.4/include >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>> -I/usr/local/MATLAB/R2020b/extern/include >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>> -lstdc++ -ldl -o matlab_ls_test >>> >>> I think there is a problem with the Matlab-R2020b version. >>> I am sharing the configure.log and make.log files. Please find the >>> attachment and do the needful. >>> >>> >>> Thanks and regards >>> Srinivas >>> >>> >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay wrote: >>> >>>> Perhaps you can try the following to get additional info - and debug >>>> >>>> Satish >>>> ---------- >>>> >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>> src/tao/leastsquares/tutorials/matlab/ >>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> make matlab_ls_test >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>> -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include >>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>> -L/scratch/balay/petsc/linux-opt/lib >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>> matlab_ls_test >>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>> -tao_smonitor -prob_id 5 -info >>>> [0] PetscInitialize(): PETSc successfully started: number of processors >>>> = 1 >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>> compute-386-07.(none) >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>> Running problem 5 >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>> -2080374784 max tags = 268435455 >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> -glnxa64 -nodisplay -nosplash >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>> TestingInitialize >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>> TestingInitialize >>>> 5 >>>> >>>> >>>> <<<< Now verify if the above matlab command actually works for you - on >>>> this machine..>>>>> >>>> >>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> -glnxa64 -nodisplay -nosplash >>>> >>>> >>>> < M A T L A B (R) > >>>> >>>> Copyright 1984-2021 The MathWorks, Inc. >>>> >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>> >>>> February 17, 2021 >>>> >>>> >>>> To get started, type doc. >>>> For product information, visit www.mathworks.com. >>>> >>>> >> >>>> >>>> >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>> >>>> > Please don't cc: both petsc-users and petsc-maint [reverting thread >>>> to petsc-users only] >>>> > >>>> > I'm not sure what is happening here. Can you send the corresponding >>>> configure.log, make.log [compressed]? >>>> > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>> with Matlab-R2021a - and that works: >>>> > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>> > main >>>> > release >>>> > * release-3.13 >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>> > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> --with-debugging=0 --with-x=0 >>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > >>>> > Compilers: >>>> >>>> >>>> >>>> > C Compiler: >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> -fvisibility=hidden -O3 >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > C++ Compiler: >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> -fvisibility=hidden -O3 -fPIC >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > Fortran Compiler: >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > Linkers: >>>> > Shared linker: >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> -fstack-protector -fvisibility=hidden -O3 >>>> > Dynamic linker: >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> -fstack-protector -fvisibility=hidden -O3 >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>> > make: >>>> > Version: 4.2 >>>> > /usr/bin/make >>>> > BlasLapack: >>>> > Library: >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>> -liomp5 -lpthread >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>>> to control the number of threads >>>> > uses 8 byte integers >>>> > MPI: >>>> > Version: 4 >>>> > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>> > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>> > MPICH_NUMVERSION: 40002300 >>>> > pthread: >>>> > Library: -lpthread >>>> > cmake: >>>> > Version: 3.16.3 >>>> > /usr/bin/cmake >>>> > regex: >>>> > Matlab: >>>> > Includes: >>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > MatlabEngine: >>>> > Library: >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>> > sowing: >>>> > Version: 1.1.25 >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>> > valgrind: >>>> > Language used to compile PETSc: C >>>> > PETSc: >>>> > PETSC_ARCH: linux-opt >>>> > PETSC_DIR: /scratch/balay/petsc >>>> > Scalar type: real >>>> > Precision: double >>>> > Support for __float128 >>>> > Integer size: 4 bytes >>>> > shared libraries: enabled >>>> > Memory alignment from malloc(): 16 bytes >>>> > >>>> xxx=========================================================================xxx >>>> > Configure stage complete. Now build PETSc libraries with: >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>> > >>>> xxx=========================================================================xxx >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>> >>>> >>>> >>>> > >>>> > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>> > Building with 'gcc'. >>>> > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>> function ?PetscBinaryWrite?: >>>> > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > | ^ >>>> > >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>> function ?PetscBinaryWrite?: >>>> > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > | ^ >>>> > >>>> > MEX completed successfully. >>>> > ========================================= >>>> > Now to check if the libraries are working do: >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>> > ========================================= >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires >>>> queryval=matlab >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>> > # ../ex72: >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>> version `GFORTRAN_9' not found (required by >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> > CC >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > CLINKER >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > TEST >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: >>>> 1 >>>> > # ../matlab_ls_test: >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>> version `GFORTRAN_9' not found (required by >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>> failed so no diff >>>> > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires >>>> queryval=matlab >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > ok ksp_ksp_tutorials-ex72_12 >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>> > TEST >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > >>>> > # ------------- >>>> > # Summary >>>> > # ------------- >>>> > # success 4/4 tests (100.0%) >>>> > # failed 0/4 tests (0.0%) >>>> > # todo 0/4 tests (0.0%) >>>> > # skip 0/4 tests (0.0%) >>>> > # >>>> > # Wall clock time for tests: 27 sec >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 sec >>>> > # >>>> > # Timing summary (actual test time / total CPU time): >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 >>>> sec >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>> > >>>> > >>>> > >>>> > >>>> > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>> > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>> configure petsc >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>> running make >>>> > > -j 10 test command I have got the following error message. >>>> > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>> code: 124 >>>> > > # Running problem 5 >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>> > > -------------------------------------------------------------- >>>> > > # [0]PETSC ERROR: Error in external library >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > # [0]PETSC ERROR: See >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > for trouble shooting. >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>> MB108SMEC028 by >>>> > > vit Sat Sep 2 12:27:22 2023 >>>> > > # [0]PETSC ERROR: Configure options >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> --with-debugging=0 >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > --with-matlab-engine=1 >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > --known-64-bit-blas-indices=1 >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>> > > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> entire >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>> > > # >>>> -------------------------------------------------------------------------- >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > > # with errorcode 126076. >>>> > > # >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>> processes. >>>> > > # You may or may not see output from other processes, depending on >>>> > > # exactly when Open MPI kills them. >>>> > > # >>>> -------------------------------------------------------------------------- >>>> > > >>>> > > I request you to help me to sort out this error. >>>> > > >>>> > > Thanks >>>> > > Srinivas >>>> > > >>>> > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>> mail2amneet at gmail.com> wrote: >>>> > > >>>> > > > I think there should be two hyphens in >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > > i.e.: >>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>> petsc-users < >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>> > > >> >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay >>>> wrote: >>>> > > >> >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>> here]. >>>> > > >>> >>>> > > >>> i.e: >>>> > > >>> >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> --with-matlab-engine=1 >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> --known-64-bit-blas-indices=1 >>>> > > >>> >>>> > > >>> Satish >>>> > > >>> >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>> wrote: >>>> > > >>> >>>> > > >>> > Hi Satish, >>>> > > >>> > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>> > > >>> > --known-64-bit-blas-indices=1 >>>> > > >>> > >>>> > > >>> > Is this what you are suggesting? >>>> > > >>> > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay >>>> wrote: >>>> > > >>> > >>>> > > >>> > > Also: >>>> > > >>> > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>> > > >>> > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>> > > >>> > > >>>> > > >>> > > [we can't really over come such dependency/conflicts across >>>> packages] >>>> > > >>> > > >>>> > > >>> > > Satish >>>> > > >>> > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>> > > >>> > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>> > > >>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>> > > >>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>> > > >>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>> -known-64-bit-blas-indices=1 >>>> > > >>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>> matlab - to >>>> > > >>> have a >>>> > > >>> > > compatible build >>>> > > >>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>> > > >>> > > > >>>> > > >>> > > > Satish >>>> > > >>> > > > >>>> > > >>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>> petsc-users >>>> > > >>> wrote: >>>> > > >>> > > > >>>> > > >>> > > > > Hi Amneet, >>>> > > >>> > > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>> working. It is >>>> > > >>> > > showing >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>> > > >>> > > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>> libmesh and >>>> > > >>> this is >>>> > > >>> > > for >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>> linking >>>> > > >>> Matlab >>>> > > >>> > > with >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>> libmesh 1.6.2 >>>> > > >>> that >>>> > > >>> > > PETSc >>>> > > >>> > > > > was not found but --enable-petsc-required is specified. >>>> > > >>> > > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>> PETSc and >>>> > > >>> Matlab >>>> > > >>> > > is in >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated geometries >>>> it is >>>> > > >>> > > mentioned to >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>> > > >>> > > > > >>>> > > >>> > > > > For the past 10 days I am trying these various things >>>> and ended >>>> > > >>> up with >>>> > > >>> > > > > errors. >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>> research work. >>>> > > >>> > > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>> > > >>> > > > > >>>> > > >>> > > > > >>>> > > >>> > > > > Thanks and Regards >>>> > > >>> > > > > Srinivas >>>> > > >>> > > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>> mail2amneet at gmail.com> >>>> > > >>> > > wrote: >>>> > > >>> > > > > >>>> > > >>> > > > > > Hi Srinivas, >>>> > > >>> > > > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for the >>>> WEC >>>> > > >>> application. >>>> > > >>> > > You >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>> Matlab. >>>> > > >>> > > > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>> libMesh? >>>> > > >>> > > > > > >>>> > > >>> > > > > > Thanks, >>>> > > >>> > > > > > ?Amneet >>>> > > >>> > > > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>> 20PHD0548 via >>>> > > >>> > > petsc-users >>>> > > >>> > > > > > wrote: >>>> > > >>> > > > > > >>>> > > >>> > > > > >> Hi, >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>> occurrences >>>> > > >>> of >>>> > > >>> > > "-lut >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" >>>> got the >>>> > > >>> > > following >>>> > > >>> > > > > >> errors >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>> > > >>> > > > > >> TEST >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > >>> > > > > >> not ok >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> > > >>> Error >>>> > > >>> > > code: 124 >>>> > > >>> > > > > >> # Running problem 5 >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >>>> > > >>> > > > > >> >>>> -------------------------------------------------------------- >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> for >>>> > > >>> trouble >>>> > > >>> > > > > >> shooting. >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>> 01, 2020 >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug >>>> named >>>> > > >>> > > MB108SMEC028 >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > >>> --with-debugging=1 >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>> --with-x=0 >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > >>> --with-matlab-engine=1 >>>> > > >>> > > > > >> >>>> > > >>> >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>> 67 in >>>> > > >>> > > > > >> >>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>> Message >>>> > > >>> -------send >>>> > > >>> > > entire >>>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >>>> > > >>> > > > > >> # >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> -------------------------------------------------------------------------- >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>> > > >>> MPI_COMM_SELF >>>> > > >>> > > > > >> # with errorcode 126076. >>>> > > >>> > > > > >> # >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>> all MPI >>>> > > >>> > > processes. >>>> > > >>> > > > > >> # You may or may not see output from other processes, >>>> > > >>> depending on >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>> > > >>> > > > > >> # >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> -------------------------------------------------------------------------- >>>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> # SKIP >>>> > > >>> Command >>>> > > >>> > > > > >> failed so no diff >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>> > > >>> > > > > >> TEST >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > >>> > > > > >> not ok >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> > > >>> Error >>>> > > >>> > > code: 124 >>>> > > >>> > > > > >> # Running problem 5 >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message >>>> > > >>> > > > > >> >>>> -------------------------------------------------------------- >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> for >>>> > > >>> trouble >>>> > > >>> > > > > >> shooting. >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>> 01, 2020 >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>> named >>>> > > >>> > > MB108SMEC028 by >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > >>> --COPTFLAGS=-O3 >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>> --PETSC_ARCH=linux-opt >>>> > > >>> > > --with-debugging=0 >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>> --download-fblaslapack=1 >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > >>> --with-matlab-engine=1 >>>> > > >>> > > > > >> >>>> > > >>> >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>> 67 in >>>> > > >>> > > > > >> >>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>> Message >>>> > > >>> -------send >>>> > > >>> > > entire >>>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- >>>> > > >>> > > > > >> # >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> -------------------------------------------------------------------------- >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>> > > >>> MPI_COMM_SELF >>>> > > >>> > > > > >> # with errorcode 126076. >>>> > > >>> > > > > >> # >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>> all MPI >>>> > > >>> > > processes. >>>> > > >>> > > > > >> # You may or may not see output from other processes, >>>> > > >>> depending on >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>> > > >>> > > > > >> # >>>> > > >>> > > > > >> >>>> > > >>> > > >>>> > > >>> >>>> -------------------------------------------------------------------------- >>>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> # SKIP >>>> > > >>> Command >>>> > > >>> > > > > >> failed so no diff. >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I >>>> am >>>> > > >>> sharing the >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>> petsc >>>> > > >>> 3.17.5. >>>> > > >>> > > Please find >>>> > > >>> > > > > >> the attachment and do the needful. >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> Thanks and regards >>>> > > >>> > > > > >> Srinivas >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>> > > >>> balay at mcs.anl.gov> >>>> > > >>> > > wrote: >>>> > > >>> > > > > >> >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>> > > >>> configure.log/make.log >>>> > > >>> > > for >>>> > > >>> > > > > >>> petsc-3.17 >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> >>>> >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> Matlab: >>>> > > >>> > > > > >>> Includes: >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>> > > >>> > > > > >>> MatlabEngine: >>>> > > >>> > > > > >>> Library: >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>> -lmex >>>> > > >>> -lmx >>>> > > >>> > > -lmat -lut >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>> > > >>> > > > > >>> <<<<< >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> >>> >>>> > > >>> > > > > >>> Matlab: >>>> > > >>> > > > > >>> Includes: >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>> > > >>> > > > > >>> Libraries: >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>> > > >>> > > > > >>> Executable: >>>> > > >>> > > > > >>> >>>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>> > > >>> > > > > >>> mex: >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>> > > >>> > > > > >>> matlab: >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>> > > >>> > > > > >>> -glnxa64 >>>> > > >>> > > > > >>> <<< >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>> preset here. >>>> > > >>> This >>>> > > >>> > > might >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> You can: >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> - edit >>>> > > >>> > > > > >>> >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>> > > >>> > > and >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n >>>> -licuuc" >>>> > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> And see if the build works now. >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> Satish >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via >>>> > > >>> petsc-users >>>> > > >>> > > wrote: >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>> petsc3.13.4 with >>>> > > >>> > > matlab and >>>> > > >>> > > > > >>> also >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>> petsc3.17.5 and >>>> > > >>> matlab. >>>> > > >>> > > > > >>> Building >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. >>>> But >>>> > > >>> libmesh is >>>> > > >>> > > not >>>> > > >>> > > > > >>> able to >>>> > > >>> > > > > >>> > find the petsc >>>> > > >>> > > > > >>> > Please find the attachments. >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>> > > >>> balay at mcs.anl.gov> >>>> > > >>> > > > > >>> wrote: >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>> petsc-3.13 and >>>> > > >>> 3.17 [or >>>> > > >>> > > 3.19]. >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to >>>> mailing >>>> > > >>> list - >>>> > > >>> > > or >>>> > > >>> > > > > >>> send >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > Satish >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>> via >>>> > > >>> petsc-users >>>> > > >>> > > wrote: >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while building >>>> > > >>> petsc-3.13.4 >>>> > > >>> > > with >>>> > > >>> > > > > >>> Matlab. >>>> > > >>> > > > > >>> > > > Please find the attachment and do the needful. >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>> SRINIVAS >>>> > > >>> 20PHD0548 < >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building >>>> of >>>> > > >>> libmesh, the >>>> > > >>> > > error >>>> > > >>> > > > > >>> shows >>>> > > >>> > > > > >>> > > > > petsc was not found >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>> Balay < >>>> > > >>> > > balay at mcs.anl.gov> >>>> > > >>> > > > > >>> > > wrote: >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>> petsc-3.17 >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >> Satish >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>> 20PHD0548 via >>>> > > >>> > > petsc-users >>>> > > >>> > > > > >>> wrote: >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >> > Hello, >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>> working on >>>> > > >>> the >>>> > > >>> > > > > >>> simulation >>>> > > >>> > > > > >>> > > using >>>> > > >>> > > > > >>> > > > >> IBAMR >>>> > > >>> > > > > >>> > > > >> > open software. While building the PETSc, >>>> using the >>>> > > >>> > > following >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>> > > >>> > > > > >>> > > > >> > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>> > > >>> > > > > >>> > > > >> > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>> > > >>> > > > > >>> > > > >> > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>> > > >>> > > > > >>> > > > >> > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> >>>> > > >>> >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> >>>> > > >>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEnginePut' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineEvaluate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGet' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEnginePut' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineEvaluate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGet' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGet' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > >>> > > > > >>> > > > >> > function `main': >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineCreate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineEvaluate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineEvaluate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGetArray' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGetArray' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGetArray' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGetArray' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineGetArray' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineEvaluate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineEvaluate' >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>> > > >>>> > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> `PetscMatlabEngineDestroy' >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>> status >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> >>>> > > >>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>> > > >>> > > > > >>> > > > >> Error 1 >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >> >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>>> Institute of >>>> > > >>> > > Technology. >>>> > > >>> > > > > >> The contents of this email may contain legally >>>> protected >>>> > > >>> > > confidential or >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>>> Technology?. >>>> > > >>> If >>>> > > >>> > > you are >>>> > > >>> > > > > >> not the intended recipient, you should not >>>> disseminate, >>>> > > >>> distribute >>>> > > >>> > > or copy >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately >>>> and destroy >>>> > > >>> all >>>> > > >>> > > copies of >>>> > > >>> > > > > >> this message and any attachments. If you have >>>> received this >>>> > > >>> email >>>> > > >>> > > in error, >>>> > > >>> > > > > >> please promptly notify the sender by reply email and >>>> delete >>>> > > >>> the >>>> > > >>> > > original >>>> > > >>> > > > > >> email and any backup copies without reading them.* >>>> > > >>> > > > > >> >>>> > > >>> > > > > > >>>> > > >>> > > > > >>>> > > >>> > > > > >>>> > > >>> > > > >>>> > > >>> > > >>>> > > >>> > >>>> > > >>> > >>>> > > >>> >>>> > > >> >>>> > > >> >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>>> Technology. >>>> > > >> The contents of this email may contain legally protected >>>> confidential or >>>> > > >> privileged information of ?Vellore Institute of Technology?. If >>>> you are >>>> > > >> not the intended recipient, you should not disseminate, >>>> distribute or copy >>>> > > >> this e-mail. Please notify the sender immediately and destroy >>>> all copies of >>>> > > >> this message and any attachments. If you have received this >>>> email in error, >>>> > > >> please promptly notify the sender by reply email and delete the >>>> original >>>> > > >> email and any backup copies without reading them.* >>>> > > >> >>>> > > > >>>> > > > >>>> > > > -- >>>> > > > --Amneet >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > >>>> > > >>>> >>> >>> >>> *Disclaimer:This message was sent from Vellore Institute of Technology. >>> The contents of this email may contain legally protected confidential or >>> privileged information of ?Vellore Institute of Technology?. If you are >>> not the intended recipient, you should not disseminate, distribute or copy >>> this e-mail. Please notify the sender immediately and destroy all copies of >>> this message and any attachments. If you have received this email in error, >>> please promptly notify the sender by reply email and delete the original >>> email and any backup copies without reading them.* >>> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> >> > > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Sun Sep 3 09:27:34 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Sun, 3 Sep 2023 09:27:34 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: <21e1bf60-a695-5ea7-b718-a5a393e01f32@mcs.anl.gov> On Sun, 3 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > Hi Sathish, > > Thank you so much for your efforts and the support you are giving me to > sort this out. > > I tried to follow the same procedure which you followed to build Petsc > 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1* > Using python3 for Python > =============================================================================== > Configuring PETSc to compile on your system > > =============================================================================== > =============================================================================== > It appears you do not have valgrind > installed on your system. > We HIGHLY recommend you install it from www.valgrind.org > Or install valgrind-devel or > equivalent using your package manager. > Then rerun ./configure > > =============================================================================== > Compilers: > > C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC > -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx -Wall > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC > Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 -fPIC > -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > Linkers: > Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared > -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared > -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector -fvisibility=hidden -O3 > Libraries linked against: -lquadmath -lstdc++ -ldl > make: > Version: 4.2 > /usr/bin/make > BlasLapack: > Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to > control the number of threads > uses 8 byte integers > MPI: > Version: 3 > Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe > OMPI_VERSION: 4.1.4 > pthread: > cmake: > Version: 3.16.3 > /usr/bin/cmake > regex: > Matlab: > Includes: -I/usr/local/MATLAB/R2020b/extern/include > /usr/local/MATLAB/R2020b > MatlabEngine: > Library: > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut > -licudata -licui18n -licuuc > Language used to compile PETSc: C > PETSc: > PETSC_ARCH: linux-opt > PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > Scalar type: real > Precision: double > Support for __float128 > Integer size: 4 bytes > shared libraries: enabled > Memory alignment from malloc(): 16 bytes > xxx=========================================================================xxx > Configure stage complete. Now build PETSc libraries with: > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all > xxx=========================================================================xxx > > Then I removed all occurrences of -lut -licudata -licui18n -licuuc as you > suggested earlier. > > *$make* > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > =============================================== > > *$make test query=requires queryval=matlab* > Using MAKEFLAGS: -- queryval=matlab query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Unable to open file > # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun Sep > 3 11:51:03 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > # [0]PETSC ERROR: #5 MatLoad() line 1225 in > /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > # [0]PETSC ERROR: #6 main() line 113 in > /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -f0 /matrices/arco1 > # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > # [0]PETSC ERROR: -pc_type lu > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 113065. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > CC > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > CLINKER > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > vit Sun Sep 3 11:51:05 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 126076. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed > so no diff > > # ------------- > # Summary > # ------------- > # FAILED ksp_ksp_tutorials-ex72_12 > tao_leastsquares_tutorials_matlab-matlab_ls_test > # success 0/2 tests (0.0%) > # failed 2/2 tests (100.0%) > # todo 0/2 tests (0.0%) > # skip 0/2 tests (0.0%) > # > # Wall clock time for tests: 3 sec > # Approximate CPU time (not incl. build time): 0.05 sec > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > # > # Timing summary (actual test time / total CPU time): > # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec > > *How to sort out this error?* > > *$cd src/tao/leastsquares/tutorials/matlab/* > *$make matlab_ls_test* > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > -I/home/vit/sfw/petsc/3.13.4/include > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > -I/usr/local/MATLAB/R2020b/extern/include > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath > -lstdc++ -ldl -o matlab_ls_test You are missing some additional debug steps. [run manually with the '-info' option. Please check my previous e-mail below] > > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test -tao_smonitor -prob_id 5 -info Satish > > I think there is a problem with the Matlab-R2020b version. > I am sharing the configure.log and make.log files. Please find the > attachment and do the needful. > > > Thanks and regards > Srinivas > > > On Sat, Sep 2, 2023 at 11:15?PM Satish Balay wrote: > > > Perhaps you can try the following to get additional info - and debug > > > > Satish > > ---------- > > > > balay at compute-386-07:/scratch/balay/petsc$ cd > > src/tao/leastsquares/tutorials/matlab/ > > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > make matlab_ls_test > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > > -L/scratch/balay/petsc/linux-opt/lib > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex > > -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi > > -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o > > matlab_ls_test > > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > > -tao_smonitor -prob_id 5 -info > > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 > > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > compute-386-07.(none) > > [0] PetscInitialize(): Running on machine: compute-386-07 > > Running problem 5 > > [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > > -2080374784 max tags = 268435455 > > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > -glnxa64 -nodisplay -nosplash > > [0] PetscMatlabEngineCreate(): Started MATLAB engine > > [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > > TestingInitialize > > [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > > TestingInitialize > > 5 > > > > > > <<<< Now verify if the above matlab command actually works for you - on > > this machine..>>>>> > > > > balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > -glnxa64 -nodisplay -nosplash > > > > > > < M A T L A B (R) > > > > > Copyright 1984-2021 The MathWorks, Inc. > > > > R2021a (9.10.0.1602886) 64-bit (glnxa64) > > > > February 17, 2021 > > > > > > To get started, type doc. > > For product information, visit www.mathworks.com. > > > > >> > > > > > > On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > > > > > Please don't cc: both petsc-users and petsc-maint [reverting thread to > > petsc-users only] > > > > > > I'm not sure what is happening here. Can you send the corresponding > > configure.log, make.log [compressed]? > > > > > > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, with > > Matlab-R2021a - and that works: > > > > > > balay at compute-386-07:/scratch/balay/petsc$ git branch > > > main > > > release > > > * release-3.13 > > > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a > > > balay at compute-386-07:/scratch/balay/petsc$ which matlab > > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > balay at compute-386-07:/scratch/balay/petsc$ ./configure > > --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > > COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 --with-x=0 > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > > > > Compilers: > > > > > > > > > C Compiler: > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fvisibility=hidden -O3 > > > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > C++ Compiler: > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall > > -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fvisibility=hidden -O3 -fPIC > > > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > Fortran Compiler: > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall > > -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > Linkers: > > > Shared linker: > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC > > -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > -fstack-protector -fvisibility=hidden -O3 > > > Dynamic linker: > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC > > -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > -fstack-protector -fvisibility=hidden -O3 > > > Libraries linked against: -lquadmath -lstdc++ -ldl > > > make: > > > Version: 4.2 > > > /usr/bin/make > > > BlasLapack: > > > Library: > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > -liomp5 -lpthread > > > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to > > control the number of threads > > > uses 8 byte integers > > > MPI: > > > Version: 4 > > > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > > > MPICH_NUMVERSION: 40002300 > > > pthread: > > > Library: -lpthread > > > cmake: > > > Version: 3.16.3 > > > /usr/bin/cmake > > > regex: > > > Matlab: > > > Includes: > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > MatlabEngine: > > > Library: > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > > > sowing: > > > Version: 1.1.25 > > > /scratch/balay/petsc/linux-opt/bin/bfort > > > valgrind: > > > Language used to compile PETSc: C > > > PETSc: > > > PETSC_ARCH: linux-opt > > > PETSC_DIR: /scratch/balay/petsc > > > Scalar type: real > > > Precision: double > > > Support for __float128 > > > Integer size: 4 bytes > > > shared libraries: enabled > > > Memory alignment from malloc(): 16 bytes > > > > > xxx=========================================================================xxx > > > Configure stage complete. Now build PETSc libraries with: > > > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > > > > > xxx=========================================================================xxx > > > balay at compute-386-07:/scratch/balay/petsc$ make > > > > > > > > > > > > > > > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > > > BEGINNING TO COMPILE MATLAB INTERFACE > > > Building with 'gcc'. > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > > | ^ > > > > > > MEX completed successfully. > > > Building with 'gcc'. > > > MEX completed successfully. > > > Building with 'gcc'. > > > MEX completed successfully. > > > Building with 'gcc'. > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > > | ^ > > > > > > MEX completed successfully. > > > ========================================= > > > Now to check if the libraries are working do: > > > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > > > ========================================= > > > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires > > queryval=matlab > > > Using MAKEFLAGS: -- queryval=matlab query=requires > > > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > > > # ../ex72: > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > version `GFORTRAN_9' not found (required by > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > CC > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > CLINKER > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > TEST > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 1 > > > # ../matlab_ls_test: > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > version `GFORTRAN_9' not found (required by > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > failed so no diff > > > > > > balay at compute-386-07:/scratch/balay/petsc$ > > LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires > > queryval=matlab > > > Using MAKEFLAGS: -- queryval=matlab query=requires > > > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > ok ksp_ksp_tutorials-ex72_12 > > > ok diff-ksp_ksp_tutorials-ex72_12 > > > TEST > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > > > # ------------- > > > # Summary > > > # ------------- > > > # success 4/4 tests (100.0%) > > > # failed 0/4 tests (0.0%) > > > # todo 0/4 tests (0.0%) > > > # skip 0/4 tests (0.0%) > > > # > > > # Wall clock time for tests: 27 sec > > > # Approximate CPU time (not incl. build time): 15.190000000000001 sec > > > # > > > # Timing summary (actual test time / total CPU time): > > > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 sec > > > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > > > balay at compute-386-07:/scratch/balay/petsc$ > > > > > > > > > > > > > > > > > > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > > > > > > > Based on the suggestions given by Sathish, I have tried to configure > > petsc > > > > 3.13.4 with Matlab-R2020b. But, it was not successful. After running > > make > > > > -j 10 test command I have got the following error message. > > > > > > > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: > > 124 > > > > # Running problem 5 > > > > # [0]PETSC ERROR: --------------------- Error Message > > > > -------------------------------------------------------------- > > > > # [0]PETSC ERROR: Error in external library > > > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > # [0]PETSC ERROR: See > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > > for trouble shooting. > > > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 > > by > > > > vit Sat Sep 2 12:27:22 2023 > > > > # [0]PETSC ERROR: Configure options > > > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > > --with-matlab-engine=1 --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > --known-64-bit-blas-indices=1 > > > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > # [0]PETSC ERROR: #2 main() line 126 in > > > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > # [0]PETSC ERROR: PETSc Option Table entries: > > > > # [0]PETSC ERROR: -prob_id 5 > > > > # [0]PETSC ERROR: -tao_smonitor > > > > # [0]PETSC ERROR: ----------------End of Error Message -------send > > entire > > > > error message to petsc-maint at mcs.anl.gov---------- > > > > # > > -------------------------------------------------------------------------- > > > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > # with errorcode 126076. > > > > # > > > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > > > # You may or may not see output from other processes, depending on > > > > # exactly when Open MPI kills them. > > > > # > > -------------------------------------------------------------------------- > > > > > > > > I request you to help me to sort out this error. > > > > > > > > Thanks > > > > Srinivas > > > > > > > > > > > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla > > wrote: > > > > > > > > > I think there should be two hyphens in > > > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > > > > > > > i.e.: > > > > > > > > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > > > > > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via > > petsc-users < > > > > > petsc-users at mcs.anl.gov> wrote: > > > > > > > > > >> Thank you Sathish.I will try this > > > > >> > > > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay wrote: > > > > >> > > > > >>> yes [and remove fblaslapack. don't know if hypre will work here]. > > > > >>> > > > > >>> i.e: > > > > >>> > > > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > > >>> --with-debugging=0 --with-x=0 \ > > > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 > > > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 > > > > >>> > > > > >>> Satish > > > > >>> > > > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > wrote: > > > > >>> > > > > >>> > Hi Satish, > > > > >>> > > > > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > > > > >>> > --known-64-bit-blas-indices=1 > > > > >>> > > > > > >>> > Is this what you are suggesting? > > > > >>> > > > > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay > > wrote: > > > > >>> > > > > > >>> > > Also: > > > > >>> > > > > > > >>> > > '-known-64-bit-blas-indices=1', > > > > >>> > > > > > > >>> > > Note: most externalpackages might not work in this mode. > > > > >>> > > > > > > >>> > > [we can't really over come such dependency/conflicts across > > packages] > > > > >>> > > > > > > >>> > > Satish > > > > >>> > > > > > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > > > >>> > > > > > > >>> > > > Here is the matlab test that runs in CI > > > > >>> > > > > > > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > >>> > > > > > > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > > >>> > > > > > > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with > > > > >>> > > > # MATLAB BLAS - hence requiring -known-64-bit-blas-indices=1 > > > > >>> > > > > > > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with matlab - > > to > > > > >>> have a > > > > >>> > > compatible build > > > > >>> > > > > > > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > > > > >>> > > > > > > > >>> > > > Satish > > > > >>> > > > > > > > >>> > > > > > > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > > > > >>> wrote: > > > > >>> > > > > > > > >>> > > > > Hi Amneet, > > > > >>> > > > > > > > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not > > working. It is > > > > >>> > > showing > > > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > > > > >>> > > > > > > > > >>> > > > > I am trying to install IBAMR in HPC cluster with libmesh > > and > > > > >>> this is > > > > >>> > > for > > > > >>> > > > > general usage not only for WEC. This I tried without > > linking > > > > >>> Matlab > > > > >>> > > with > > > > >>> > > > > PETSc. Here also I got the error while configuring libmesh > > 1.6.2 > > > > >>> that > > > > >>> > > PETSc > > > > >>> > > > > was not found but --enable-petsc-required is specified. > > > > >>> > > > > > > > > >>> > > > > The reason for specifically asking for libmesh with PETSc > > and > > > > >>> Matlab > > > > >>> > > is in > > > > >>> > > > > the cfd-mpc-wecs application for complicated geometries it > > is > > > > >>> > > mentioned to > > > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > > > > >>> > > > > > > > > >>> > > > > For the past 10 days I am trying these various things and > > ended > > > > >>> up with > > > > >>> > > > > errors. > > > > >>> > > > > I want to solve this and proceed further to do my research > > work. > > > > >>> > > > > > > > > >>> > > > > Please help me to solve this as soon as possible. > > > > >>> > > > > > > > > >>> > > > > > > > > >>> > > > > Thanks and Regards > > > > >>> > > > > Srinivas > > > > >>> > > > > > > > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > > mail2amneet at gmail.com> > > > > >>> > > wrote: > > > > >>> > > > > > > > > >>> > > > > > Hi Srinivas, > > > > >>> > > > > > > > > > >>> > > > > > As discussed earlier you don?t need libMesh for the WEC > > > > >>> application. > > > > >>> > > You > > > > >>> > > > > > can just work with PETSc 3.17.5 that builds with Matlab. > > > > >>> > > > > > > > > > >>> > > > > > Do you have a specific reason for wanting to build > > libMesh? > > > > >>> > > > > > > > > > >>> > > > > > Thanks, > > > > >>> > > > > > ?Amneet > > > > >>> > > > > > > > > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS > > 20PHD0548 via > > > > >>> > > petsc-users > > > > >>> > > > > > wrote: > > > > >>> > > > > > > > > > >>> > > > > >> Hi, > > > > >>> > > > > >> > > > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all > > occurrences > > > > >>> of > > > > >>> > > "-lut > > > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" > > got the > > > > >>> > > following > > > > >>> > > > > >> errors > > > > >>> > > > > >> in petsc/3.13.4/linux-debug: > > > > >>> > > > > >> TEST > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > # > > > > >>> Error > > > > >>> > > code: 124 > > > > >>> > > > > >> # Running problem 5 > > > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > > >>> > > > > >> > > -------------------------------------------------------------- > > > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > >>> > > > > >> # [0]PETSC ERROR: See > > > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html > > for > > > > >>> trouble > > > > >>> > > > > >> shooting. > > > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > > 2020 > > > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug > > named > > > > >>> > > MB108SMEC028 > > > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > > > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > > >>> --with-debugging=1 > > > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 --with-x=0 > > > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>> --with-matlab-engine=1 > > > > >>> > > > > >> > > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 > > in > > > > >>> > > > > >> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > > > > >>> -------send > > > > >>> > > entire > > > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > > >>> > > > > >> # > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > -------------------------------------------------------------------------- > > > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > > > >>> MPI_COMM_SELF > > > > >>> > > > > >> # with errorcode 126076. > > > > >>> > > > > >> # > > > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all > > MPI > > > > >>> > > processes. > > > > >>> > > > > >> # You may or may not see output from other processes, > > > > >>> depending on > > > > >>> > > > > >> # exactly when Open MPI kills them. > > > > >>> > > > > >> # > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > -------------------------------------------------------------------------- > > > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > > SKIP > > > > >>> Command > > > > >>> > > > > >> failed so no diff > > > > >>> > > > > >> > > > > >>> > > > > >> in petsc/3.13.4/linux-opt > > > > >>> > > > > >> TEST > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>> > > > > >> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > # > > > > >>> Error > > > > >>> > > code: 124 > > > > >>> > > > > >> # Running problem 5 > > > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > > > > >>> > > > > >> > > -------------------------------------------------------------- > > > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > >>> > > > > >> # [0]PETSC ERROR: See > > > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html > > for > > > > >>> trouble > > > > >>> > > > > >> shooting. > > > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > > 2020 > > > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > > > >>> > > MB108SMEC028 by > > > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > > > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > > >>> --COPTFLAGS=-O3 > > > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 --PETSC_ARCH=linux-opt > > > > >>> > > --with-debugging=0 > > > > >>> > > > > >> --download-hypre=1 --with-x=0 --download-fblaslapack=1 > > > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>> --with-matlab-engine=1 > > > > >>> > > > > >> > > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 > > in > > > > >>> > > > > >> > > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error Message > > > > >>> -------send > > > > >>> > > entire > > > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > > > > >>> > > > > >> # > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > -------------------------------------------------------------------------- > > > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > > > >>> MPI_COMM_SELF > > > > >>> > > > > >> # with errorcode 126076. > > > > >>> > > > > >> # > > > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all > > MPI > > > > >>> > > processes. > > > > >>> > > > > >> # You may or may not see output from other processes, > > > > >>> depending on > > > > >>> > > > > >> # exactly when Open MPI kills them. > > > > >>> > > > > >> # > > > > >>> > > > > >> > > > > >>> > > > > > > >>> > > -------------------------------------------------------------------------- > > > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > > SKIP > > > > >>> Command > > > > >>> > > > > >> failed so no diff. > > > > >>> > > > > >> > > > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I am > > > > >>> sharing the > > > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and petsc > > > > >>> 3.17.5. > > > > >>> > > Please find > > > > >>> > > > > >> the attachment and do the needful. > > > > >>> > > > > >> > > > > >>> > > > > >> Thanks and regards > > > > >>> > > > > >> Srinivas > > > > >>> > > > > >> > > > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > > > > >>> balay at mcs.anl.gov> > > > > >>> > > wrote: > > > > >>> > > > > >> > > > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > > > > >>> configure.log/make.log > > > > >>> > > for > > > > >>> > > > > >>> petsc-3.17 > > > > >>> > > > > >>> > > > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > > > >>> > > > > >>> > > > > >>> > > > > >>> >>>> > > > > >>> > > > > >>> > > > > >>> > > > > >>> Matlab: > > > > >>> > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > > >>> > > > > >>> /usr/local/MATLAB/R2020b > > > > >>> > > > > >>> MatlabEngine: > > > > >>> > > > > >>> Library: > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng > > -lmex > > > > >>> -lmx > > > > >>> > > -lmat -lut > > > > >>> > > > > >>> -licudata -licui18n -licuuc > > > > >>> > > > > >>> Language used to compile PETSc: C > > > > >>> > > > > >>> <<<<< > > > > >>> > > > > >>> > > > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > > > > >>> > > > > >>> > > > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > >>> > > > > >>> > > > > >>> > > > > >>> >>> > > > > >>> > > > > >>> Matlab: > > > > >>> > > > > >>> Includes: > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > > >>> > > > > >>> Libraries: > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > >>> > > > > >>> -leng -lmex -lmx -lmat > > > > >>> > > > > >>> Executable: > > > > >>> > > > > >>> > > > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > > >>> > > > > >>> mex: > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > > >>> > > > > >>> matlab: > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > > >>> > > > > >>> -glnxa64 > > > > >>> > > > > >>> <<< > > > > >>> > > > > >>> > > > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not preset > > here. > > > > >>> This > > > > >>> > > might > > > > >>> > > > > >>> be a change wrt newer matlab versions. > > > > >>> > > > > >>> > > > > >>> > > > > >>> You can: > > > > >>> > > > > >>> > > > > >>> > > > > >>> - edit > > > > >>> > > > > >>> > > > > >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > > > >>> > > and > > > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n > > -licuuc" > > > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > > > > >>> > > > > >>> > > > > >>> > > > > >>> And see if the build works now. > > > > >>> > > > > >>> > > > > >>> > > > > >>> Satish > > > > >>> > > > > >>> > > > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > > > >>> petsc-users > > > > >>> > > wrote: > > > > >>> > > > > >>> > > > > >>> > > > > >>> > I am sharing the log files while building > > petsc3.13.4 with > > > > >>> > > matlab and > > > > >>> > > > > >>> also > > > > >>> > > > > >>> > the log file while building libmesh with petsc3.17.5 > > and > > > > >>> matlab. > > > > >>> > > > > >>> Building > > > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. But > > > > >>> libmesh is > > > > >>> > > not > > > > >>> > > > > >>> able to > > > > >>> > > > > >>> > find the petsc > > > > >>> > > > > >>> > Please find the attachments. > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > > > > >>> balay at mcs.anl.gov> > > > > >>> > > > > >>> wrote: > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > Send configure.log, make.log from both petsc-3.13 > > and > > > > >>> 3.17 [or > > > > >>> > > 3.19]. > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to > > mailing > > > > >>> list - > > > > >>> > > or > > > > >>> > > > > >>> send > > > > >>> > > > > >>> > > them to petsc-maint] > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > Satish > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > > > > >>> petsc-users > > > > >>> > > wrote: > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > I am sharing the make.log file while building > > > > >>> petsc-3.13.4 > > > > >>> > > with > > > > >>> > > > > >>> Matlab. > > > > >>> > > > > >>> > > > Please find the attachment and do the needful. > > > > >>> > > > > >>> > > > > > > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU SRINIVAS > > > > >>> 20PHD0548 < > > > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > >>> > > > > >>> > > > > > > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building of > > > > >>> libmesh, the > > > > >>> > > error > > > > >>> > > > > >>> shows > > > > >>> > > > > >>> > > > > petsc was not found > > > > >>> > > > > >>> > > > > > > > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish Balay < > > > > >>> > > balay at mcs.anl.gov> > > > > >>> > > > > >>> > > wrote: > > > > >>> > > > > >>> > > > > > > > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says petsc-3.17 > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> Here you are using 3.13 > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> Satish > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS > > 20PHD0548 via > > > > >>> > > petsc-users > > > > >>> > > > > >>> wrote: > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > Hello, > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for > > working on > > > > >>> the > > > > >>> > > > > >>> simulation > > > > >>> > > > > >>> > > using > > > > >>> > > > > >>> > > > >> IBAMR > > > > >>> > > > > >>> > > > >> > open software. While building the PETSc, > > using the > > > > >>> > > following > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > > >>> > > > > >>> > > > >> > ./configure \ > > > > >>> > > > > >>> > > > >> > > > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > > >>> > > > > >>> > > > >> > > > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > > >>> > > > > >>> > > > >> > > > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > > > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > > > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > > > > >>> > > > > >>> > > > >> > --with-x=0 \ > > > > >>> > > > > >>> > > > >> > > > --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > > >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > make -j4 > > > > >>> > > > > >>> > > > >> > make -j4 test > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > I got the following error > > > > >>> > > > > >>> > > > >> > CLINKER > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEnginePut' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineEvaluate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGet' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEnginePut' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineEvaluate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGet' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > > >>> > > > >> > function `TaoPounders': > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGet' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > > >>> > > > > >>> > > > >> > function `main': > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineCreate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineEvaluate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineEvaluate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGetArray' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGetArray' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGetArray' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGetArray' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineGetArray' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineEvaluate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineEvaluate' > > > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > >>> > > > > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > > >>> > > > > >>> > > > >> > undefined reference to > > `PetscMatlabEngineDestroy' > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit status > > > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > > >>> > > > > >>> > > > >> Error 1 > > > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > Please help me to solve this issue > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > Thank you > > > > >>> > > > > >>> > > > >> > Srinivas > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > >> > > > > >>> > > > > >>> > > > > > > > >>> > > > > >>> > > > > > > > >>> > > > > >>> > > > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > > >>> > > > > >>> > > > > >>> > > > > >> > > > > >>> > > > > >> > > > > >>> > > > > >> *Disclaimer:This message was sent from Vellore > > Institute of > > > > >>> > > Technology. > > > > >>> > > > > >> The contents of this email may contain legally protected > > > > >>> > > confidential or > > > > >>> > > > > >> privileged information of ?Vellore Institute of > > Technology?. > > > > >>> If > > > > >>> > > you are > > > > >>> > > > > >> not the intended recipient, you should not disseminate, > > > > >>> distribute > > > > >>> > > or copy > > > > >>> > > > > >> this e-mail. Please notify the sender immediately and > > destroy > > > > >>> all > > > > >>> > > copies of > > > > >>> > > > > >> this message and any attachments. If you have received > > this > > > > >>> email > > > > >>> > > in error, > > > > >>> > > > > >> please promptly notify the sender by reply email and > > delete > > > > >>> the > > > > >>> > > original > > > > >>> > > > > >> email and any backup copies without reading them.* > > > > >>> > > > > >> > > > > >>> > > > > > > > > > >>> > > > > > > > > >>> > > > > > > > > >>> > > > > > > > >>> > > > > > > >>> > > > > > >>> > > > > > >>> > > > > >> > > > > >> > > > > >> *Disclaimer:This message was sent from Vellore Institute of > > Technology. > > > > >> The contents of this email may contain legally protected > > confidential or > > > > >> privileged information of ?Vellore Institute of Technology?. If > > you are > > > > >> not the intended recipient, you should not disseminate, distribute > > or copy > > > > >> this e-mail. Please notify the sender immediately and destroy all > > copies of > > > > >> this message and any attachments. If you have received this email > > in error, > > > > >> please promptly notify the sender by reply email and delete the > > original > > > > >> email and any backup copies without reading them.* > > > > >> > > > > > > > > > > > > > > > -- > > > > > --Amneet > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > From balay at mcs.anl.gov Sun Sep 3 09:30:51 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Sun, 3 Sep 2023 09:30:51 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> Message-ID: <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> To use datafiles in the test suite: cd $HOME git clone https://gitlab.com/petsc/datafiles make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles Satish On Sun, 3 Sep 2023, Matthew Knepley wrote: > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > Hi Matthew, > > > > I am using PETSc to simulate the problems using IBAMR. I do not have any > > separate test files to test PETSc alone. Can you please help me how to > > define this DATAFILESPATH? > > > > That test you tried uses a certain matrix. On our machine, we point to this > matrix using an environment variable, DATAFILESPATH. You don't have those > matrices, since they are just for testing here. That > is why I suggested just using a different matrix, or running a problem you > care about in IBAMR. > > Thanks, > > Matt > > > > Thanks and regards > > Srinivas. > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley wrote: > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via petsc-users < > >> petsc-users at mcs.anl.gov> wrote: > >> > >>> Hi Sathish, > >>> > >>> Thank you so much for your efforts and the support you are giving me to > >>> sort this out. > >>> > >>> I tried to follow the same procedure which you followed to build Petsc > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > >>> > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>> --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* > >>> Using python3 for Python > >>> > >>> =============================================================================== > >>> Configuring PETSc to compile on your system > >>> > >>> > >>> =============================================================================== > >>> =============================================================================== > >>> It appears you do not have valgrind > >>> installed on your system. > >>> We HIGHLY recommend you install it from www.valgrind.org > >>> Or install valgrind-devel or > >>> equivalent using your package manager. > >>> Then rerun ./configure > >>> > >>> =============================================================================== > >>> Compilers: > >>> > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>> -fstack-protector -fvisibility=hidden -O3 > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>> Linkers: > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>> -fstack-protector -fvisibility=hidden -O3 > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>> -fstack-protector -fvisibility=hidden -O3 > >>> Libraries linked against: -lquadmath -lstdc++ -ldl > >>> make: > >>> Version: 4.2 > >>> /usr/bin/make > >>> BlasLapack: > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to > >>> control the number of threads > >>> uses 8 byte integers > >>> MPI: > >>> Version: 3 > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe > >>> OMPI_VERSION: 4.1.4 > >>> pthread: > >>> cmake: > >>> Version: 3.16.3 > >>> /usr/bin/cmake > >>> regex: > >>> Matlab: > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > >>> /usr/local/MATLAB/R2020b > >>> MatlabEngine: > >>> Library: > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut > >>> -licudata -licui18n -licuuc > >>> Language used to compile PETSc: C > >>> PETSc: > >>> PETSC_ARCH: linux-opt > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > >>> Scalar type: real > >>> Precision: double > >>> Support for __float128 > >>> Integer size: 4 bytes > >>> shared libraries: enabled > >>> Memory alignment from malloc(): 16 bytes > >>> > >>> xxx=========================================================================xxx > >>> Configure stage complete. Now build PETSc libraries with: > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all > >>> > >>> xxx=========================================================================xxx > >>> > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as > >>> you suggested earlier. > >>> > >>> *$make* > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > >>> BEGINNING TO COMPILE MATLAB INTERFACE > >>> Building with 'gcc'. > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > >>> In function ?PetscBinaryWrite?: > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>> warning: ?err? may be used uninitialized in this function > >>> [-Wmaybe-uninitialized] > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>> | ^ > >>> > >>> MEX completed successfully. > >>> Building with 'gcc'. > >>> MEX completed successfully. > >>> Building with 'gcc'. > >>> MEX completed successfully. > >>> Building with 'gcc'. > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > >>> In function ?PetscBinaryWrite?: > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>> warning: ?err? may be used uninitialized in this function > >>> [-Wmaybe-uninitialized] > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>> | ^ > >>> > >>> MEX completed successfully. > >>> ========================================= > >>> Now to check if the libraries are working do: > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > >>> =============================================== > >>> > >>> *$make test query=requires queryval=matlab* > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > >>> # [0]PETSC ERROR: --------------------- Error Message > >>> -------------------------------------------------------------- > >>> # [0]PETSC ERROR: Unable to open file > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > >>> > >> > >> No, the problem is that you do not have DATAFILESPATH defined, so it > >> cannot find the matrix to test. Try running some test of yours. > >> > >> Thanks, > >> > >> Matt > >> > >> > >>> # [0]PETSC ERROR: See > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > >>> shooting. > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun > >>> Sep 3 11:51:03 2023 > >>> # [0]PETSC ERROR: Configure options > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > >>> # [0]PETSC ERROR: #6 main() line 113 in > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > >>> # [0]PETSC ERROR: PETSc Option Table entries: > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > >>> # [0]PETSC ERROR: -pc_type lu > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > >>> entire error message to petsc-maint at mcs.anl.gov---------- > >>> # > >>> -------------------------------------------------------------------------- > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>> # with errorcode 113065. > >>> # > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>> # You may or may not see output from other processes, depending on > >>> # exactly when Open MPI kills them. > >>> # > >>> -------------------------------------------------------------------------- > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>> CC > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > >>> CLINKER > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>> TEST > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > >>> # Running problem 5 > >>> # [0]PETSC ERROR: --------------------- Error Message > >>> -------------------------------------------------------------- > >>> # [0]PETSC ERROR: Error in external library > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on > >>> # [0]PETSC ERROR: See > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > >>> shooting. > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > >>> vit Sun Sep 3 11:51:05 2023 > >>> # [0]PETSC ERROR: Configure options > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>> # [0]PETSC ERROR: #2 main() line 126 in > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>> # [0]PETSC ERROR: PETSc Option Table entries: > >>> # [0]PETSC ERROR: -prob_id 5 > >>> # [0]PETSC ERROR: -tao_smonitor > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > >>> entire error message to petsc-maint at mcs.anl.gov---------- > >>> # > >>> -------------------------------------------------------------------------- > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>> # with errorcode 126076. > >>> # > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>> # You may or may not see output from other processes, depending on > >>> # exactly when Open MPI kills them. > >>> # > >>> -------------------------------------------------------------------------- > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > >>> failed so no diff > >>> > >>> # ------------- > >>> # Summary > >>> # ------------- > >>> # FAILED ksp_ksp_tutorials-ex72_12 > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test > >>> # success 0/2 tests (0.0%) > >>> # failed 2/2 tests (100.0%) > >>> # todo 0/2 tests (0.0%) > >>> # skip 0/2 tests (0.0%) > >>> # > >>> # Wall clock time for tests: 3 sec > >>> # Approximate CPU time (not incl. build time): 0.05 sec > >>> # > >>> # To rerun failed tests: > >>> # /usr/bin/make -f gmakefile test test-fail=1 > >>> # > >>> # Timing summary (actual test time / total CPU time): > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec > >>> > >>> *How to sort out this error?* > >>> > >>> *$cd src/tao/leastsquares/tutorials/matlab/* > >>> *$make matlab_ls_test* > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > >>> -I/home/vit/sfw/petsc/3.13.4/include > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > >>> -I/usr/local/MATLAB/R2020b/extern/include > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath > >>> -lstdc++ -ldl -o matlab_ls_test > >>> > >>> I think there is a problem with the Matlab-R2020b version. > >>> I am sharing the configure.log and make.log files. Please find the > >>> attachment and do the needful. > >>> > >>> > >>> Thanks and regards > >>> Srinivas > >>> > >>> > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay wrote: > >>> > >>>> Perhaps you can try the following to get additional info - and debug > >>>> > >>>> Satish > >>>> ---------- > >>>> > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd > >>>> src/tao/leastsquares/tutorials/matlab/ > >>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > >>>> make matlab_ls_test > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > >>>> -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include > >>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > >>>> -L/scratch/balay/petsc/linux-opt/lib > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o > >>>> matlab_ls_test > >>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > >>>> -tao_smonitor -prob_id 5 -info > >>>> [0] PetscInitialize(): PETSc successfully started: number of processors > >>>> = 1 > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS > >>>> compute-386-07.(none) > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 > >>>> Running problem 5 > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > >>>> -2080374784 max tags = 268435455 > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>> -glnxa64 -nodisplay -nosplash > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > >>>> TestingInitialize > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > >>>> TestingInitialize > >>>> 5 > >>>> > >>>> > >>>> <<<< Now verify if the above matlab command actually works for you - on > >>>> this machine..>>>>> > >>>> > >>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>> -glnxa64 -nodisplay -nosplash > >>>> > >>>> > >>>> < M A T L A B (R) > > >>>> > >>>> Copyright 1984-2021 The MathWorks, Inc. > >>>> > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) > >>>> > >>>> February 17, 2021 > >>>> > >>>> > >>>> To get started, type doc. > >>>> For product information, visit www.mathworks.com. > >>>> > >>>> >> > >>>> > >>>> > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > >>>> > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting thread > >>>> to petsc-users only] > >>>> > > >>>> > I'm not sure what is happening here. Can you send the corresponding > >>>> configure.log, make.log [compressed]? > >>>> > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, > >>>> with Matlab-R2021a - and that works: > >>>> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch > >>>> > main > >>>> > release > >>>> > * release-3.13 > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab > >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>>> --with-debugging=0 --with-x=0 > >>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > >>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>> > > >>>> > Compilers: > >>>> > >>>> > >>>> > >>>> > C Compiler: > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > >>>> -fvisibility=hidden -O3 > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>> > C++ Compiler: > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > >>>> -fvisibility=hidden -O3 -fPIC > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>> > Fortran Compiler: > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>> > Linkers: > >>>> > Shared linker: > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>> -fstack-protector -fvisibility=hidden -O3 > >>>> > Dynamic linker: > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>> -fstack-protector -fvisibility=hidden -O3 > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl > >>>> > make: > >>>> > Version: 4.2 > >>>> > /usr/bin/make > >>>> > BlasLapack: > >>>> > Library: > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > >>>> -liomp5 -lpthread > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

> >>>> to control the number of threads > >>>> > uses 8 byte integers > >>>> > MPI: > >>>> > Version: 4 > >>>> > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > >>>> > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > >>>> > MPICH_NUMVERSION: 40002300 > >>>> > pthread: > >>>> > Library: -lpthread > >>>> > cmake: > >>>> > Version: 3.16.3 > >>>> > /usr/bin/cmake > >>>> > regex: > >>>> > Matlab: > >>>> > Includes: > >>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > >>>> > MatlabEngine: > >>>> > Library: > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > >>>> > sowing: > >>>> > Version: 1.1.25 > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort > >>>> > valgrind: > >>>> > Language used to compile PETSc: C > >>>> > PETSc: > >>>> > PETSC_ARCH: linux-opt > >>>> > PETSC_DIR: /scratch/balay/petsc > >>>> > Scalar type: real > >>>> > Precision: double > >>>> > Support for __float128 > >>>> > Integer size: 4 bytes > >>>> > shared libraries: enabled > >>>> > Memory alignment from malloc(): 16 bytes > >>>> > > >>>> xxx=========================================================================xxx > >>>> > Configure stage complete. Now build PETSc libraries with: > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > >>>> > > >>>> xxx=========================================================================xxx > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make > >>>> > >>>> > >>>> > >>>> > > >>>> > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE > >>>> > Building with 'gcc'. > >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > >>>> function ?PetscBinaryWrite?: > >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>> warning: ?err? may be used uninitialized in this function > >>>> [-Wmaybe-uninitialized] > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>> > | ^ > >>>> > > >>>> > MEX completed successfully. > >>>> > Building with 'gcc'. > >>>> > MEX completed successfully. > >>>> > Building with 'gcc'. > >>>> > MEX completed successfully. > >>>> > Building with 'gcc'. > >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > >>>> function ?PetscBinaryWrite?: > >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>> warning: ?err? may be used uninitialized in this function > >>>> [-Wmaybe-uninitialized] > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>> > | ^ > >>>> > > >>>> > MEX completed successfully. > >>>> > ========================================= > >>>> > Now to check if the libraries are working do: > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > >>>> > ========================================= > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires > >>>> queryval=matlab > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > >>>> > # ../ex72: > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > >>>> version `GFORTRAN_9' not found (required by > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>>> > CC > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > >>>> > CLINKER > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>>> > TEST > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: > >>>> 1 > >>>> > # ../matlab_ls_test: > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > >>>> version `GFORTRAN_9' not found (required by > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > >>>> failed so no diff > >>>> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires > >>>> queryval=matlab > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > >>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>> > ok ksp_ksp_tutorials-ex72_12 > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 > >>>> > TEST > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>> > > >>>> > # ------------- > >>>> > # Summary > >>>> > # ------------- > >>>> > # success 4/4 tests (100.0%) > >>>> > # failed 0/4 tests (0.0%) > >>>> > # todo 0/4 tests (0.0%) > >>>> > # skip 0/4 tests (0.0%) > >>>> > # > >>>> > # Wall clock time for tests: 27 sec > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 sec > >>>> > # > >>>> > # Timing summary (actual test time / total CPU time): > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54 > >>>> sec > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > >>>> > > >>>> > > >>>> > > >>>> > > >>>> > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > >>>> > > >>>> > > Based on the suggestions given by Sathish, I have tried to > >>>> configure petsc > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After > >>>> running make > >>>> > > -j 10 test command I have got the following error message. > >>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > >>>> code: 124 > >>>> > > # Running problem 5 > >>>> > > # [0]PETSC ERROR: --------------------- Error Message > >>>> > > -------------------------------------------------------------- > >>>> > > # [0]PETSC ERROR: Error in external library > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>> > > # [0]PETSC ERROR: See > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>> > > for trouble shooting. > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > >>>> MB108SMEC028 by > >>>> > > vit Sat Sep 2 12:27:22 2023 > >>>> > > # [0]PETSC ERROR: Configure options > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>>> --with-debugging=0 > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>> > > --with-matlab-engine=1 > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>> > > --known-64-bit-blas-indices=1 > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in > >>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: > >>>> > > # [0]PETSC ERROR: -prob_id 5 > >>>> > > # [0]PETSC ERROR: -tao_smonitor > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message -------send > >>>> entire > >>>> > > error message to petsc-maint at mcs.anl.gov---------- > >>>> > > # > >>>> -------------------------------------------------------------------------- > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>>> > > # with errorcode 126076. > >>>> > > # > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > >>>> processes. > >>>> > > # You may or may not see output from other processes, depending on > >>>> > > # exactly when Open MPI kills them. > >>>> > > # > >>>> -------------------------------------------------------------------------- > >>>> > > > >>>> > > I request you to help me to sort out this error. > >>>> > > > >>>> > > Thanks > >>>> > > Srinivas > >>>> > > > >>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < > >>>> mail2amneet at gmail.com> wrote: > >>>> > > > >>>> > > > I think there should be two hyphens in > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>> > > > > >>>> > > > i.e.: > >>>> > > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>> > > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via > >>>> petsc-users < > >>>> > > > petsc-users at mcs.anl.gov> wrote: > >>>> > > > > >>>> > > >> Thank you Sathish.I will try this > >>>> > > >> > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>> wrote: > >>>> > > >> > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work > >>>> here]. > >>>> > > >>> > >>>> > > >>> i.e: > >>>> > > >>> > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>>> > > >>> --with-debugging=0 --with-x=0 \ > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>> --with-matlab-engine=1 > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>> --known-64-bit-blas-indices=1 > >>>> > > >>> > >>>> > > >>> Satish > >>>> > > >>> > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users > >>>> wrote: > >>>> > > >>> > >>>> > > >>> > Hi Satish, > >>>> > > >>> > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > >>>> > > >>> > --known-64-bit-blas-indices=1 > >>>> > > >>> > > >>>> > > >>> > Is this what you are suggesting? > >>>> > > >>> > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay > >>>> wrote: > >>>> > > >>> > > >>>> > > >>> > > Also: > >>>> > > >>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', > >>>> > > >>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. > >>>> > > >>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts across > >>>> packages] > >>>> > > >>> > > > >>>> > > >>> > > Satish > >>>> > > >>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > >>>> > > >>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI > >>>> > > >>> > > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>>> > > >>> > > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > >>>> > > >>> > > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with > >>>> > > >>> > > > # MATLAB BLAS - hence requiring > >>>> -known-64-bit-blas-indices=1 > >>>> > > >>> > > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with > >>>> matlab - to > >>>> > > >>> have a > >>>> > > >>> > > compatible build > >>>> > > >>> > > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > >>>> > > >>> > > > > >>>> > > >>> > > > Satish > >>>> > > >>> > > > > >>>> > > >>> > > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > >>>> petsc-users > >>>> > > >>> wrote: > >>>> > > >>> > > > > >>>> > > >>> > > > > Hi Amneet, > >>>> > > >>> > > > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not > >>>> working. It is > >>>> > > >>> > > showing > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > >>>> > > >>> > > > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with > >>>> libmesh and > >>>> > > >>> this is > >>>> > > >>> > > for > >>>> > > >>> > > > > general usage not only for WEC. This I tried without > >>>> linking > >>>> > > >>> Matlab > >>>> > > >>> > > with > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring > >>>> libmesh 1.6.2 > >>>> > > >>> that > >>>> > > >>> > > PETSc > >>>> > > >>> > > > > was not found but --enable-petsc-required is specified. > >>>> > > >>> > > > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with > >>>> PETSc and > >>>> > > >>> Matlab > >>>> > > >>> > > is in > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated geometries > >>>> it is > >>>> > > >>> > > mentioned to > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > >>>> > > >>> > > > > > >>>> > > >>> > > > > For the past 10 days I am trying these various things > >>>> and ended > >>>> > > >>> up with > >>>> > > >>> > > > > errors. > >>>> > > >>> > > > > I want to solve this and proceed further to do my > >>>> research work. > >>>> > > >>> > > > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. > >>>> > > >>> > > > > > >>>> > > >>> > > > > > >>>> > > >>> > > > > Thanks and Regards > >>>> > > >>> > > > > Srinivas > >>>> > > >>> > > > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > >>>> mail2amneet at gmail.com> > >>>> > > >>> > > wrote: > >>>> > > >>> > > > > > >>>> > > >>> > > > > > Hi Srinivas, > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for the > >>>> WEC > >>>> > > >>> application. > >>>> > > >>> > > You > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with > >>>> Matlab. > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build > >>>> libMesh? > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > Thanks, > >>>> > > >>> > > > > > ?Amneet > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS > >>>> 20PHD0548 via > >>>> > > >>> > > petsc-users > >>>> > > >>> > > > > > wrote: > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >> Hi, > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all > >>>> occurrences > >>>> > > >>> of > >>>> > > >>> > > "-lut > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test" > >>>> got the > >>>> > > >>> > > following > >>>> > > >>> > > > > >> errors > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: > >>>> > > >>> > > > > >> TEST > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>> > > >>> > > > > >> not ok > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > >>>> > > >>> Error > >>>> > > >>> > > code: 124 > >>>> > > >>> > > > > >> # Running problem 5 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > >>>> > > >>> > > > > >> > >>>> -------------------------------------------------------------- > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > >>>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>> for > >>>> > > >>> trouble > >>>> > > >>> > > > > >> shooting. > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug > >>>> 01, 2020 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug > >>>> named > >>>> > > >>> > > MB108SMEC028 > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>>> > > >>> --with-debugging=1 > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 > >>>> --with-x=0 > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>>> > > >>> --with-matlab-engine=1 > >>>> > > >>> > > > > >> > >>>> > > >>> > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line > >>>> 67 in > >>>> > > >>> > > > > >> > >>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > >>>> Message > >>>> > > >>> -------send > >>>> > > >>> > > entire > >>>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > >>>> > > >>> > > > > >> # > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> -------------------------------------------------------------------------- > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > >>>> > > >>> MPI_COMM_SELF > >>>> > > >>> > > > > >> # with errorcode 126076. > >>>> > > >>> > > > > >> # > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill > >>>> all MPI > >>>> > > >>> > > processes. > >>>> > > >>> > > > > >> # You may or may not see output from other processes, > >>>> > > >>> depending on > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > >>>> > > >>> > > > > >> # > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> -------------------------------------------------------------------------- > >>>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>> # SKIP > >>>> > > >>> Command > >>>> > > >>> > > > > >> failed so no diff > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt > >>>> > > >>> > > > > >> TEST > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>> > > >>> > > > > >> not ok > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > >>>> > > >>> Error > >>>> > > >>> > > code: 124 > >>>> > > >>> > > > > >> # Running problem 5 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message > >>>> > > >>> > > > > >> > >>>> -------------------------------------------------------------- > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > >>>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>> for > >>>> > > >>> trouble > >>>> > > >>> > > > > >> shooting. > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug > >>>> 01, 2020 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt > >>>> named > >>>> > > >>> > > MB108SMEC028 by > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>>> > > >>> --COPTFLAGS=-O3 > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 > >>>> --PETSC_ARCH=linux-opt > >>>> > > >>> > > --with-debugging=0 > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 > >>>> --download-fblaslapack=1 > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>>> > > >>> --with-matlab-engine=1 > >>>> > > >>> > > > > >> > >>>> > > >>> > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line > >>>> 67 in > >>>> > > >>> > > > > >> > >>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > >>>> Message > >>>> > > >>> -------send > >>>> > > >>> > > entire > >>>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov---------- > >>>> > > >>> > > > > >> # > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> -------------------------------------------------------------------------- > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > >>>> > > >>> MPI_COMM_SELF > >>>> > > >>> > > > > >> # with errorcode 126076. > >>>> > > >>> > > > > >> # > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill > >>>> all MPI > >>>> > > >>> > > processes. > >>>> > > >>> > > > > >> # You may or may not see output from other processes, > >>>> > > >>> depending on > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > >>>> > > >>> > > > > >> # > >>>> > > >>> > > > > >> > >>>> > > >>> > > > >>>> > > >>> > >>>> -------------------------------------------------------------------------- > >>>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>> # SKIP > >>>> > > >>> Command > >>>> > > >>> > > > > >> failed so no diff. > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I > >>>> am > >>>> > > >>> sharing the > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and > >>>> petsc > >>>> > > >>> 3.17.5. > >>>> > > >>> > > Please find > >>>> > > >>> > > > > >> the attachment and do the needful. > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> Thanks and regards > >>>> > > >>> > > > > >> Srinivas > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > >>>> > > >>> balay at mcs.anl.gov> > >>>> > > >>> > > wrote: > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > >>>> > > >>> configure.log/make.log > >>>> > > >>> > > for > >>>> > > >>> > > > > >>> petsc-3.17 > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> >>>> > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> Matlab: > >>>> > > >>> > > > > >>> Includes: > >>>> -I/usr/local/MATLAB/R2020b/extern/include > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b > >>>> > > >>> > > > > >>> MatlabEngine: > >>>> > > >>> > > > > >>> Library: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng > >>>> -lmex > >>>> > > >>> -lmx > >>>> > > >>> > > -lmat -lut > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc > >>>> > > >>> > > > > >>> Language used to compile PETSc: C > >>>> > > >>> > > > > >>> <<<<< > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> >>> > >>>> > > >>> > > > > >>> Matlab: > >>>> > > >>> > > > > >>> Includes: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > >>>> > > >>> > > > > >>> Libraries: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat > >>>> > > >>> > > > > >>> Executable: > >>>> > > >>> > > > > >>> > >>>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > >>>> > > >>> > > > > >>> mex: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > >>>> > > >>> > > > > >>> matlab: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > >>>> > > >>> > > > > >>> -glnxa64 > >>>> > > >>> > > > > >>> <<< > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not > >>>> preset here. > >>>> > > >>> This > >>>> > > >>> > > might > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> You can: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> - edit > >>>> > > >>> > > > > >>> > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > >>>> > > >>> > > and > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n > >>>> -licuuc" > >>>> > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4' > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> And see if the build works now. > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> Satish > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via > >>>> > > >>> petsc-users > >>>> > > >>> > > wrote: > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >>> > I am sharing the log files while building > >>>> petsc3.13.4 with > >>>> > > >>> > > matlab and > >>>> > > >>> > > > > >>> also > >>>> > > >>> > > > > >>> > the log file while building libmesh with > >>>> petsc3.17.5 and > >>>> > > >>> matlab. > >>>> > > >>> > > > > >>> Building > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully. > >>>> But > >>>> > > >>> libmesh is > >>>> > > >>> > > not > >>>> > > >>> > > > > >>> able to > >>>> > > >>> > > > > >>> > find the petsc > >>>> > > >>> > > > > >>> > Please find the attachments. > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > >>>> > > >>> balay at mcs.anl.gov> > >>>> > > >>> > > > > >>> wrote: > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both > >>>> petsc-3.13 and > >>>> > > >>> 3.17 [or > >>>> > > >>> > > 3.19]. > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to > >>>> mailing > >>>> > > >>> list - > >>>> > > >>> > > or > >>>> > > >>> > > > > >>> send > >>>> > > >>> > > > > >>> > > them to petsc-maint] > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?] > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > Satish > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 > >>>> via > >>>> > > >>> petsc-users > >>>> > > >>> > > wrote: > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while building > >>>> > > >>> petsc-3.13.4 > >>>> > > >>> > > with > >>>> > > >>> > > > > >>> Matlab. > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the needful. > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU > >>>> SRINIVAS > >>>> > > >>> 20PHD0548 < > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building > >>>> of > >>>> > > >>> libmesh, the > >>>> > > >>> > > error > >>>> > > >>> > > > > >>> shows > >>>> > > >>> > > > > >>> > > > > petsc was not found > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish > >>>> Balay < > >>>> > > >>> > > balay at mcs.anl.gov> > >>>> > > >>> > > > > >>> > > wrote: > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says > >>>> petsc-3.17 > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> Satish > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS > >>>> 20PHD0548 via > >>>> > > >>> > > petsc-users > >>>> > > >>> > > > > >>> wrote: > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > Hello, > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for > >>>> working on > >>>> > > >>> the > >>>> > > >>> > > > > >>> simulation > >>>> > > >>> > > > > >>> > > using > >>>> > > >>> > > > > >>> > > > >> IBAMR > >>>> > > >>> > > > > >>> > > > >> > open software. While building the PETSc, > >>>> using the > >>>> > > >>> > > following > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > >>>> > > >>> > > > > >>> > > > >> > ./configure \ > >>>> > > >>> > > > > >>> > > > >> > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > >>>> > > >>> > > > > >>> > > > >> > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > >>>> > > >>> > > > > >>> > > > >> > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ > >>>> > > >>> > > > > >>> > > > >> > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > >>>> > > >>> > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > make -j4 > >>>> > > >>> > > > > >>> > > > >> > make -j4 test > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > I got the following error > >>>> > > >>> > > > > >>> > > > >> > CLINKER > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > >>>> > > >>> > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEnginePut' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineEvaluate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGet' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEnginePut' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineEvaluate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGet' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGet' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>> > > >>> > > > > >>> > > > >> > function `main': > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineCreate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineEvaluate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineEvaluate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGetArray' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGetArray' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGetArray' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGetArray' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineGetArray' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineEvaluate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineEvaluate' > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > >>>> > > >>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>> `PetscMatlabEngineDestroy' > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit > >>>> status > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > >>>> > > >>> > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > >>>> > > >>> > > > > >>> > > > >> Error 1 > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs.... > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > Thank you > >>>> > > >>> > > > > >>> > > > >> > Srinivas > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > >> > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore > >>>> Institute of > >>>> > > >>> > > Technology. > >>>> > > >>> > > > > >> The contents of this email may contain legally > >>>> protected > >>>> > > >>> > > confidential or > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of > >>>> Technology?. > >>>> > > >>> If > >>>> > > >>> > > you are > >>>> > > >>> > > > > >> not the intended recipient, you should not > >>>> disseminate, > >>>> > > >>> distribute > >>>> > > >>> > > or copy > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately > >>>> and destroy > >>>> > > >>> all > >>>> > > >>> > > copies of > >>>> > > >>> > > > > >> this message and any attachments. If you have > >>>> received this > >>>> > > >>> email > >>>> > > >>> > > in error, > >>>> > > >>> > > > > >> please promptly notify the sender by reply email and > >>>> delete > >>>> > > >>> the > >>>> > > >>> > > original > >>>> > > >>> > > > > >> email and any backup copies without reading them.* > >>>> > > >>> > > > > >> > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > >>>> > > >>> > > > > > >>>> > > >>> > > > > >>>> > > >>> > > > >>>> > > >>> > > >>>> > > >>> > > >>>> > > >>> > >>>> > > >> > >>>> > > >> > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of > >>>> Technology. > >>>> > > >> The contents of this email may contain legally protected > >>>> confidential or > >>>> > > >> privileged information of ?Vellore Institute of Technology?. If > >>>> you are > >>>> > > >> not the intended recipient, you should not disseminate, > >>>> distribute or copy > >>>> > > >> this e-mail. Please notify the sender immediately and destroy > >>>> all copies of > >>>> > > >> this message and any attachments. If you have received this > >>>> email in error, > >>>> > > >> please promptly notify the sender by reply email and delete the > >>>> original > >>>> > > >> email and any backup copies without reading them.* > >>>> > > >> > >>>> > > > > >>>> > > > > >>>> > > > -- > >>>> > > > --Amneet > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > >>>> > > > >>>> > >>> > >>> > >>> *Disclaimer:This message was sent from Vellore Institute of Technology. > >>> The contents of this email may contain legally protected confidential or > >>> privileged information of ?Vellore Institute of Technology?. If you are > >>> not the intended recipient, you should not disseminate, distribute or copy > >>> this e-mail. Please notify the sender immediately and destroy all copies of > >>> this message and any attachments. If you have received this email in error, > >>> please promptly notify the sender by reply email and delete the original > >>> email and any backup copies without reading them.* > >>> > >> > >> > >> -- > >> What most experimenters take for granted before they begin their > >> experiments is infinitely more interesting than any results to which their > >> experiments lead. > >> -- Norbert Wiener > >> > >> https://www.cse.buffalo.edu/~knepley/ > >> > >> > > > > > > *Disclaimer:This message was sent from Vellore Institute of Technology. > > The contents of this email may contain legally protected confidential or > > privileged information of ?Vellore Institute of Technology?. If you are > > not the intended recipient, you should not disseminate, distribute or copy > > this e-mail. Please notify the sender immediately and destroy all copies of > > this message and any attachments. If you have received this email in error, > > please promptly notify the sender by reply email and delete the original > > email and any backup copies without reading them.* > > > > > From david.knezevic at akselos.com Sun Sep 3 13:09:39 2023 From: david.knezevic at akselos.com (David Knezevic) Date: Sun, 3 Sep 2023 14:09:39 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: > > > https://petsc.org/release/manualpages/SNES/SNESSetForceIteration/#snessetforceiteration Great, thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.knezevic at akselos.com Sun Sep 3 13:12:19 2023 From: david.knezevic at akselos.com (David Knezevic) Date: Sun, 3 Sep 2023 14:12:19 -0400 Subject: [petsc-users] Can we force SNES solver to do at least Newton step? In-Reply-To: References: Message-ID: > > Hmm, it sounds like the convergence measure is bad. Maybe using a weighted >>> norm would be better? >> >> >> That's a good thought, I'd like to look into that idea too. Could you >> please give me some guidance on how to use a weighted norm in the >> convergence test? (Or are there any examples of doing that in the example >> suite?) >> > > I guess the idea would be the following: > > You have exponential terms in your equation. You get a relatively small > residual, but unacceptable > error. This leads me to believe that some part of the residual is > swamping other parts you care about. > This should be confirmed by plotting the residual for one of these > 0-iterate cases. To prevent this > imbalance, you would scale the residual to give more weight to the > underrepresented parts, probably > with an inverse of the exponential. This is just a more complicated > form of the diagonal scaling > commonly used to give all fields the same scale. > OK, I see what you mean, thanks. I'll investigate that idea. And I'll also try SNESSetForceIteration, as suggested by Barry, since it looks like that takes care of my initial request (to always perform at least one iteration) without needing a custom convergence test. Thanks, David On Sat, Sep 2, 2023 at 5:54?PM Matthew Knepley wrote: >> >>> On Sat, Sep 2, 2023 at 5:45?PM David Knezevic < >>> david.knezevic at akselos.com> wrote: >>> >>>> OK, thanks, I'll look into the custom convergence test. >>>> >>>> I do not understand this comment. What do you mean by "inaccurate"? >>>>> Since we do not have the true solution, we usually say "inaccurate" for >>>>> large residual, but you already said that the residual is small. Why would >>>>> you want to do another iterate? >>>> >>>> >>>> I agree with your comments, but the specific case I'm considering is >>>> very numerically sensitive since it includes creep (which unfortunately has >>>> large exponential terms in it) which is the root cause of the issues I'm >>>> facing. Based on test cases with a known reference solution we're finding >>>> that we get inaccurate results due to steps with "zero iterations". We can >>>> fix this by tightening the tolerance but then we do an excessive number of >>>> iterations in other steps. So it seems to me that ensuring that we do at >>>> least one iteration will help here, so that's what I wanted to try. >>>> >>> >>> Hmm, it sounds like the convergence measure is bad. Maybe using a >>> weighted norm would be better? >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> Thanks again for your help. >>>> >>>> Best, >>>> David >>>> >>>> On Sat, Sep 2, 2023 at 3:23?PM Matthew Knepley >>>> wrote: >>>> >>>>> On Sat, Sep 2, 2023 at 3:05?PM David Knezevic via petsc-users < >>>>> petsc-users at mcs.anl.gov> wrote: >>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm using the SNES solver for a plasticity model, and the issue I've >>>>>> run into is that in some time steps the solver terminates after "NL step 0" >>>>>> since the initial residual (based on the solution from the previous time >>>>>> step) is below the specified tolerance. >>>>>> >>>>>> I gather that "NL step 0" only checks the residual and doesn't >>>>>> actually do a Newtown update, and hence it seems that this is leading to >>>>>> inaccurate results in some cases. >>>>>> >>>>> >>>>> I do not understand this comment. What do you mean by "inaccurate"? >>>>> Since we do not have the true solution, we usually say "inaccurate" for >>>>> large residual, but you already said that the residual is small. >>>>> Why would you want to do another iterate? >>>>> >>>>> >>>>>> I can of course specify a smaller convergence tolerance to avoid this >>>>>> issue, but I've found it difficult to find a smaller tolerance that works >>>>>> well in all cases (e.g. it leads to too many iterations or >>>>>> non-convergence). So instead what I would like to do is ensure that the >>>>>> solver does at least 1 Newton iteration instead of terminating at "NL step >>>>>> 0". Is there a way to enforce this behavior, e.g. by skipping "NL step 0", >>>>>> or specifying a "minimum number of iterations"? I didn't see anything like >>>>>> this in the documentation, so I was wondering if there are any suggestions >>>>>> on how to proceed for this. >>>>>> >>>>> >>>>> The easiest way to do this is to write a custom convergence test that >>>>> looks like this >>>>> >>>>> PetscErrorCode SNESConvergedDefault(SNES snes, PetscInt it, PetscReal >>>>> xnorm, PetscReal snorm, PetscReal fnorm, SNESConvergedReason *reason, void >>>>> *dummy) >>>>> { >>>>> PetscFunctionBeginUser; >>>>> if (!it) { >>>>> *reason = SNES_CONVERGED_ITERATING; >>>>> PetscFunctionReturn(PETSC_SUCCESS); >>>>> } >>>>> PetscCall(SNESConvergedDefault(snes, it, xnorm, snorm, fnorm, >>>>> reason, dummy)); >>>>> PetscFunctionReturn(PETSC_SUCCESS); >>>>> } >>>>> >>>>> Thanks, >>>>> >>>>> Matt >>>>> >>>>> >>>>>> Thanks, >>>>>> David >>>>>> >>>>> >>>>> >>>>> -- >>>>> What most experimenters take for granted before they begin their >>>>> experiments is infinitely more interesting than any results to which their >>>>> experiments lead. >>>>> -- Norbert Wiener >>>>> >>>>> https://www.cse.buffalo.edu/~knepley/ >>>>> >>>>> >>>> >>> >>> -- >>> What most experimenters take for granted before they begin their >>> experiments is infinitely more interesting than any results to which their >>> experiments lead. >>> -- Norbert Wiener >>> >>> https://www.cse.buffalo.edu/~knepley/ >>> >>> >> > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Sun Sep 3 23:53:34 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Mon, 4 Sep 2023 10:23:34 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> Message-ID: Hi Sathish, I tried the following procedure *$make * CLINKER linux-opt/lib/libpetsc.so.3.13.4 BEGINNING TO COMPILE MATLAB INTERFACE Building with 'gcc'. /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. ========================================= Now to check if the libraries are working do: make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check *$make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/* Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires CC linux-opt/tests/ksp/ksp/tutorials/ex72.o CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine on # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep 4 10:02:32 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Petsc has generated inconsistent data # [0]PETSC ERROR: # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep 4 10:02:32 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: ------------------------------------------------------------------------ # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger # [0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run # [0]PETSC ERROR: to get more information on the crash. # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Signal received # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep 4 10:02:32 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD # with errorcode 50162059. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff CC linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o CLINKER linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 # Running problem 5 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine on # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by vit Mon Sep 4 10:02:34 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c # [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -prob_id 5 # [0]PETSC ERROR: -tao_smonitor # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF # with errorcode 126076. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff # ------------- # Summary # ------------- # FAILED ksp_ksp_tutorials-ex72_12 tao_leastsquares_tutorials_matlab-matlab_ls_test # success 0/2 tests (0.0%) # failed 2/2 tests (100.0%) # todo 0/2 tests (0.0%) # skip 0/2 tests (0.0%) # # Wall clock time for tests: 4 sec # Approximate CPU time (not incl. build time): 0.03 sec # # To rerun failed tests: # /usr/bin/make -f gmakefile test test-fail=1 # # Timing summary (actual test time / total CPU time): # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec *$cd src/tao/leastsquares/tutorials/matlab/* *$make matlab_ls_test* /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 -I/home/vit/sfw/petsc/3.13.4/include -I/home/vit/sfw/petsc/3.13.4/linux-opt/include -I/usr/local/MATLAB/R2020b/extern/include -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib -L/home/vit/sfw/linux/openmpi/4.1.4/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath -lstdc++ -ldl -o matlab_ls_test *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test -tao_smonitor -prob_id 5 -info* [0] PetscInitialize(): PETSc successfully started: number of processors = 1 [0] PetscGetHostName(): Rejecting domainname, likely is NIS MB108SMEC028.(none) [0] PetscInitialize(): Running on machine: MB108SMEC028 Running problem 5 [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 94202473157392 max tags = 2147483647 [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Error in external library [0]PETSC ERROR: Unable to start MATLAB engine on [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit Mon Sep 4 10:09:56 2023 [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c [0]PETSC ERROR: PETSc Option Table entries: [0]PETSC ERROR: -info [0]PETSC ERROR: -prob_id 5 [0]PETSC ERROR: -tao_smonitor [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF with errorcode 126076. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. Please find the attachment for configure.log and make.log files On Sun, Sep 3, 2023 at 8:00?PM Satish Balay wrote: > To use datafiles in the test suite: > > cd $HOME > git clone https://gitlab.com/petsc/datafiles > manually with make> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles > > Satish > > On Sun, 3 Sep 2023, Matthew Knepley wrote: > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > Hi Matthew, > > > > > > I am using PETSc to simulate the problems using IBAMR. I do not have > any > > > separate test files to test PETSc alone. Can you please help me how to > > > define this DATAFILESPATH? > > > > > > > That test you tried uses a certain matrix. On our machine, we point to > this > > matrix using an environment variable, DATAFILESPATH. You don't have those > > matrices, since they are just for testing here. That > > is why I suggested just using a different matrix, or running a problem > you > > care about in IBAMR. > > > > Thanks, > > > > Matt > > > > > > > Thanks and regards > > > Srinivas. > > > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > wrote: > > > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via > petsc-users < > > >> petsc-users at mcs.anl.gov> wrote: > > >> > > >>> Hi Sathish, > > >>> > > >>> Thank you so much for your efforts and the support you are giving me > to > > >>> sort this out. > > >>> > > >>> I tried to follow the same procedure which you followed to build > Petsc > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > >>> > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > >>> --with-debugging=0 --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* > > >>> Using python3 for Python > > >>> > > >>> > =============================================================================== > > >>> Configuring PETSc to compile on your system > > >>> > > >>> > > >>> > =============================================================================== > > >>> > =============================================================================== > > >>> It appears you do not have > valgrind > > >>> installed on your system. > > >>> We HIGHLY recommend you install it from www.valgrind.org > > >>> Or install > valgrind-devel or > > >>> equivalent using your package manager. > > >>> Then rerun ./configure > > >>> > > >>> > =============================================================================== > > >>> Compilers: > > >>> > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > -fPIC > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > >>> -fstack-protector -fvisibility=hidden -O3 > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>> Linkers: > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > -shared > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas > > >>> -fstack-protector -fvisibility=hidden -O3 > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > -shared > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas > > >>> -fstack-protector -fvisibility=hidden -O3 > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl > > >>> make: > > >>> Version: 4.2 > > >>> /usr/bin/make > > >>> BlasLapack: > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >

to > > >>> control the number of threads > > >>> uses 8 byte integers > > >>> MPI: > > >>> Version: 3 > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec > --oversubscribe > > >>> OMPI_VERSION: 4.1.4 > > >>> pthread: > > >>> cmake: > > >>> Version: 3.16.3 > > >>> /usr/bin/cmake > > >>> regex: > > >>> Matlab: > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > >>> /usr/local/MATLAB/R2020b > > >>> MatlabEngine: > > >>> Library: > > >>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat > -lut > > >>> -licudata -licui18n -licuuc > > >>> Language used to compile PETSc: C > > >>> PETSc: > > >>> PETSC_ARCH: linux-opt > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > > >>> Scalar type: real > > >>> Precision: double > > >>> Support for __float128 > > >>> Integer size: 4 bytes > > >>> shared libraries: enabled > > >>> Memory alignment from malloc(): 16 bytes > > >>> > > >>> > xxx=========================================================================xxx > > >>> Configure stage complete. Now build PETSc libraries with: > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all > > >>> > > >>> > xxx=========================================================================xxx > > >>> > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as > > >>> you suggested earlier. > > >>> > > >>> *$make* > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > >>> BEGINNING TO COMPILE MATLAB INTERFACE > > >>> Building with 'gcc'. > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > >>> In function ?PetscBinaryWrite?: > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>> warning: ?err? may be used uninitialized in this function > > >>> [-Wmaybe-uninitialized] > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > >>> | ^ > > >>> > > >>> MEX completed successfully. > > >>> Building with 'gcc'. > > >>> MEX completed successfully. > > >>> Building with 'gcc'. > > >>> MEX completed successfully. > > >>> Building with 'gcc'. > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > >>> In function ?PetscBinaryWrite?: > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>> warning: ?err? may be used uninitialized in this function > > >>> [-Wmaybe-uninitialized] > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > >>> | ^ > > >>> > > >>> MEX completed successfully. > > >>> ========================================= > > >>> Now to check if the libraries are working do: > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > > >>> =============================================== > > >>> > > >>> *$make test query=requires queryval=matlab* > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > > >>> # [0]PETSC ERROR: --------------------- Error Message > > >>> -------------------------------------------------------------- > > >>> # [0]PETSC ERROR: Unable to open file > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > > >>> > > >> > > >> No, the problem is that you do not have DATAFILESPATH defined, so it > > >> cannot find the matrix to test. Try running some test of yours. > > >> > > >> Thanks, > > >> > > >> Matt > > >> > > >> > > >>> # [0]PETSC ERROR: See > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > >>> shooting. > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit > Sun > > >>> Sep 3 11:51:03 2023 > > >>> # [0]PETSC ERROR: Configure options > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > > >>> # [0]PETSC ERROR: #6 main() line 113 in > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > >>> # [0]PETSC ERROR: -pc_type lu > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > > >>> # > > >>> > -------------------------------------------------------------------------- > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > >>> # with errorcode 113065. > > >>> # > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > >>> # You may or may not see output from other processes, depending on > > >>> # exactly when Open MPI kills them. > > >>> # > > >>> > -------------------------------------------------------------------------- > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > >>> CC > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > >>> CLINKER > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>> TEST > > >>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > code: 124 > > >>> # Running problem 5 > > >>> # [0]PETSC ERROR: --------------------- Error Message > > >>> -------------------------------------------------------------- > > >>> # [0]PETSC ERROR: Error in external library > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on > > >>> # [0]PETSC ERROR: See > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > >>> shooting. > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > MB108SMEC028 by > > >>> vit Sun Sep 3 11:51:05 2023 > > >>> # [0]PETSC ERROR: Configure options > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>> # [0]PETSC ERROR: #2 main() line 126 in > > >>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > >>> # [0]PETSC ERROR: -prob_id 5 > > >>> # [0]PETSC ERROR: -tao_smonitor > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > > >>> # > > >>> > -------------------------------------------------------------------------- > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > >>> # with errorcode 126076. > > >>> # > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > >>> # You may or may not see output from other processes, depending on > > >>> # exactly when Open MPI kills them. > > >>> # > > >>> > -------------------------------------------------------------------------- > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > >>> failed so no diff > > >>> > > >>> # ------------- > > >>> # Summary > > >>> # ------------- > > >>> # FAILED ksp_ksp_tutorials-ex72_12 > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test > > >>> # success 0/2 tests (0.0%) > > >>> # failed 2/2 tests (100.0%) > > >>> # todo 0/2 tests (0.0%) > > >>> # skip 0/2 tests (0.0%) > > >>> # > > >>> # Wall clock time for tests: 3 sec > > >>> # Approximate CPU time (not incl. build time): 0.05 sec > > >>> # > > >>> # To rerun failed tests: > > >>> # /usr/bin/make -f gmakefile test test-fail=1 > > >>> # > > >>> # Timing summary (actual test time / total CPU time): > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / > 0.02 sec > > >>> > > >>> *How to sort out this error?* > > >>> > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* > > >>> *$make matlab_ls_test* > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall > -Wwrite-strings > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > >>> -I/home/vit/sfw/petsc/3.13.4/include > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > > >>> -I/usr/local/MATLAB/R2020b/extern/include > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex > -lmx > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr > -lmpi_mpifh > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread > -lquadmath > > >>> -lstdc++ -ldl -o matlab_ls_test > > >>> > > >>> I think there is a problem with the Matlab-R2020b version. > > >>> I am sharing the configure.log and make.log files. Please find the > > >>> attachment and do the needful. > > >>> > > >>> > > >>> Thanks and regards > > >>> Srinivas > > >>> > > >>> > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > wrote: > > >>> > > >>>> Perhaps you can try the following to get additional info - and debug > > >>>> > > >>>> Satish > > >>>> ---------- > > >>>> > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd > > >>>> src/tao/leastsquares/tutorials/matlab/ > > >>>> balay at compute-386-07 > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > >>>> make matlab_ls_test > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > -Wall > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > >>>> -I/scratch/balay/petsc/include > -I/scratch/balay/petsc/linux-opt/include > > >>>> > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > > >>>> -L/scratch/balay/petsc/linux-opt/lib > > >>>> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > >>>> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > >>>> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng > -lmex > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort > -lmpi > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o > > >>>> matlab_ls_test > > >>>> balay at compute-386-07 > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > > >>>> -tao_smonitor -prob_id 5 -info > > >>>> [0] PetscInitialize(): PETSc successfully started: number of > processors > > >>>> = 1 > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > >>>> compute-386-07.(none) > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 > > >>>> Running problem 5 > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > > >>>> -2080374784 max tags = 268435455 > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > >>>> -glnxa64 -nodisplay -nosplash > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > > >>>> TestingInitialize > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > > >>>> TestingInitialize > > >>>> 5 > > >>>> > > >>>> > > >>>> <<<< Now verify if the above matlab command actually works for you > - on > > >>>> this machine..>>>>> > > >>>> > > >>>> balay at compute-386-07 > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > >>>> -glnxa64 -nodisplay -nosplash > > >>>> > > >>>> > > >>>> < M A T L A B (R) > > > >>>> > > >>>> Copyright 1984-2021 The MathWorks, Inc. > > >>>> > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) > > >>>> > > >>>> February 17, 2021 > > >>>> > > >>>> > > >>>> To get started, type doc. > > >>>> For product information, visit www.mathworks.com. > > >>>> > > >>>> >> > > >>>> > > >>>> > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > > >>>> > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting > thread > > >>>> to petsc-users only] > > >>>> > > > >>>> > I'm not sure what is happening here. Can you send the > corresponding > > >>>> configure.log, make.log [compressed]? > > >>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, > > >>>> with Matlab-R2021a - and that works: > > >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch > > >>>> > main > > >>>> > release > > >>>> > * release-3.13 > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load > matlab/R2021a > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab > > >>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > >>>> --with-debugging=0 --with-x=0 > > >>>> > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > >>>> > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>> > > > >>>> > Compilers: > > >>>> > > >>>> > > >>>> > > >>>> > C Compiler: > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > -Wall > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector > > >>>> -fvisibility=hidden -O3 > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>>> > C++ Compiler: > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > -fstack-protector > > >>>> -fvisibility=hidden -O3 -fPIC > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>>> > Fortran Compiler: > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC > -Wall > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>>> > Linkers: > > >>>> > Shared linker: > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > -shared -fPIC > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > >>>> -fstack-protector -fvisibility=hidden -O3 > > >>>> > Dynamic linker: > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > -shared -fPIC > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > >>>> -fstack-protector -fvisibility=hidden -O3 > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl > > >>>> > make: > > >>>> > Version: 4.2 > > >>>> > /usr/bin/make > > >>>> > BlasLapack: > > >>>> > Library: > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > > >>>> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > >>>> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > >>>> -liomp5 -lpthread > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >

> > >>>> to control the number of threads > > >>>> > uses 8 byte integers > > >>>> > MPI: > > >>>> > Version: 4 > > >>>> > Includes: > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > >>>> > Mpiexec: > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > > >>>> > MPICH_NUMVERSION: 40002300 > > >>>> > pthread: > > >>>> > Library: -lpthread > > >>>> > cmake: > > >>>> > Version: 3.16.3 > > >>>> > /usr/bin/cmake > > >>>> > regex: > > >>>> > Matlab: > > >>>> > Includes: > > >>>> > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > >>>> > MatlabEngine: > > >>>> > Library: > > >>>> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > >>>> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > >>>> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > > >>>> > sowing: > > >>>> > Version: 1.1.25 > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort > > >>>> > valgrind: > > >>>> > Language used to compile PETSc: C > > >>>> > PETSc: > > >>>> > PETSC_ARCH: linux-opt > > >>>> > PETSC_DIR: /scratch/balay/petsc > > >>>> > Scalar type: real > > >>>> > Precision: double > > >>>> > Support for __float128 > > >>>> > Integer size: 4 bytes > > >>>> > shared libraries: enabled > > >>>> > Memory alignment from malloc(): 16 bytes > > >>>> > > > >>>> > xxx=========================================================================xxx > > >>>> > Configure stage complete. Now build PETSc libraries with: > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > > >>>> > > > >>>> > xxx=========================================================================xxx > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make > > >>>> > > >>>> > > >>>> > > >>>> > > > >>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE > > >>>> > Building with 'gcc'. > > >>>> > > > >>>> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > > >>>> function ?PetscBinaryWrite?: > > >>>> > > > >>>> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>>> warning: ?err? may be used uninitialized in this function > > >>>> [-Wmaybe-uninitialized] > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>> > | ^ > > >>>> > > > >>>> > MEX completed successfully. > > >>>> > Building with 'gcc'. > > >>>> > MEX completed successfully. > > >>>> > Building with 'gcc'. > > >>>> > MEX completed successfully. > > >>>> > Building with 'gcc'. > > >>>> > > > >>>> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > > >>>> function ?PetscBinaryWrite?: > > >>>> > > > >>>> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>>> warning: ?err? may be used uninitialized in this function > > >>>> [-Wmaybe-uninitialized] > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>> > | ^ > > >>>> > > > >>>> > MEX completed successfully. > > >>>> > ========================================= > > >>>> > Now to check if the libraries are working do: > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > > >>>> > ========================================= > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test > query=requires > > >>>> queryval=matlab > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > >>>> > TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > > >>>> > # ../ex72: > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > >>>> version `GFORTRAN_9' not found (required by > > >>>> > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > >>>> > CC > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > >>>> > CLINKER > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>>> > TEST > > >>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > code: > > >>>> 1 > > >>>> > # ../matlab_ls_test: > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > >>>> version `GFORTRAN_9' not found (required by > > >>>> > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > Command > > >>>> failed so no diff > > >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test > query=requires > > >>>> queryval=matlab > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > > >>>> > TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>>> > ok ksp_ksp_tutorials-ex72_12 > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 > > >>>> > TEST > > >>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > > >>>> > > > >>>> > # ------------- > > >>>> > # Summary > > >>>> > # ------------- > > >>>> > # success 4/4 tests (100.0%) > > >>>> > # failed 0/4 tests (0.0%) > > >>>> > # todo 0/4 tests (0.0%) > > >>>> > # skip 0/4 tests (0.0%) > > >>>> > # > > >>>> > # Wall clock time for tests: 27 sec > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 > sec > > >>>> > # > > >>>> > # Timing summary (actual test time / total CPU time): > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / > 7.54 > > >>>> sec > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > > >>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to > > >>>> configure petsc > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After > > >>>> running make > > >>>> > > -j 10 test command I have got the following error message. > > >>>> > > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > >>>> code: 124 > > >>>> > > # Running problem 5 > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message > > >>>> > > -------------------------------------------------------------- > > >>>> > > # [0]PETSC ERROR: Error in external library > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > >>>> > > # [0]PETSC ERROR: See > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>> > > for trouble shooting. > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > >>>> MB108SMEC028 by > > >>>> > > vit Sat Sep 2 12:27:22 2023 > > >>>> > > # [0]PETSC ERROR: Configure options > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > >>>> --with-debugging=0 > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>> > > --with-matlab-engine=1 > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>> > > --known-64-bit-blas-indices=1 > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in > > >>>> > > > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: > > >>>> > > # [0]PETSC ERROR: -prob_id 5 > > >>>> > > # [0]PETSC ERROR: -tao_smonitor > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message > -------send > > >>>> entire > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- > > >>>> > > # > > >>>> > -------------------------------------------------------------------------- > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > >>>> > > # with errorcode 126076. > > >>>> > > # > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > >>>> processes. > > >>>> > > # You may or may not see output from other processes, depending > on > > >>>> > > # exactly when Open MPI kills them. > > >>>> > > # > > >>>> > -------------------------------------------------------------------------- > > >>>> > > > > >>>> > > I request you to help me to sort out this error. > > >>>> > > > > >>>> > > Thanks > > >>>> > > Srinivas > > >>>> > > > > >>>> > > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < > > >>>> mail2amneet at gmail.com> wrote: > > >>>> > > > > >>>> > > > I think there should be two hyphens in > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>> > > > > > >>>> > > > i.e.: > > >>>> > > > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>> > > > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via > > >>>> petsc-users < > > >>>> > > > petsc-users at mcs.anl.gov> wrote: > > >>>> > > > > > >>>> > > >> Thank you Sathish.I will try this > > >>>> > > >> > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > > >>>> wrote: > > >>>> > > >> > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work > > >>>> here]. > > >>>> > > >>> > > >>>> > > >>> i.e: > > >>>> > > >>> > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > PETSC_ARCH=linux-opt > > >>>> > > >>> --with-debugging=0 --with-x=0 \ > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>> --with-matlab-engine=1 > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>> --known-64-bit-blas-indices=1 > > >>>> > > >>> > > >>>> > > >>> Satish > > >>>> > > >>> > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > petsc-users > > >>>> wrote: > > >>>> > > >>> > > >>>> > > >>> > Hi Satish, > > >>>> > > >>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > > >>>> > > >>> > --known-64-bit-blas-indices=1 > > >>>> > > >>> > > > >>>> > > >>> > Is this what you are suggesting? > > >>>> > > >>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < > balay at mcs.anl.gov> > > >>>> wrote: > > >>>> > > >>> > > > >>>> > > >>> > > Also: > > >>>> > > >>> > > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', > > >>>> > > >>> > > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. > > >>>> > > >>> > > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts > across > > >>>> packages] > > >>>> > > >>> > > > > >>>> > > >>> > > Satish > > >>>> > > >>> > > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > >>>> > > >>> > > > > >>>> > > >>> > > > Here is the matlab test that runs in CI > > >>>> > > >>> > > > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > >>>> > > >>> > > > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > > >>>> > > >>> > > > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict > with > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring > > >>>> -known-64-bit-blas-indices=1 > > >>>> > > >>> > > > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with > > >>>> matlab - to > > >>>> > > >>> have a > > >>>> > > >>> > > compatible build > > >>>> > > >>> > > > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > > >>>> > > >>> > > > > > >>>> > > >>> > > > Satish > > >>>> > > >>> > > > > > >>>> > > >>> > > > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > > >>>> petsc-users > > >>>> > > >>> wrote: > > >>>> > > >>> > > > > > >>>> > > >>> > > > > Hi Amneet, > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not > > >>>> working. It is > > >>>> > > >>> > > showing > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with > > >>>> libmesh and > > >>>> > > >>> this is > > >>>> > > >>> > > for > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without > > >>>> linking > > >>>> > > >>> Matlab > > >>>> > > >>> > > with > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring > > >>>> libmesh 1.6.2 > > >>>> > > >>> that > > >>>> > > >>> > > PETSc > > >>>> > > >>> > > > > was not found but --enable-petsc-required is > specified. > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with > > >>>> PETSc and > > >>>> > > >>> Matlab > > >>>> > > >>> > > is in > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated > geometries > > >>>> it is > > >>>> > > >>> > > mentioned to > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > For the past 10 days I am trying these various > things > > >>>> and ended > > >>>> > > >>> up with > > >>>> > > >>> > > > > errors. > > >>>> > > >>> > > > > I want to solve this and proceed further to do my > > >>>> research work. > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > Thanks and Regards > > >>>> > > >>> > > > > Srinivas > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > > >>>> mail2amneet at gmail.com> > > >>>> > > >>> > > wrote: > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > Hi Srinivas, > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for > the > > >>>> WEC > > >>>> > > >>> application. > > >>>> > > >>> > > You > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with > > >>>> Matlab. > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build > > >>>> libMesh? > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > Thanks, > > >>>> > > >>> > > > > > ?Amneet > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS > > >>>> 20PHD0548 via > > >>>> > > >>> > > petsc-users > > >>>> > > >>> > > > > > wrote: > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > >> Hi, > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all > > >>>> occurrences > > >>>> > > >>> of > > >>>> > > >>> > > "-lut > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make > test" > > >>>> got the > > >>>> > > >>> > > following > > >>>> > > >>> > > > > >> errors > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: > > >>>> > > >>> > > > > >> TEST > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>>> > > >>> > > > > >> not ok > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > > >>>> > > >>> Error > > >>>> > > >>> > > code: 124 > > >>>> > > >>> > > > > >> # Running problem 5 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > Message > > >>>> > > >>> > > > > >> > > >>>> -------------------------------------------------------------- > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine > on > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > > >>>> > > >>> > > > > >> > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>> for > > >>>> > > >>> trouble > > >>>> > > >>> > > > > >> shooting. > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > Aug > > >>>> 01, 2020 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > linux-debug > > >>>> named > > >>>> > > >>> > > MB108SMEC028 > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>>> > > >>> > > > > >> > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > >>>> > > >>> --with-debugging=1 > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 > > >>>> --with-x=0 > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>>> > > >>> --with-matlab-engine=1 > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() > line > > >>>> 67 in > > >>>> > > >>> > > > > >> > > >>>> > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > > >>>> Message > > >>>> > > >>> -------send > > >>>> > > >>> > > entire > > >>>> > > >>> > > > > >> error message to > petsc-maint at mcs.anl.gov---------- > > >>>> > > >>> > > > > >> # > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -------------------------------------------------------------------------- > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > >>>> > > >>> MPI_COMM_SELF > > >>>> > > >>> > > > > >> # with errorcode 126076. > > >>>> > > >>> > > > > >> # > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > kill > > >>>> all MPI > > >>>> > > >>> > > processes. > > >>>> > > >>> > > > > >> # You may or may not see output from other > processes, > > >>>> > > >>> depending on > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > > >>>> > > >>> > > > > >> # > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -------------------------------------------------------------------------- > > >>>> > > >>> > > > > >> ok > tao_leastsquares_tutorials_matlab-matlab_ls_test > > >>>> # SKIP > > >>>> > > >>> Command > > >>>> > > >>> > > > > >> failed so no diff > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt > > >>>> > > >>> > > > > >> TEST > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>>> > > >>> > > > > >> not ok > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > > >>>> > > >>> Error > > >>>> > > >>> > > code: 124 > > >>>> > > >>> > > > > >> # Running problem 5 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > Message > > >>>> > > >>> > > > > >> > > >>>> -------------------------------------------------------------- > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine > on > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > > >>>> > > >>> > > > > >> > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>> for > > >>>> > > >>> trouble > > >>>> > > >>> > > > > >> shooting. > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > Aug > > >>>> 01, 2020 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > linux-opt > > >>>> named > > >>>> > > >>> > > MB108SMEC028 by > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>>> > > >>> > > > > >> > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > >>>> > > >>> --COPTFLAGS=-O3 > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 > > >>>> --PETSC_ARCH=linux-opt > > >>>> > > >>> > > --with-debugging=0 > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 > > >>>> --download-fblaslapack=1 > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>>> > > >>> --with-matlab-engine=1 > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() > line > > >>>> 67 in > > >>>> > > >>> > > > > >> > > >>>> > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > > >>>> Message > > >>>> > > >>> -------send > > >>>> > > >>> > > entire > > >>>> > > >>> > > > > >> error message to > petsc-maint at mcs.anl.gov---------- > > >>>> > > >>> > > > > >> # > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -------------------------------------------------------------------------- > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > >>>> > > >>> MPI_COMM_SELF > > >>>> > > >>> > > > > >> # with errorcode 126076. > > >>>> > > >>> > > > > >> # > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > kill > > >>>> all MPI > > >>>> > > >>> > > processes. > > >>>> > > >>> > > > > >> # You may or may not see output from other > processes, > > >>>> > > >>> depending on > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > > >>>> > > >>> > > > > >> # > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -------------------------------------------------------------------------- > > >>>> > > >>> > > > > >> ok > tao_leastsquares_tutorials_matlab-matlab_ls_test > > >>>> # SKIP > > >>>> > > >>> Command > > >>>> > > >>> > > > > >> failed so no diff. > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 > version. I > > >>>> am > > >>>> > > >>> sharing the > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and > > >>>> petsc > > >>>> > > >>> 3.17.5. > > >>>> > > >>> > > Please find > > >>>> > > >>> > > > > >> the attachment and do the needful. > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> Thanks and regards > > >>>> > > >>> > > > > >> Srinivas > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > > >>>> > > >>> balay at mcs.anl.gov> > > >>>> > > >>> > > wrote: > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > > >>>> > > >>> configure.log/make.log > > >>>> > > >>> > > for > > >>>> > > >>> > > > > >>> petsc-3.17 > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>>> > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> Matlab: > > >>>> > > >>> > > > > >>> Includes: > > >>>> -I/usr/local/MATLAB/R2020b/extern/include > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b > > >>>> > > >>> > > > > >>> MatlabEngine: > > >>>> > > >>> > > > > >>> Library: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -leng > > >>>> -lmex > > >>>> > > >>> -lmx > > >>>> > > >>> > > -lmat -lut > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C > > >>>> > > >>> > > > > >>> <<<<< > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are > seeing: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> >>> > > >>>> > > >>> > > > > >>> Matlab: > > >>>> > > >>> > > > > >>> Includes: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > >>>> > > >>> > > > > >>> Libraries: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat > > >>>> > > >>> > > > > >>> Executable: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > >>>> > > >>> > > > > >>> mex: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > >>>> > > >>> > > > > >>> matlab: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > >>>> > > >>> > > > > >>> -glnxa64 > > >>>> > > >>> > > > > >>> <<< > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not > > >>>> preset here. > > >>>> > > >>> This > > >>>> > > >>> > > might > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> You can: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> - edit > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > >>>> > > >>> > > and > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata > -licui18n > > >>>> -licuuc" > > >>>> > > >>> > > > > >>> - now run 'make all' in > '/home/vit/sfw/petsc/3.13.4' > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> And see if the build works now. > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> Satish > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 > via > > >>>> > > >>> petsc-users > > >>>> > > >>> > > wrote: > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>> > I am sharing the log files while building > > >>>> petsc3.13.4 with > > >>>> > > >>> > > matlab and > > >>>> > > >>> > > > > >>> also > > >>>> > > >>> > > > > >>> > the log file while building libmesh with > > >>>> petsc3.17.5 and > > >>>> > > >>> matlab. > > >>>> > > >>> > > > > >>> Building > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done > successfully. > > >>>> But > > >>>> > > >>> libmesh is > > >>>> > > >>> > > not > > >>>> > > >>> > > > > >>> able to > > >>>> > > >>> > > > > >>> > find the petsc > > >>>> > > >>> > > > > >>> > Please find the attachments. > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > > >>>> > > >>> balay at mcs.anl.gov> > > >>>> > > >>> > > > > >>> wrote: > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both > > >>>> petsc-3.13 and > > >>>> > > >>> 3.17 [or > > >>>> > > >>> > > 3.19]. > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs > friendly to > > >>>> mailing > > >>>> > > >>> list - > > >>>> > > >>> > > or > > >>>> > > >>> > > > > >>> send > > >>>> > > >>> > > > > >>> > > them to petsc-maint] > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or > 3.19?] > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > Satish > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS > 20PHD0548 > > >>>> via > > >>>> > > >>> petsc-users > > >>>> > > >>> > > wrote: > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while > building > > >>>> > > >>> petsc-3.13.4 > > >>>> > > >>> > > with > > >>>> > > >>> > > > > >>> Matlab. > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the > needful. > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU > > >>>> SRINIVAS > > >>>> > > >>> 20PHD0548 < > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> > wrote: > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During > building > > >>>> of > > >>>> > > >>> libmesh, the > > >>>> > > >>> > > error > > >>>> > > >>> > > > > >>> shows > > >>>> > > >>> > > > > >>> > > > > petsc was not found > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish > > >>>> Balay < > > >>>> > > >>> > > balay at mcs.anl.gov> > > >>>> > > >>> > > > > >>> > > wrote: > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says > > >>>> petsc-3.17 > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> Satish > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS > > >>>> 20PHD0548 via > > >>>> > > >>> > > petsc-users > > >>>> > > >>> > > > > >>> wrote: > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > Hello, > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for > > >>>> working on > > >>>> > > >>> the > > >>>> > > >>> > > > > >>> simulation > > >>>> > > >>> > > > > >>> > > using > > >>>> > > >>> > > > > >>> > > > >> IBAMR > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the > PETSc, > > >>>> using the > > >>>> > > >>> > > following > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error > > >>>> > > >>> > > > > >>> > > > >> > CLINKER > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEnginePut' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineEvaluate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGet' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEnginePut' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineEvaluate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGet' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGet' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > >>>> > > >>> > > > > >>> > > > >> > function `main': > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineCreate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineEvaluate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineEvaluate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGetArray' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGetArray' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGetArray' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGetArray' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineGetArray' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineEvaluate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineEvaluate' > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >>>> > > >>> > > >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > >>>> `PetscMatlabEngineDestroy' > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit > > >>>> status > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > >>>> > > >>> > > > > >>> > > > >> Error 1 > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished > jobs.... > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you > > >>>> > > >>> > > > > >>> > > > >> > Srinivas > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > >> > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore > > >>>> Institute of > > >>>> > > >>> > > Technology. > > >>>> > > >>> > > > > >> The contents of this email may contain legally > > >>>> protected > > >>>> > > >>> > > confidential or > > >>>> > > >>> > > > > >> privileged information of ?Vellore 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Name: configure.log.gz Type: application/gzip Size: 1479 bytes Desc: not available URL: From balay at mcs.anl.gov Sun Sep 3 23:49:36 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Sun, 3 Sep 2023 23:49:36 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> Message-ID: <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> You are missing one more step: > [0] PetscInitialize(): Running on machine: MB108SMEC028 > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. Satish On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > Hi Sathish, > > I tried the following procedure > > *$make * > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > > *$make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/* > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab > query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > 4 10:02:32 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Petsc has generated inconsistent data > # [0]PETSC ERROR: > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > 4 10:02:32 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: > ------------------------------------------------------------------------ > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > # [0]PETSC ERROR: or see > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS > X to find memory corruption errors > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > and run > # [0]PETSC ERROR: to get more information on the crash. > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Signal received > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > 4 10:02:32 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > # with errorcode 50162059. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > CC > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > CLINKER > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > vit Mon Sep 4 10:02:34 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > # with errorcode 126076. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed > so no diff > > # ------------- > # Summary > # ------------- > # FAILED ksp_ksp_tutorials-ex72_12 > tao_leastsquares_tutorials_matlab-matlab_ls_test > # success 0/2 tests (0.0%) > # failed 2/2 tests (100.0%) > # todo 0/2 tests (0.0%) > # skip 0/2 tests (0.0%) > # > # Wall clock time for tests: 4 sec > # Approximate CPU time (not incl. build time): 0.03 sec > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > # > # Timing summary (actual test time / total CPU time): > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec > > *$cd src/tao/leastsquares/tutorials/matlab/* > *$make matlab_ls_test* > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > -I/home/vit/sfw/petsc/3.13.4/include > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > -I/usr/local/MATLAB/R2020b/extern/include > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath > -lstdc++ -ldl -o matlab_ls_test > > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > -tao_smonitor -prob_id 5 -info* > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > MB108SMEC028.(none) > [0] PetscInitialize(): Running on machine: MB108SMEC028 > Running problem 5 > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 > 94202473157392 max tags = 2147483647 > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Error in external library > [0]PETSC ERROR: Unable to start MATLAB engine on > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit > Mon Sep 4 10:09:56 2023 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -info > [0]PETSC ERROR: -prob_id 5 > [0]PETSC ERROR: -tao_smonitor > [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > with errorcode 126076. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > > Please find the attachment for configure.log and make.log files > > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay wrote: > > > To use datafiles in the test suite: > > > > cd $HOME > > git clone https://gitlab.com/petsc/datafiles > > > manually with make> > > > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles > > > > Satish > > > > On Sun, 3 Sep 2023, Matthew Knepley wrote: > > > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > > > Hi Matthew, > > > > > > > > I am using PETSc to simulate the problems using IBAMR. I do not have > > any > > > > separate test files to test PETSc alone. Can you please help me how to > > > > define this DATAFILESPATH? > > > > > > > > > > That test you tried uses a certain matrix. On our machine, we point to > > this > > > matrix using an environment variable, DATAFILESPATH. You don't have those > > > matrices, since they are just for testing here. That > > > is why I suggested just using a different matrix, or running a problem > > you > > > care about in IBAMR. > > > > > > Thanks, > > > > > > Matt > > > > > > > > > > Thanks and regards > > > > Srinivas. > > > > > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > > wrote: > > > > > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via > > petsc-users < > > > >> petsc-users at mcs.anl.gov> wrote: > > > >> > > > >>> Hi Sathish, > > > >>> > > > >>> Thank you so much for your efforts and the support you are giving me > > to > > > >>> sort this out. > > > >>> > > > >>> I tried to follow the same procedure which you followed to build > > Petsc > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > > >>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > >>> --with-debugging=0 --with-x=0 > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* > > > >>> Using python3 for Python > > > >>> > > > >>> > > =============================================================================== > > > >>> Configuring PETSc to compile on your system > > > >>> > > > >>> > > > >>> > > =============================================================================== > > > >>> > > =============================================================================== > > > >>> It appears you do not have > > valgrind > > > >>> installed on your system. > > > >>> We HIGHLY recommend you install it from www.valgrind.org > > > >>> Or install > > valgrind-devel or > > > >>> equivalent using your package manager. > > > >>> Then rerun ./configure > > > >>> > > > >>> > > =============================================================================== > > > >>> Compilers: > > > >>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > -fPIC > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>> Linkers: > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > -shared > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > -shared > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl > > > >>> make: > > > >>> Version: 4.2 > > > >>> /usr/bin/make > > > >>> BlasLapack: > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads > >

to > > > >>> control the number of threads > > > >>> uses 8 byte integers > > > >>> MPI: > > > >>> Version: 3 > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec > > --oversubscribe > > > >>> OMPI_VERSION: 4.1.4 > > > >>> pthread: > > > >>> cmake: > > > >>> Version: 3.16.3 > > > >>> /usr/bin/cmake > > > >>> regex: > > > >>> Matlab: > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > >>> /usr/local/MATLAB/R2020b > > > >>> MatlabEngine: > > > >>> Library: > > > >>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat > > -lut > > > >>> -licudata -licui18n -licuuc > > > >>> Language used to compile PETSc: C > > > >>> PETSc: > > > >>> PETSC_ARCH: linux-opt > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > > > >>> Scalar type: real > > > >>> Precision: double > > > >>> Support for __float128 > > > >>> Integer size: 4 bytes > > > >>> shared libraries: enabled > > > >>> Memory alignment from malloc(): 16 bytes > > > >>> > > > >>> > > xxx=========================================================================xxx > > > >>> Configure stage complete. Now build PETSc libraries with: > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all > > > >>> > > > >>> > > xxx=========================================================================xxx > > > >>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as > > > >>> you suggested earlier. > > > >>> > > > >>> *$make* > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE > > > >>> Building with 'gcc'. > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > >>> In function ?PetscBinaryWrite?: > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>> warning: ?err? may be used uninitialized in this function > > > >>> [-Wmaybe-uninitialized] > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > > >>> | ^ > > > >>> > > > >>> MEX completed successfully. > > > >>> Building with 'gcc'. > > > >>> MEX completed successfully. > > > >>> Building with 'gcc'. > > > >>> MEX completed successfully. > > > >>> Building with 'gcc'. > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > >>> In function ?PetscBinaryWrite?: > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>> warning: ?err? may be used uninitialized in this function > > > >>> [-Wmaybe-uninitialized] > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > > >>> | ^ > > > >>> > > > >>> MEX completed successfully. > > > >>> ========================================= > > > >>> Now to check if the libraries are working do: > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > > > >>> =============================================== > > > >>> > > > >>> *$make test query=requires queryval=matlab* > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > > > >>> # [0]PETSC ERROR: --------------------- Error Message > > > >>> -------------------------------------------------------------- > > > >>> # [0]PETSC ERROR: Unable to open file > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > > > >>> > > > >> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it > > > >> cannot find the matrix to test. Try running some test of yours. > > > >> > > > >> Thanks, > > > >> > > > >> Matt > > > >> > > > >> > > > >>> # [0]PETSC ERROR: See > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > >>> shooting. > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit > > Sun > > > >>> Sep 3 11:51:03 2023 > > > >>> # [0]PETSC ERROR: Configure options > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > > > >>> # [0]PETSC ERROR: #6 main() line 113 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > > >>> # [0]PETSC ERROR: -pc_type lu > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > > > >>> # > > > >>> > > -------------------------------------------------------------------------- > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > >>> # with errorcode 113065. > > > >>> # > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > > >>> # You may or may not see output from other processes, depending on > > > >>> # exactly when Open MPI kills them. > > > >>> # > > > >>> > > -------------------------------------------------------------------------- > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > >>> CC > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > >>> CLINKER > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>> TEST > > > >>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > code: 124 > > > >>> # Running problem 5 > > > >>> # [0]PETSC ERROR: --------------------- Error Message > > > >>> -------------------------------------------------------------- > > > >>> # [0]PETSC ERROR: Error in external library > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>> # [0]PETSC ERROR: See > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > >>> shooting. > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > MB108SMEC028 by > > > >>> vit Sun Sep 3 11:51:05 2023 > > > >>> # [0]PETSC ERROR: Configure options > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>> # [0]PETSC ERROR: #2 main() line 126 in > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>> # [0]PETSC ERROR: -prob_id 5 > > > >>> # [0]PETSC ERROR: -tao_smonitor > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > > > >>> # > > > >>> > > -------------------------------------------------------------------------- > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > >>> # with errorcode 126076. > > > >>> # > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > > >>> # You may or may not see output from other processes, depending on > > > >>> # exactly when Open MPI kills them. > > > >>> # > > > >>> > > -------------------------------------------------------------------------- > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > > > >>> failed so no diff > > > >>> > > > >>> # ------------- > > > >>> # Summary > > > >>> # ------------- > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test > > > >>> # success 0/2 tests (0.0%) > > > >>> # failed 2/2 tests (100.0%) > > > >>> # todo 0/2 tests (0.0%) > > > >>> # skip 0/2 tests (0.0%) > > > >>> # > > > >>> # Wall clock time for tests: 3 sec > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec > > > >>> # > > > >>> # To rerun failed tests: > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 > > > >>> # > > > >>> # Timing summary (actual test time / total CPU time): > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / > > 0.02 sec > > > >>> > > > >>> *How to sort out this error?* > > > >>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* > > > >>> *$make matlab_ls_test* > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall > > -Wwrite-strings > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > > -Wno-strict-aliasing > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > > >>> -I/home/vit/sfw/petsc/3.13.4/include > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > > > >>> -I/usr/local/MATLAB/R2020b/extern/include > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex > > -lmx > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr > > -lmpi_mpifh > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread > > -lquadmath > > > >>> -lstdc++ -ldl -o matlab_ls_test > > > >>> > > > >>> I think there is a problem with the Matlab-R2020b version. > > > >>> I am sharing the configure.log and make.log files. Please find the > > > >>> attachment and do the needful. > > > >>> > > > >>> > > > >>> Thanks and regards > > > >>> Srinivas > > > >>> > > > >>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > > wrote: > > > >>> > > > >>>> Perhaps you can try the following to get additional info - and debug > > > >>>> > > > >>>> Satish > > > >>>> ---------- > > > >>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd > > > >>>> src/tao/leastsquares/tutorials/matlab/ > > > >>>> balay at compute-386-07 > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > > >>>> make matlab_ls_test > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > > -Wall > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > -fstack-protector > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > > -Wno-strict-aliasing > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > > >>>> -I/scratch/balay/petsc/include > > -I/scratch/balay/petsc/linux-opt/include > > > >>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > > > >>>> -L/scratch/balay/petsc/linux-opt/lib > > > >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > > >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng > > -lmex > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort > > -lmpi > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o > > > >>>> matlab_ls_test > > > >>>> balay at compute-386-07 > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > > > >>>> -tao_smonitor -prob_id 5 -info > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of > > processors > > > >>>> = 1 > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > > >>>> compute-386-07.(none) > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 > > > >>>> Running problem 5 > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > > > >>>> -2080374784 max tags = 268435455 > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > >>>> -glnxa64 -nodisplay -nosplash > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > > > >>>> TestingInitialize > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > > > >>>> TestingInitialize > > > >>>> 5 > > > >>>> > > > >>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you > > - on > > > >>>> this machine..>>>>> > > > >>>> > > > >>>> balay at compute-386-07 > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > >>>> -glnxa64 -nodisplay -nosplash > > > >>>> > > > >>>> > > > >>>> < M A T L A B (R) > > > > >>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. > > > >>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) > > > >>>> > > > >>>> February 17, 2021 > > > >>>> > > > >>>> > > > >>>> To get started, type doc. > > > >>>> For product information, visit www.mathworks.com. > > > >>>> > > > >>>> >> > > > >>>> > > > >>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > > > >>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting > > thread > > > >>>> to petsc-users only] > > > >>>> > > > > >>>> > I'm not sure what is happening here. Can you send the > > corresponding > > > >>>> configure.log, make.log [compressed]? > > > >>>> > > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, > > > >>>> with Matlab-R2021a - and that works: > > > >>>> > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch > > > >>>> > main > > > >>>> > release > > > >>>> > * release-3.13 > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load > > matlab/R2021a > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab > > > >>>> > > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > >>>> --with-debugging=0 --with-x=0 > > > >>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > >>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>> > > > > >>>> > Compilers: > > > >>>> > > > >>>> > > > >>>> > > > >>>> > C Compiler: > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > > -Wall > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > -fstack-protector > > > >>>> -fvisibility=hidden -O3 > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>>> > C++ Compiler: > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > -fstack-protector > > > >>>> -fvisibility=hidden -O3 -fPIC > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>>> > Fortran Compiler: > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC > > -Wall > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>>> > Linkers: > > > >>>> > Shared linker: > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > > -shared -fPIC > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > >>>> -fstack-protector -fvisibility=hidden -O3 > > > >>>> > Dynamic linker: > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > > -shared -fPIC > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > >>>> -fstack-protector -fvisibility=hidden -O3 > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl > > > >>>> > make: > > > >>>> > Version: 4.2 > > > >>>> > /usr/bin/make > > > >>>> > BlasLapack: > > > >>>> > Library: > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > > > >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > > >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > > >>>> -liomp5 -lpthread > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads > >

> > > >>>> to control the number of threads > > > >>>> > uses 8 byte integers > > > >>>> > MPI: > > > >>>> > Version: 4 > > > >>>> > Includes: > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > > >>>> > Mpiexec: > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > > > >>>> > MPICH_NUMVERSION: 40002300 > > > >>>> > pthread: > > > >>>> > Library: -lpthread > > > >>>> > cmake: > > > >>>> > Version: 3.16.3 > > > >>>> > /usr/bin/cmake > > > >>>> > regex: > > > >>>> > Matlab: > > > >>>> > Includes: > > > >>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > >>>> > MatlabEngine: > > > >>>> > Library: > > > >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > > >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > > > >>>> > sowing: > > > >>>> > Version: 1.1.25 > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort > > > >>>> > valgrind: > > > >>>> > Language used to compile PETSc: C > > > >>>> > PETSc: > > > >>>> > PETSC_ARCH: linux-opt > > > >>>> > PETSC_DIR: /scratch/balay/petsc > > > >>>> > Scalar type: real > > > >>>> > Precision: double > > > >>>> > Support for __float128 > > > >>>> > Integer size: 4 bytes > > > >>>> > shared libraries: enabled > > > >>>> > Memory alignment from malloc(): 16 bytes > > > >>>> > > > > >>>> > > xxx=========================================================================xxx > > > >>>> > Configure stage complete. Now build PETSc libraries with: > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > > > >>>> > > > > >>>> > > xxx=========================================================================xxx > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > > >>>> > > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE > > > >>>> > Building with 'gcc'. > > > >>>> > > > > >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > > > >>>> function ?PetscBinaryWrite?: > > > >>>> > > > > >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>>> warning: ?err? may be used uninitialized in this function > > > >>>> [-Wmaybe-uninitialized] > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>> > | ^ > > > >>>> > > > > >>>> > MEX completed successfully. > > > >>>> > Building with 'gcc'. > > > >>>> > MEX completed successfully. > > > >>>> > Building with 'gcc'. > > > >>>> > MEX completed successfully. > > > >>>> > Building with 'gcc'. > > > >>>> > > > > >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > > > >>>> function ?PetscBinaryWrite?: > > > >>>> > > > > >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>>> warning: ?err? may be used uninitialized in this function > > > >>>> [-Wmaybe-uninitialized] > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>> > | ^ > > > >>>> > > > > >>>> > MEX completed successfully. > > > >>>> > ========================================= > > > >>>> > Now to check if the libraries are working do: > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > > > >>>> > ========================================= > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test > > query=requires > > > >>>> queryval=matlab > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > >>>> > TEST > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > > > >>>> > # ../ex72: > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > > >>>> version `GFORTRAN_9' not found (required by > > > >>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > >>>> > CC > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > >>>> > CLINKER > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>>> > TEST > > > >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > code: > > > >>>> 1 > > > >>>> > # ../matlab_ls_test: > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > > >>>> version `GFORTRAN_9' not found (required by > > > >>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > > Command > > > >>>> failed so no diff > > > >>>> > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test > > query=requires > > > >>>> queryval=matlab > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > > > >>>> > TEST > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>>> > ok ksp_ksp_tutorials-ex72_12 > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 > > > >>>> > TEST > > > >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > > > >>>> > > > > >>>> > # ------------- > > > >>>> > # Summary > > > >>>> > # ------------- > > > >>>> > # success 4/4 tests (100.0%) > > > >>>> > # failed 0/4 tests (0.0%) > > > >>>> > # todo 0/4 tests (0.0%) > > > >>>> > # skip 0/4 tests (0.0%) > > > >>>> > # > > > >>>> > # Wall clock time for tests: 27 sec > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 > > sec > > > >>>> > # > > > >>>> > # Timing summary (actual test time / total CPU time): > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / > > 7.54 > > > >>>> sec > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > > > >>>> > > > > >>>> > > Based on the suggestions given by Sathish, I have tried to > > > >>>> configure petsc > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After > > > >>>> running make > > > >>>> > > -j 10 test command I have got the following error message. > > > >>>> > > > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > > >>>> code: 124 > > > >>>> > > # Running problem 5 > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message > > > >>>> > > -------------------------------------------------------------- > > > >>>> > > # [0]PETSC ERROR: Error in external library > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>>> > > # [0]PETSC ERROR: See > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>> > > for trouble shooting. > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > > >>>> MB108SMEC028 by > > > >>>> > > vit Sat Sep 2 12:27:22 2023 > > > >>>> > > # [0]PETSC ERROR: Configure options > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > >>>> --with-debugging=0 > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>> > > --with-matlab-engine=1 > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>> > > --known-64-bit-blas-indices=1 > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in > > > >>>> > > > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message > > -------send > > > >>>> entire > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- > > > >>>> > > # > > > >>>> > > -------------------------------------------------------------------------- > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > >>>> > > # with errorcode 126076. > > > >>>> > > # > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > > >>>> processes. > > > >>>> > > # You may or may not see output from other processes, depending > > on > > > >>>> > > # exactly when Open MPI kills them. > > > >>>> > > # > > > >>>> > > -------------------------------------------------------------------------- > > > >>>> > > > > > >>>> > > I request you to help me to sort out this error. > > > >>>> > > > > > >>>> > > Thanks > > > >>>> > > Srinivas > > > >>>> > > > > > >>>> > > > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < > > > >>>> mail2amneet at gmail.com> wrote: > > > >>>> > > > > > >>>> > > > I think there should be two hyphens in > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>> > > > > > > >>>> > > > i.e.: > > > >>>> > > > > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>> > > > > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via > > > >>>> petsc-users < > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: > > > >>>> > > > > > > >>>> > > >> Thank you Sathish.I will try this > > > >>>> > > >> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > > > >>>> wrote: > > > >>>> > > >> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work > > > >>>> here]. > > > >>>> > > >>> > > > >>>> > > >>> i.e: > > > >>>> > > >>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > > PETSC_ARCH=linux-opt > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>> --with-matlab-engine=1 > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>> --known-64-bit-blas-indices=1 > > > >>>> > > >>> > > > >>>> > > >>> Satish > > > >>>> > > >>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > > petsc-users > > > >>>> wrote: > > > >>>> > > >>> > > > >>>> > > >>> > Hi Satish, > > > >>>> > > >>> > > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > > > >>>> > > >>> > --known-64-bit-blas-indices=1 > > > >>>> > > >>> > > > > >>>> > > >>> > Is this what you are suggesting? > > > >>>> > > >>> > > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < > > balay at mcs.anl.gov> > > > >>>> wrote: > > > >>>> > > >>> > > > > >>>> > > >>> > > Also: > > > >>>> > > >>> > > > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', > > > >>>> > > >>> > > > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. > > > >>>> > > >>> > > > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts > > across > > > >>>> packages] > > > >>>> > > >>> > > > > > >>>> > > >>> > > Satish > > > >>>> > > >>> > > > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > > > >>>> > > >>> > > > > > >>>> > > >>> > > > Here is the matlab test that runs in CI > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict > > with > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring > > > >>>> -known-64-bit-blas-indices=1 > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with > > > >>>> matlab - to > > > >>>> > > >>> have a > > > >>>> > > >>> > > compatible build > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > Satish > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > > > >>>> petsc-users > > > >>>> > > >>> wrote: > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > Hi Amneet, > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not > > > >>>> working. It is > > > >>>> > > >>> > > showing > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with > > > >>>> libmesh and > > > >>>> > > >>> this is > > > >>>> > > >>> > > for > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without > > > >>>> linking > > > >>>> > > >>> Matlab > > > >>>> > > >>> > > with > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring > > > >>>> libmesh 1.6.2 > > > >>>> > > >>> that > > > >>>> > > >>> > > PETSc > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is > > specified. > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with > > > >>>> PETSc and > > > >>>> > > >>> Matlab > > > >>>> > > >>> > > is in > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated > > geometries > > > >>>> it is > > > >>>> > > >>> > > mentioned to > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > For the past 10 days I am trying these various > > things > > > >>>> and ended > > > >>>> > > >>> up with > > > >>>> > > >>> > > > > errors. > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my > > > >>>> research work. > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > Thanks and Regards > > > >>>> > > >>> > > > > Srinivas > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > > > >>>> mail2amneet at gmail.com> > > > >>>> > > >>> > > wrote: > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > Hi Srinivas, > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for > > the > > > >>>> WEC > > > >>>> > > >>> application. > > > >>>> > > >>> > > You > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with > > > >>>> Matlab. > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build > > > >>>> libMesh? > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > Thanks, > > > >>>> > > >>> > > > > > ?Amneet > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS > > > >>>> 20PHD0548 via > > > >>>> > > >>> > > petsc-users > > > >>>> > > >>> > > > > > wrote: > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > >> Hi, > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all > > > >>>> occurrences > > > >>>> > > >>> of > > > >>>> > > >>> > > "-lut > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make > > test" > > > >>>> got the > > > >>>> > > >>> > > following > > > >>>> > > >>> > > > > >> errors > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: > > > >>>> > > >>> > > > > >> TEST > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>>> > > >>> > > > > >> not ok > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > > > >>>> > > >>> Error > > > >>>> > > >>> > > code: 124 > > > >>>> > > >>> > > > > >> # Running problem 5 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > > Message > > > >>>> > > >>> > > > > >> > > > >>>> -------------------------------------------------------------- > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine > > on > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > > > >>>> > > >>> > > > > >> > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>> for > > > >>>> > > >>> trouble > > > >>>> > > >>> > > > > >> shooting. > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > > Aug > > > >>>> 01, 2020 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > > linux-debug > > > >>>> named > > > >>>> > > >>> > > MB108SMEC028 > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>>> > > >>> > > > > >> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > >>>> > > >>> --with-debugging=1 > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 > > > >>>> --with-x=0 > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>>> > > >>> --with-matlab-engine=1 > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() > > line > > > >>>> 67 in > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > > > >>>> Message > > > >>>> > > >>> -------send > > > >>>> > > >>> > > entire > > > >>>> > > >>> > > > > >> error message to > > petsc-maint at mcs.anl.gov---------- > > > >>>> > > >>> > > > > >> # > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -------------------------------------------------------------------------- > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > > >>>> > > >>> MPI_COMM_SELF > > > >>>> > > >>> > > > > >> # with errorcode 126076. > > > >>>> > > >>> > > > > >> # > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > > kill > > > >>>> all MPI > > > >>>> > > >>> > > processes. > > > >>>> > > >>> > > > > >> # You may or may not see output from other > > processes, > > > >>>> > > >>> depending on > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > > > >>>> > > >>> > > > > >> # > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -------------------------------------------------------------------------- > > > >>>> > > >>> > > > > >> ok > > tao_leastsquares_tutorials_matlab-matlab_ls_test > > > >>>> # SKIP > > > >>>> > > >>> Command > > > >>>> > > >>> > > > > >> failed so no diff > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt > > > >>>> > > >>> > > > > >> TEST > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>>> > > >>> > > > > >> not ok > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > > > >>>> > > >>> Error > > > >>>> > > >>> > > code: 124 > > > >>>> > > >>> > > > > >> # Running problem 5 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > > Message > > > >>>> > > >>> > > > > >> > > > >>>> -------------------------------------------------------------- > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine > > on > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > > > >>>> > > >>> > > > > >> > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>> for > > > >>>> > > >>> trouble > > > >>>> > > >>> > > > > >> shooting. > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > > Aug > > > >>>> 01, 2020 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > > linux-opt > > > >>>> named > > > >>>> > > >>> > > MB108SMEC028 by > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>>> > > >>> > > > > >> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > >>>> > > >>> --COPTFLAGS=-O3 > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 > > > >>>> --PETSC_ARCH=linux-opt > > > >>>> > > >>> > > --with-debugging=0 > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 > > > >>>> --download-fblaslapack=1 > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>>> > > >>> --with-matlab-engine=1 > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() > > line > > > >>>> 67 in > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > > > >>>> Message > > > >>>> > > >>> -------send > > > >>>> > > >>> > > entire > > > >>>> > > >>> > > > > >> error message to > > petsc-maint at mcs.anl.gov---------- > > > >>>> > > >>> > > > > >> # > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -------------------------------------------------------------------------- > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > > > >>>> > > >>> MPI_COMM_SELF > > > >>>> > > >>> > > > > >> # with errorcode 126076. > > > >>>> > > >>> > > > > >> # > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > > kill > > > >>>> all MPI > > > >>>> > > >>> > > processes. > > > >>>> > > >>> > > > > >> # You may or may not see output from other > > processes, > > > >>>> > > >>> depending on > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > > > >>>> > > >>> > > > > >> # > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -------------------------------------------------------------------------- > > > >>>> > > >>> > > > > >> ok > > tao_leastsquares_tutorials_matlab-matlab_ls_test > > > >>>> # SKIP > > > >>>> > > >>> Command > > > >>>> > > >>> > > > > >> failed so no diff. > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 > > version. I > > > >>>> am > > > >>>> > > >>> sharing the > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and > > > >>>> petsc > > > >>>> > > >>> 3.17.5. > > > >>>> > > >>> > > Please find > > > >>>> > > >>> > > > > >> the attachment and do the needful. > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> Thanks and regards > > > >>>> > > >>> > > > > >> Srinivas > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > > > >>>> > > >>> balay at mcs.anl.gov> > > > >>>> > > >>> > > wrote: > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > > > >>>> > > >>> configure.log/make.log > > > >>>> > > >>> > > for > > > >>>> > > >>> > > > > >>> petsc-3.17 > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> Matlab: > > > >>>> > > >>> > > > > >>> Includes: > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b > > > >>>> > > >>> > > > > >>> MatlabEngine: > > > >>>> > > >>> > > > > >>> Library: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > -leng > > > >>>> -lmex > > > >>>> > > >>> -lmx > > > >>>> > > >>> > > -lmat -lut > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C > > > >>>> > > >>> > > > > >>> <<<<< > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are > > seeing: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> Matlab: > > > >>>> > > >>> > > > > >>> Includes: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > >>>> > > >>> > > > > >>> Libraries: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat > > > >>>> > > >>> > > > > >>> Executable: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > >>>> > > >>> > > > > >>> mex: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > >>>> > > >>> > > > > >>> matlab: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > >>>> > > >>> > > > > >>> -glnxa64 > > > >>>> > > >>> > > > > >>> <<< > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not > > > >>>> preset here. > > > >>>> > > >>> This > > > >>>> > > >>> > > might > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> You can: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> - edit > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > > >>>> > > >>> > > and > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata > > -licui18n > > > >>>> -licuuc" > > > >>>> > > >>> > > > > >>> - now run 'make all' in > > '/home/vit/sfw/petsc/3.13.4' > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> And see if the build works now. > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> Satish > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 > > via > > > >>>> > > >>> petsc-users > > > >>>> > > >>> > > wrote: > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building > > > >>>> petsc3.13.4 with > > > >>>> > > >>> > > matlab and > > > >>>> > > >>> > > > > >>> also > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with > > > >>>> petsc3.17.5 and > > > >>>> > > >>> matlab. > > > >>>> > > >>> > > > > >>> Building > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done > > successfully. > > > >>>> But > > > >>>> > > >>> libmesh is > > > >>>> > > >>> > > not > > > >>>> > > >>> > > > > >>> able to > > > >>>> > > >>> > > > > >>> > find the petsc > > > >>>> > > >>> > > > > >>> > Please find the attachments. > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > > > >>>> > > >>> balay at mcs.anl.gov> > > > >>>> > > >>> > > > > >>> wrote: > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both > > > >>>> petsc-3.13 and > > > >>>> > > >>> 3.17 [or > > > >>>> > > >>> > > 3.19]. > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs > > friendly to > > > >>>> mailing > > > >>>> > > >>> list - > > > >>>> > > >>> > > or > > > >>>> > > >>> > > > > >>> send > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or > > 3.19?] > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > Satish > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS > > 20PHD0548 > > > >>>> via > > > >>>> > > >>> petsc-users > > > >>>> > > >>> > > wrote: > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while > > building > > > >>>> > > >>> petsc-3.13.4 > > > >>>> > > >>> > > with > > > >>>> > > >>> > > > > >>> Matlab. > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the > > needful. > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU > > > >>>> SRINIVAS > > > >>>> > > >>> 20PHD0548 < > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> > > wrote: > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During > > building > > > >>>> of > > > >>>> > > >>> libmesh, the > > > >>>> > > >>> > > error > > > >>>> > > >>> > > > > >>> shows > > > >>>> > > >>> > > > > >>> > > > > petsc was not found > > > >>>> > > >>> > > > > >>> > > > > > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish > > > >>>> Balay < > > > >>>> > > >>> > > balay at mcs.anl.gov> > > > >>>> > > >>> > > > > >>> > > wrote: > > > >>>> > > >>> > > > > >>> > > > > > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says > > > >>>> petsc-3.17 > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> Satish > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS > > > >>>> 20PHD0548 via > > > >>>> > > >>> > > petsc-users > > > >>>> > > >>> > > > > >>> wrote: > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for > > > >>>> working on > > > >>>> > > >>> the > > > >>>> > > >>> > > > > >>> simulation > > > >>>> > > >>> > > > > >>> > > using > > > >>>> > > >>> > > > > >>> > > > >> IBAMR > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the > > PETSc, > > > >>>> using the > > > >>>> > > >>> > > following > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEnginePut' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineEvaluate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGet' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEnginePut' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineEvaluate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGet' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGet' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > > > >>>> > > >>> > > > > >>> > > > >> > function `main': > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineCreate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineEvaluate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineEvaluate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGetArray' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGetArray' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGetArray' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGetArray' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineGetArray' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineEvaluate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineEvaluate' > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > >>>> > > >>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > >>>> `PetscMatlabEngineDestroy' > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit > > > >>>> status > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > >>>> > > >>> > > > > >>> > > > >> Error 1 > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished > > jobs.... > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > Thank you > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > >> > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore > > > >>>> Institute of > > > >>>> > > >>> > > Technology. > > > >>>> > > >>> > > > > >> The contents of this email may contain legally > > > >>>> protected > > > >>>> > > >>> > > confidential or > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of > > > >>>> Technology?. > > > >>>> > > >>> If > > > >>>> > > >>> > > you are > > > >>>> > > >>> > > > > >> not the intended recipient, you should not > > > >>>> disseminate, > > > >>>> > > >>> distribute > > > >>>> > > >>> > > or copy > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately > > > >>>> and destroy > > > >>>> > > >>> all > > > >>>> > > >>> > > copies of > > > >>>> > > >>> > > > > >> this message and any attachments. If you have > > > >>>> received this > > > >>>> > > >>> email > > > >>>> > > >>> > > in error, > > > >>>> > > >>> > > > > >> please promptly notify the sender by reply email > > and > > > >>>> delete > > > >>>> > > >>> the > > > >>>> > > >>> > > original > > > >>>> > > >>> > > > > >> email and any backup copies without reading > > them.* > > > >>>> > > >>> > > > > >> > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > > >>>> > > >>> > > > > >>>> > > >>> > > > > >>>> > > >>> > > > >>>> > > >> > > > >>>> > > >> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of > > > >>>> Technology. > > > >>>> > > >> The contents of this email may contain legally protected > > > >>>> confidential or > > > >>>> > > >> privileged information of ?Vellore Institute of > > Technology?. If > > > >>>> you are > > > >>>> > > >> not the intended recipient, you should not disseminate, > > > >>>> distribute or copy > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy > > > >>>> all copies of > > > >>>> > > >> this message and any attachments. If you have received this > > > >>>> email in error, > > > >>>> > > >> please promptly notify the sender by reply email and delete > > the > > > >>>> original > > > >>>> > > >> email and any backup copies without reading them.* > > > >>>> > > >> > > > >>>> > > > > > > >>>> > > > > > > >>>> > > > -- > > > >>>> > > > --Amneet > > > >>>> > > > > > > >>>> > > > > > > >>>> > > > > > > >>>> > > > > > > >>>> > > > > > >>>> > > > > > >>>> > > > >>> > > > >>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of > > Technology. > > > >>> The contents of this email may contain legally protected > > confidential or > > > >>> privileged information of ?Vellore Institute of Technology?. If you > > are > > > >>> not the intended recipient, you should not disseminate, distribute > > or copy > > > >>> this e-mail. Please notify the sender immediately and destroy all > > copies of > > > >>> this message and any attachments. If you have received this email in > > error, > > > >>> please promptly notify the sender by reply email and delete the > > original > > > >>> email and any backup copies without reading them.* > > > >>> > > > >> > > > >> > > > >> -- > > > >> What most experimenters take for granted before they begin their > > > >> experiments is infinitely more interesting than any results to which > > their > > > >> experiments lead. > > > >> -- Norbert Wiener > > > >> > > > >> https://www.cse.buffalo.edu/~knepley/ > > > >> > > > >> > > > > > > > > > > > > *Disclaimer:This message was sent from Vellore Institute of Technology. > > > > The contents of this email may contain legally protected confidential > > or > > > > privileged information of ?Vellore Institute of Technology?. If you > > are > > > > not the intended recipient, you should not disseminate, distribute or > > copy > > > > this e-mail. Please notify the sender immediately and destroy all > > copies of > > > > this message and any attachments. If you have received this email in > > error, > > > > please promptly notify the sender by reply email and delete the > > original > > > > email and any backup copies without reading them.* > > > > > > > > > > > > > > > > > From inturu.srinivas2020 at vitstudent.ac.in Mon Sep 4 00:32:19 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Mon, 4 Sep 2023 11:02:19 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> Message-ID: Sorry for missing that. */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* < M A T L A B (R) > Copyright 1984-2020 The MathWorks, Inc. R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) November 23, 2020 To get started, type doc. For product information, visit www.mathworks.com. Thanks and regards Srinivas On Mon, Sep 4, 2023 at 10:19?AM Satish Balay wrote: > You are missing one more step: > > > [0] PetscInitialize(): Running on machine: MB108SMEC028 > > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > No run matlab manually on "MB108SMEC028" with the command > "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" > > Does this work for you? As the message indicates this command is invoked > by "matlab_ls_test" - and that is failing. > > Satish > > > On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > > Hi Sathish, > > > > I tried the following procedure > > > > *$make * > > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > BEGINNING TO COMPILE MATLAB INTERFACE > > Building with 'gcc'. > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > | ^ > > > > MEX completed successfully. > > Building with 'gcc'. > > MEX completed successfully. > > Building with 'gcc'. > > MEX completed successfully. > > Building with 'gcc'. > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > > | ^ > > > > MEX completed successfully. > > ========================================= > > Now to check if the libraries are working do: > > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > > > > *$make test query=requires queryval=matlab > > DATAFILESPATH=/home/vit/datafiles/* > > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab > > query=requires > > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 > > # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > # [0]PETSC ERROR: Error in external library > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon > Sep > > 4 10:02:32 2023 > > # [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > # [0]PETSC ERROR: Petsc has generated inconsistent data > > # [0]PETSC ERROR: > > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon > Sep > > 4 10:02:32 2023 > > # [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > # [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > probably memory access out of range > > # [0]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > # [0]PETSC ERROR: or see > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac > OS > > X to find memory corruption errors > > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > > and run > > # [0]PETSC ERROR: to get more information on the crash. > > # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > # [0]PETSC ERROR: Signal received > > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon > Sep > > 4 10:02:32 2023 > > # [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file > > # > -------------------------------------------------------------------------- > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > # with errorcode 50162059. > > # > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > # You may or may not see output from other processes, depending on > > # exactly when Open MPI kills them. > > # > -------------------------------------------------------------------------- > > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > CC > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > CLINKER > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > TEST > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > > # Running problem 5 > > # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > # [0]PETSC ERROR: Error in external library > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > > vit Mon Sep 4 10:02:34 2023 > > # [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > # [0]PETSC ERROR: #2 main() line 126 in > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > # [0]PETSC ERROR: PETSc Option Table entries: > > # [0]PETSC ERROR: -prob_id 5 > > # [0]PETSC ERROR: -tao_smonitor > > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > > error message to petsc-maint at mcs.anl.gov---------- > > # > -------------------------------------------------------------------------- > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > # with errorcode 126076. > > # > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > # You may or may not see output from other processes, depending on > > # exactly when Open MPI kills them. > > # > -------------------------------------------------------------------------- > > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > failed > > so no diff > > > > # ------------- > > # Summary > > # ------------- > > # FAILED ksp_ksp_tutorials-ex72_12 > > tao_leastsquares_tutorials_matlab-matlab_ls_test > > # success 0/2 tests (0.0%) > > # failed 2/2 tests (100.0%) > > # todo 0/2 tests (0.0%) > > # skip 0/2 tests (0.0%) > > # > > # Wall clock time for tests: 4 sec > > # Approximate CPU time (not incl. build time): 0.03 sec > > # > > # To rerun failed tests: > > # /usr/bin/make -f gmakefile test test-fail=1 > > # > > # Timing summary (actual test time / total CPU time): > > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec > > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec > > > > *$cd src/tao/leastsquares/tutorials/matlab/* > > *$make matlab_ls_test* > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > -I/home/vit/sfw/petsc/3.13.4/include > > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > > -I/usr/local/MATLAB/R2020b/extern/include > > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread > -lquadmath > > -lstdc++ -ldl -o matlab_ls_test > > > > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > > -tao_smonitor -prob_id 5 -info* > > [0] PetscInitialize(): PETSc successfully started: number of processors > = 1 > > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > MB108SMEC028.(none) > > [0] PetscInitialize(): Running on machine: MB108SMEC028 > > Running problem 5 > > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 > > 94202473157392 max tags = 2147483647 > > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > [0]PETSC ERROR: Error in external library > > [0]PETSC ERROR: Unable to start MATLAB engine on > > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > > for trouble shooting. > > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit > > Mon Sep 4 10:09:56 2023 > > [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c > > [0]PETSC ERROR: PETSc Option Table entries: > > [0]PETSC ERROR: -info > > [0]PETSC ERROR: -prob_id 5 > > [0]PETSC ERROR: -tao_smonitor > > [0]PETSC ERROR: ----------------End of Error Message -------send entire > > error message to petsc-maint at mcs.anl.gov---------- > > > -------------------------------------------------------------------------- > > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > with errorcode 126076. > > > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > > You may or may not see output from other processes, depending on > > exactly when Open MPI kills them. > > > > Please find the attachment for configure.log and make.log files > > > > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay wrote: > > > > > To use datafiles in the test suite: > > > > > > cd $HOME > > > git clone https://gitlab.com/petsc/datafiles > > > set > > > manually with make> > > > > > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles > > > > > > Satish > > > > > > On Sun, 3 Sep 2023, Matthew Knepley wrote: > > > > > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < > > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > > > > > Hi Matthew, > > > > > > > > > > I am using PETSc to simulate the problems using IBAMR. I do not > have > > > any > > > > > separate test files to test PETSc alone. Can you please help me > how to > > > > > define this DATAFILESPATH? > > > > > > > > > > > > > That test you tried uses a certain matrix. On our machine, we point > to > > > this > > > > matrix using an environment variable, DATAFILESPATH. You don't have > those > > > > matrices, since they are just for testing here. That > > > > is why I suggested just using a different matrix, or running a > problem > > > you > > > > care about in IBAMR. > > > > > > > > Thanks, > > > > > > > > Matt > > > > > > > > > > > > > Thanks and regards > > > > > Srinivas. > > > > > > > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > > > wrote: > > > > > > > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via > > > petsc-users < > > > > >> petsc-users at mcs.anl.gov> wrote: > > > > >> > > > > >>> Hi Sathish, > > > > >>> > > > > >>> Thank you so much for your efforts and the support you are > giving me > > > to > > > > >>> sort this out. > > > > >>> > > > > >>> I tried to follow the same procedure which you followed to build > > > Petsc > > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > > > >>> > > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > > >>> --with-debugging=0 --with-x=0 > > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* > > > > >>> Using python3 for Python > > > > >>> > > > > >>> > > > > =============================================================================== > > > > >>> Configuring PETSc to compile on your system > > > > >>> > > > > >>> > > > > >>> > > > > =============================================================================== > > > > >>> > > > > =============================================================================== > > > > >>> It appears you do not > have > > > valgrind > > > > >>> installed on your system. > > > > >>> We HIGHLY recommend you install it from www.valgrind.org > > > > >>> Or install > > > valgrind-devel or > > > > >>> equivalent using your package manager. > > > > >>> Then rerun ./configure > > > > >>> > > > > >>> > > > > =============================================================================== > > > > >>> Compilers: > > > > >>> > > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > -fPIC > > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > > >>> C++ Compiler: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > > > > >>> Fortran Compiler: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > > >>> Linkers: > > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > -shared > > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > > -Wno-unknown-pragmas > > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > -shared > > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > > -Wno-unknown-pragmas > > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl > > > > >>> make: > > > > >>> Version: 4.2 > > > > >>> /usr/bin/make > > > > >>> BlasLapack: > > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads > > >

to > > > > >>> control the number of threads > > > > >>> uses 8 byte integers > > > > >>> MPI: > > > > >>> Version: 3 > > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec > > > --oversubscribe > > > > >>> OMPI_VERSION: 4.1.4 > > > > >>> pthread: > > > > >>> cmake: > > > > >>> Version: 3.16.3 > > > > >>> /usr/bin/cmake > > > > >>> regex: > > > > >>> Matlab: > > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > > >>> /usr/local/MATLAB/R2020b > > > > >>> MatlabEngine: > > > > >>> Library: > > > > >>> > > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx > -lmat > > > -lut > > > > >>> -licudata -licui18n -licuuc > > > > >>> Language used to compile PETSc: C > > > > >>> PETSc: > > > > >>> PETSC_ARCH: linux-opt > > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > > > > >>> Scalar type: real > > > > >>> Precision: double > > > > >>> Support for __float128 > > > > >>> Integer size: 4 bytes > > > > >>> shared libraries: enabled > > > > >>> Memory alignment from malloc(): 16 bytes > > > > >>> > > > > >>> > > > > xxx=========================================================================xxx > > > > >>> Configure stage complete. Now build PETSc libraries with: > > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > PETSC_ARCH=linux-opt all > > > > >>> > > > > >>> > > > > xxx=========================================================================xxx > > > > >>> > > > > >>> Then I removed all occurrences of -lut -licudata -licui18n > -licuuc as > > > > >>> you suggested earlier. > > > > >>> > > > > >>> *$make* > > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE > > > > >>> Building with 'gcc'. > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > > >>> In function ?PetscBinaryWrite?: > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > > >>> warning: ?err? may be used uninitialized in this function > > > > >>> [-Wmaybe-uninitialized] > > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > > > >>> | ^ > > > > >>> > > > > >>> MEX completed successfully. > > > > >>> Building with 'gcc'. > > > > >>> MEX completed successfully. > > > > >>> Building with 'gcc'. > > > > >>> MEX completed successfully. > > > > >>> Building with 'gcc'. > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > > >>> In function ?PetscBinaryWrite?: > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > > >>> warning: ?err? may be used uninitialized in this function > > > > >>> [-Wmaybe-uninitialized] > > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > > > >>> | ^ > > > > >>> > > > > >>> MEX completed successfully. > > > > >>> ========================================= > > > > >>> Now to check if the libraries are working do: > > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt > check > > > > >>> =============================================== > > > > >>> > > > > >>> *$make test query=requires queryval=matlab* > > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > > >>> TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > > > > >>> # [0]PETSC ERROR: --------------------- Error Message > > > > >>> -------------------------------------------------------------- > > > > >>> # [0]PETSC ERROR: Unable to open file > > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > > > > >>> > > > > >> > > > > >> No, the problem is that you do not have DATAFILESPATH defined, so > it > > > > >> cannot find the matrix to test. Try running some test of yours. > > > > >> > > > > >> Thanks, > > > > >> > > > > >> Matt > > > > >> > > > > >> > > > > >>> # [0]PETSC ERROR: See > > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > > >>> shooting. > > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by > vit > > > Sun > > > > >>> Sep 3 11:51:03 2023 > > > > >>> # [0]PETSC ERROR: Configure options > > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line > 1444 in > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > > > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > > > > >>> # [0]PETSC ERROR: #6 main() line 113 in > > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > > > >>> # [0]PETSC ERROR: -pc_type lu > > > > >>> # [0]PETSC ERROR: ----------------End of Error Message > -------send > > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > > > > >>> # > > > > >>> > > > > -------------------------------------------------------------------------- > > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > >>> # with errorcode 113065. > > > > >>> # > > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > > > >>> # You may or may not see output from other processes, depending > on > > > > >>> # exactly when Open MPI kills them. > > > > >>> # > > > > >>> > > > > -------------------------------------------------------------------------- > > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > > >>> CC > > > > >>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > > >>> CLINKER > > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > >>> TEST > > > > >>> > > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > > code: 124 > > > > >>> # Running problem 5 > > > > >>> # [0]PETSC ERROR: --------------------- Error Message > > > > >>> -------------------------------------------------------------- > > > > >>> # [0]PETSC ERROR: Error in external library > > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > >>> # [0]PETSC ERROR: See > > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > > >>> shooting. > > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > > MB108SMEC028 by > > > > >>> vit Sun Sep 3 11:51:05 2023 > > > > >>> # [0]PETSC ERROR: Configure options > > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >>> # [0]PETSC ERROR: #2 main() line 126 in > > > > >>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>> # [0]PETSC ERROR: -prob_id 5 > > > > >>> # [0]PETSC ERROR: -tao_smonitor > > > > >>> # [0]PETSC ERROR: ----------------End of Error Message > -------send > > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > > > > >>> # > > > > >>> > > > > -------------------------------------------------------------------------- > > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > > > > >>> # with errorcode 126076. > > > > >>> # > > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > > > >>> # You may or may not see output from other processes, depending > on > > > > >>> # exactly when Open MPI kills them. > > > > >>> # > > > > >>> > > > > -------------------------------------------------------------------------- > > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > Command > > > > >>> failed so no diff > > > > >>> > > > > >>> # ------------- > > > > >>> # Summary > > > > >>> # ------------- > > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 > > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > >>> # success 0/2 tests (0.0%) > > > > >>> # failed 2/2 tests (100.0%) > > > > >>> # todo 0/2 tests (0.0%) > > > > >>> # skip 0/2 tests (0.0%) > > > > >>> # > > > > >>> # Wall clock time for tests: 3 sec > > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec > > > > >>> # > > > > >>> # To rerun failed tests: > > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 > > > > >>> # > > > > >>> # Timing summary (actual test time / total CPU time): > > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / > > > 0.02 sec > > > > >>> > > > > >>> *How to sort out this error?* > > > > >>> > > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* > > > > >>> *$make matlab_ls_test* > > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall > > > -Wwrite-strings > > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > > > -Wno-strict-aliasing > > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > > > >>> -I/home/vit/sfw/petsc/3.13.4/include > > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > > > > >>> -I/usr/local/MATLAB/R2020b/extern/include > > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > > >>> > > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib > > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex > > > -lmx > > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr > > > -lmpi_mpifh > > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread > > > -lquadmath > > > > >>> -lstdc++ -ldl -o matlab_ls_test > > > > >>> > > > > >>> I think there is a problem with the Matlab-R2020b version. > > > > >>> I am sharing the configure.log and make.log files. Please find > the > > > > >>> attachment and do the needful. > > > > >>> > > > > >>> > > > > >>> Thanks and regards > > > > >>> Srinivas > > > > >>> > > > > >>> > > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > > > wrote: > > > > >>> > > > > >>>> Perhaps you can try the following to get additional info - and > debug > > > > >>>> > > > > >>>> Satish > > > > >>>> ---------- > > > > >>>> > > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd > > > > >>>> src/tao/leastsquares/tutorials/matlab/ > > > > >>>> balay at compute-386-07 > > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > > > >>>> make matlab_ls_test > > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > > > -Wall > > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > -fstack-protector > > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > > > -Wno-strict-aliasing > > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > > > > >>>> -I/scratch/balay/petsc/include > > > -I/scratch/balay/petsc/linux-opt/include > > > > >>>> > > > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > > > > >>>> -L/scratch/balay/petsc/linux-opt/lib > > > > >>>> > > > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > > >>>> > > > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > > > >>>> > > > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm > -leng > > > -lmex > > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl > -lmpifort > > > -lmpi > > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl > -o > > > > >>>> matlab_ls_test > > > > >>>> balay at compute-386-07 > > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 > ./matlab_ls_test > > > > >>>> -tao_smonitor -prob_id 5 -info > > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of > > > processors > > > > >>>> = 1 > > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > > > >>>> compute-386-07.(none) > > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 > > > > >>>> Running problem 5 > > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > > > > >>>> -2080374784 max tags = 268435455 > > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with > command > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > > >>>> -glnxa64 -nodisplay -nosplash > > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine > > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > > > > >>>> TestingInitialize > > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > > > > >>>> TestingInitialize > > > > >>>> 5 > > > > >>>> > > > > >>>> > > > > >>>> <<<< Now verify if the above matlab command actually works for > you > > > - on > > > > >>>> this machine..>>>>> > > > > >>>> > > > > >>>> balay at compute-386-07 > > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > > >>>> -glnxa64 -nodisplay -nosplash > > > > >>>> > > > > >>>> > > > > >>>> < M A T L A B (R) > > > > > >>>> > > > > >>>> Copyright 1984-2021 The MathWorks, Inc. > > > > >>>> > > > > >>>> R2021a (9.10.0.1602886) 64-bit > (glnxa64) > > > > >>>> > > > > >>>> February 17, 2021 > > > > >>>> > > > > >>>> > > > > >>>> To get started, type doc. > > > > >>>> For product information, visit www.mathworks.com. > > > > >>>> > > > > >>>> >> > > > > >>>> > > > > >>>> > > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > > > > >>>> > > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting > > > thread > > > > >>>> to petsc-users only] > > > > >>>> > > > > > >>>> > I'm not sure what is happening here. Can you send the > > > corresponding > > > > >>>> configure.log, make.log [compressed]? > > > > >>>> > > > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on > Ubuntu-20.04, > > > > >>>> with Matlab-R2021a - and that works: > > > > >>>> > > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch > > > > >>>> > main > > > > >>>> > release > > > > >>>> > * release-3.13 > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load > > > matlab/R2021a > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab > > > > >>>> > > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure > > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > > >>>> --with-debugging=0 --with-x=0 > > > > >>>> > > > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > > >>>> > > > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > > >>>> > > > > > >>>> > Compilers: > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > C Compiler: > > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > -fPIC > > > -Wall > > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > -fstack-protector > > > > >>>> -fvisibility=hidden -O3 > > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > > >>>> > C++ Compiler: > > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx > -Wall > > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > -fstack-protector > > > > >>>> -fvisibility=hidden -O3 -fPIC > > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > > >>>> > Fortran Compiler: > > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 > -fPIC > > > -Wall > > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > > >>>> > Linkers: > > > > >>>> > Shared linker: > > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > > > -shared -fPIC > > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > > >>>> -fstack-protector -fvisibility=hidden -O3 > > > > >>>> > Dynamic linker: > > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > > > -shared -fPIC > > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > > > > >>>> -fstack-protector -fvisibility=hidden -O3 > > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl > > > > >>>> > make: > > > > >>>> > Version: 4.2 > > > > >>>> > /usr/bin/make > > > > >>>> > BlasLapack: > > > > >>>> > Library: > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > > > > >>>> > > > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > > > >>>> > > > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > > > > >>>> -liomp5 -lpthread > > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or > -omp_num_threads > > >

> > > > >>>> to control the number of threads > > > > >>>> > uses 8 byte integers > > > > >>>> > MPI: > > > > >>>> > Version: 4 > > > > >>>> > Includes: > > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > > > > >>>> > Mpiexec: > > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > > > > >>>> > MPICH_NUMVERSION: 40002300 > > > > >>>> > pthread: > > > > >>>> > Library: -lpthread > > > > >>>> > cmake: > > > > >>>> > Version: 3.16.3 > > > > >>>> > /usr/bin/cmake > > > > >>>> > regex: > > > > >>>> > Matlab: > > > > >>>> > Includes: > > > > >>>> > > > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > > > > >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > > > > >>>> > MatlabEngine: > > > > >>>> > Library: > > > > >>>> > > > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > > >>>> > > > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > > > > >>>> > > > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > > > > >>>> > sowing: > > > > >>>> > Version: 1.1.25 > > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort > > > > >>>> > valgrind: > > > > >>>> > Language used to compile PETSc: C > > > > >>>> > PETSc: > > > > >>>> > PETSC_ARCH: linux-opt > > > > >>>> > PETSC_DIR: /scratch/balay/petsc > > > > >>>> > Scalar type: real > > > > >>>> > Precision: double > > > > >>>> > Support for __float128 > > > > >>>> > Integer size: 4 bytes > > > > >>>> > shared libraries: enabled > > > > >>>> > Memory alignment from malloc(): 16 bytes > > > > >>>> > > > > > >>>> > > > > xxx=========================================================================xxx > > > > >>>> > Configure stage complete. Now build PETSc libraries with: > > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt > all > > > > >>>> > > > > > >>>> > > > > xxx=========================================================================xxx > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>> > > > > > >>>> > > > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE > > > > >>>> > Building with 'gcc'. > > > > >>>> > > > > > >>>> > > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > > > > >>>> function ?PetscBinaryWrite?: > > > > >>>> > > > > > >>>> > > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > > >>>> warning: ?err? may be used uninitialized in this function > > > > >>>> [-Wmaybe-uninitialized] > > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > > socket\n"); > > > > >>>> > | ^ > > > > >>>> > > > > > >>>> > MEX completed successfully. > > > > >>>> > Building with 'gcc'. > > > > >>>> > MEX completed successfully. > > > > >>>> > Building with 'gcc'. > > > > >>>> > MEX completed successfully. > > > > >>>> > Building with 'gcc'. > > > > >>>> > > > > > >>>> > > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > > > > >>>> function ?PetscBinaryWrite?: > > > > >>>> > > > > > >>>> > > > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > > >>>> warning: ?err? may be used uninitialized in this function > > > > >>>> [-Wmaybe-uninitialized] > > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > > socket\n"); > > > > >>>> > | ^ > > > > >>>> > > > > > >>>> > MEX completed successfully. > > > > >>>> > ========================================= > > > > >>>> > Now to check if the libraries are working do: > > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > > > > >>>> > ========================================= > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test > > > query=requires > > > > >>>> queryval=matlab > > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > > >>>> > TEST > > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > > > > >>>> > # ../ex72: > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > > > >>>> version `GFORTRAN_9' not found (required by > > > > >>>> > > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > > >>>> > CC > > > > >>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > > >>>> > CLINKER > > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > >>>> > TEST > > > > >>>> > > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > Error > > > code: > > > > >>>> 1 > > > > >>>> > # ../matlab_ls_test: > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > > > > >>>> version `GFORTRAN_9' not found (required by > > > > >>>> > > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > > > Command > > > > >>>> failed so no diff > > > > >>>> > > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test > > > query=requires > > > > >>>> queryval=matlab > > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > > > > >>>> > TEST > > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > > >>>> > ok ksp_ksp_tutorials-ex72_12 > > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 > > > > >>>> > TEST > > > > >>>> > > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > >>>> > > > > > >>>> > # ------------- > > > > >>>> > # Summary > > > > >>>> > # ------------- > > > > >>>> > # success 4/4 tests (100.0%) > > > > >>>> > # failed 0/4 tests (0.0%) > > > > >>>> > # todo 0/4 tests (0.0%) > > > > >>>> > # skip 0/4 tests (0.0%) > > > > >>>> > # > > > > >>>> > # Wall clock time for tests: 27 sec > > > > >>>> > # Approximate CPU time (not incl. build time): > 15.190000000000001 > > > sec > > > > >>>> > # > > > > >>>> > # Timing summary (actual test time / total CPU time): > > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 > sec / > > > 7.54 > > > > >>>> sec > > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > > > > >>>> > > > > > >>>> > > > > > >>>> > > > > > >>>> > > > > > >>>> > > > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > > > > >>>> > > > > > >>>> > > Based on the suggestions given by Sathish, I have tried to > > > > >>>> configure petsc > > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After > > > > >>>> running make > > > > >>>> > > -j 10 test command I have got the following error message. > > > > >>>> > > > > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > Error > > > > >>>> code: 124 > > > > >>>> > > # Running problem 5 > > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message > > > > >>>> > > > -------------------------------------------------------------- > > > > >>>> > > # [0]PETSC ERROR: Error in external library > > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on > > > > >>>> > > # [0]PETSC ERROR: See > > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html > > > > >>>> > > for trouble shooting. > > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > > > >>>> MB108SMEC028 by > > > > >>>> > > vit Sat Sep 2 12:27:22 2023 > > > > >>>> > > # [0]PETSC ERROR: Configure options > > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > > > >>>> --with-debugging=0 > > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > > >>>> > > --with-matlab-engine=1 > > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>>> > > --known-64-bit-blas-indices=1 > > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > > >>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in > > > > >>>> > > > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 > > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor > > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message > > > -------send > > > > >>>> entire > > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- > > > > >>>> > > # > > > > >>>> > > > > -------------------------------------------------------------------------- > > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator > MPI_COMM_SELF > > > > >>>> > > # with errorcode 126076. > > > > >>>> > > # > > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > > > >>>> processes. > > > > >>>> > > # You may or may not see output from other processes, > depending > > > on > > > > >>>> > > # exactly when Open MPI kills them. > > > > >>>> > > # > > > > >>>> > > > > -------------------------------------------------------------------------- > > > > >>>> > > > > > > >>>> > > I request you to help me to sort out this error. > > > > >>>> > > > > > > >>>> > > Thanks > > > > >>>> > > Srinivas > > > > >>>> > > > > > > >>>> > > > > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < > > > > >>>> mail2amneet at gmail.com> wrote: > > > > >>>> > > > > > > >>>> > > > I think there should be two hyphens in > > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>>> > > > > > > > >>>> > > > i.e.: > > > > >>>> > > > > > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>>> > > > > > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 > via > > > > >>>> petsc-users < > > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: > > > > >>>> > > > > > > > >>>> > > >> Thank you Sathish.I will try this > > > > >>>> > > >> > > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < > balay at mcs.anl.gov> > > > > >>>> wrote: > > > > >>>> > > >> > > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will > work > > > > >>>> here]. > > > > >>>> > > >>> > > > > >>>> > > >>> i.e: > > > > >>>> > > >>> > > > > >>>> > > >>> ./configure > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > > > PETSC_ARCH=linux-opt > > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ > > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b > > > > >>>> --with-matlab-engine=1 > > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > > >>>> --known-64-bit-blas-indices=1 > > > > >>>> > > >>> > > > > >>>> > > >>> Satish > > > > >>>> > > >>> > > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > > > petsc-users > > > > >>>> wrote: > > > > >>>> > > >>> > > > > >>>> > > >>> > Hi Satish, > > > > >>>> > > >>> > > > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > > > > >>>> > > >>> > --known-64-bit-blas-indices=1 > > > > >>>> > > >>> > > > > > >>>> > > >>> > Is this what you are suggesting? > > > > >>>> > > >>> > > > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < > > > balay at mcs.anl.gov> > > > > >>>> wrote: > > > > >>>> > > >>> > > > > > >>>> > > >>> > > Also: > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > Note: most externalpackages might not work in this > mode. > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts > > > across > > > > >>>> packages] > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > Satish > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users > wrote: > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > Here is the matlab test that runs in CI > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] > conflict > > > with > > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring > > > > >>>> -known-64-bit-blas-indices=1 > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with > > > > >>>> matlab - to > > > > >>>> > > >>> have a > > > > >>>> > > >>> > > compatible build > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > Satish > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > > > > >>>> petsc-users > > > > >>>> > > >>> wrote: > > > > >>>> > > >>> > > > > > > > >>>> > > >>> > > > > Hi Amneet, > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is > not > > > > >>>> working. It is > > > > >>>> > > >>> > > showing > > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with > > > > >>>> libmesh and > > > > >>>> > > >>> this is > > > > >>>> > > >>> > > for > > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried > without > > > > >>>> linking > > > > >>>> > > >>> Matlab > > > > >>>> > > >>> > > with > > > > >>>> > > >>> > > > > PETSc. Here also I got the error while > configuring > > > > >>>> libmesh 1.6.2 > > > > >>>> > > >>> that > > > > >>>> > > >>> > > PETSc > > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is > > > specified. > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh > with > > > > >>>> PETSc and > > > > >>>> > > >>> Matlab > > > > >>>> > > >>> > > is in > > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated > > > geometries > > > > >>>> it is > > > > >>>> > > >>> > > mentioned to > > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > For the past 10 days I am trying these various > > > things > > > > >>>> and ended > > > > >>>> > > >>> up with > > > > >>>> > > >>> > > > > errors. > > > > >>>> > > >>> > > > > I want to solve this and proceed further to do > my > > > > >>>> research work. > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > Please help me to solve this as soon as > possible. > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > Thanks and Regards > > > > >>>> > > >>> > > > > Srinivas > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > > > > >>>> mail2amneet at gmail.com> > > > > >>>> > > >>> > > wrote: > > > > >>>> > > >>> > > > > > > > > >>>> > > >>> > > > > > Hi Srinivas, > > > > >>>> > > >>> > > > > > > > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh > for > > > the > > > > >>>> WEC > > > > >>>> > > >>> application. > > > > >>>> > > >>> > > You > > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds > with > > > > >>>> Matlab. > > > > >>>> > > >>> > > > > > > > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to > build > > > > >>>> libMesh? > > > > >>>> > > >>> > > > > > > > > > >>>> > > >>> > > > > > Thanks, > > > > >>>> > > >>> > > > > > ?Amneet > > > > >>>> > > >>> > > > > > > > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU > SRINIVAS > > > > >>>> 20PHD0548 via > > > > >>>> > > >>> > > petsc-users > > > > >>>> > > >>> > > > > > wrote: > > > > >>>> > > >>> > > > > > > > > > >>>> > > >>> > > > > >> Hi, > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by > removing all > > > > >>>> occurrences > > > > >>>> > > >>> of > > > > >>>> > > >>> > > "-lut > > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran > "make > > > test" > > > > >>>> got the > > > > >>>> > > >>> > > following > > > > >>>> > > >>> > > > > >> errors > > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: > > > > >>>> > > >>> > > > > >> TEST > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>>> > > >>> > > > > >> not ok > > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > > > > >>>> > > >>> Error > > > > >>>> > > >>> > > code: 124 > > > > >>>> > > >>> > > > > >> # Running problem 5 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > > > Message > > > > >>>> > > >>> > > > > >> > > > > >>>> -------------------------------------------------------------- > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB > engine > > > on > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > > > > >>>> > > >>> > > > > >> > > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > > >>>> for > > > > >>>> > > >>> trouble > > > > >>>> > > >>> > > > > >> shooting. > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version > 3.13.4, > > > Aug > > > > >>>> 01, 2020 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > > > linux-debug > > > > >>>> named > > > > >>>> > > >>> > > MB108SMEC028 > > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > > >>>> > > >>> > > > > >> > --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > >>>> > > >>> > > > > >> > > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >>>> > > >>> > > > > >> > --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > > >>>> > > >>> --with-debugging=1 > > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 > > > > >>>> --with-x=0 > > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>>> > > >>> --with-matlab-engine=1 > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >>>> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 > PetscMatlabEngineCreate() > > > line > > > > >>>> 67 in > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of > Error > > > > >>>> Message > > > > >>>> > > >>> -------send > > > > >>>> > > >>> > > entire > > > > >>>> > > >>> > > > > >> error message to > > > petsc-maint at mcs.anl.gov---------- > > > > >>>> > > >>> > > > > >> # > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -------------------------------------------------------------------------- > > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in > communicator > > > > >>>> > > >>> MPI_COMM_SELF > > > > >>>> > > >>> > > > > >> # with errorcode 126076. > > > > >>>> > > >>> > > > > >> # > > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > > > kill > > > > >>>> all MPI > > > > >>>> > > >>> > > processes. > > > > >>>> > > >>> > > > > >> # You may or may not see output from other > > > processes, > > > > >>>> > > >>> depending on > > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > > > > >>>> > > >>> > > > > >> # > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -------------------------------------------------------------------------- > > > > >>>> > > >>> > > > > >> ok > > > tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > >>>> # SKIP > > > > >>>> > > >>> Command > > > > >>>> > > >>> > > > > >> failed so no diff > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt > > > > >>>> > > >>> > > > > >> TEST > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > > >>>> > > >>> > > > > >> not ok > > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > > > > >>>> > > >>> Error > > > > >>>> > > >>> > > code: 124 > > > > >>>> > > >>> > > > > >> # Running problem 5 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > > > Message > > > > >>>> > > >>> > > > > >> > > > > >>>> -------------------------------------------------------------- > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB > engine > > > on > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > > > > >>>> > > >>> > > > > >> > > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > > >>>> for > > > > >>>> > > >>> trouble > > > > >>>> > > >>> > > > > >> shooting. > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version > 3.13.4, > > > Aug > > > > >>>> 01, 2020 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > > > linux-opt > > > > >>>> named > > > > >>>> > > >>> > > MB108SMEC028 by > > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > > > > >>>> > > >>> > > > > >> > --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > > >>>> > > >>> > > > > >> > > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > > >>>> > > >>> > > > > >> > --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > > >>>> > > >>> --COPTFLAGS=-O3 > > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 > > > > >>>> --PETSC_ARCH=linux-opt > > > > >>>> > > >>> > > --with-debugging=0 > > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 > > > > >>>> --download-fblaslapack=1 > > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>>> > > >>> --with-matlab-engine=1 > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >>>> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 > PetscMatlabEngineCreate() > > > line > > > > >>>> 67 in > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of > Error > > > > >>>> Message > > > > >>>> > > >>> -------send > > > > >>>> > > >>> > > entire > > > > >>>> > > >>> > > > > >> error message to > > > petsc-maint at mcs.anl.gov---------- > > > > >>>> > > >>> > > > > >> # > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -------------------------------------------------------------------------- > > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in > communicator > > > > >>>> > > >>> MPI_COMM_SELF > > > > >>>> > > >>> > > > > >> # with errorcode 126076. > > > > >>>> > > >>> > > > > >> # > > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > > > kill > > > > >>>> all MPI > > > > >>>> > > >>> > > processes. > > > > >>>> > > >>> > > > > >> # You may or may not see output from other > > > processes, > > > > >>>> > > >>> depending on > > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > > > > >>>> > > >>> > > > > >> # > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -------------------------------------------------------------------------- > > > > >>>> > > >>> > > > > >> ok > > > tao_leastsquares_tutorials_matlab-matlab_ls_test > > > > >>>> # SKIP > > > > >>>> > > >>> Command > > > > >>>> > > >>> > > > > >> failed so no diff. > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 > > > version. I > > > > >>>> am > > > > >>>> > > >>> sharing the > > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc > 3.13.4 and > > > > >>>> petsc > > > > >>>> > > >>> 3.17.5. > > > > >>>> > > >>> > > Please find > > > > >>>> > > >>> > > > > >> the attachment and do the needful. > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> Thanks and regards > > > > >>>> > > >>> > > > > >> Srinivas > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish > Balay < > > > > >>>> > > >>> balay at mcs.anl.gov> > > > > >>>> > > >>> > > wrote: > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > > > > >>>> > > >>> configure.log/make.log > > > > >>>> > > >>> > > for > > > > >>>> > > >>> > > > > >>> petsc-3.17 > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> >>>> > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> Matlab: > > > > >>>> > > >>> > > > > >>> Includes: > > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include > > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b > > > > >>>> > > >>> > > > > >>> MatlabEngine: > > > > >>>> > > >>> > > > > >>> Library: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > > >>>> > > >>> > > > > >>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > -leng > > > > >>>> -lmex > > > > >>>> > > >>> -lmx > > > > >>>> > > >>> > > -lmat -lut > > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc > > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C > > > > >>>> > > >>> > > > > >>> <<<<< > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are > > > seeing: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> >>> > > > > >>>> > > >>> > > > > >>> Matlab: > > > > >>>> > > >>> > > > > >>> Includes: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > > > > >>>> > > >>> > > > > >>> Libraries: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat > > > > >>>> > > >>> > > > > >>> Executable: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > > > > >>>> > > >>> > > > > >>> mex: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > > > > >>>> > > >>> > > > > >>> matlab: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > > > > >>>> > > >>> > > > > >>> -glnxa64 > > > > >>>> > > >>> > > > > >>> <<< > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are > not > > > > >>>> preset here. > > > > >>>> > > >>> This > > > > >>>> > > >>> > > might > > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> You can: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> - edit > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>>> > /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > > > > >>>> > > >>> > > and > > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata > > > -licui18n > > > > >>>> -licuuc" > > > > >>>> > > >>> > > > > >>> - now run 'make all' in > > > '/home/vit/sfw/petsc/3.13.4' > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> And see if the build works now. > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> Satish > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS > 20PHD0548 > > > via > > > > >>>> > > >>> petsc-users > > > > >>>> > > >>> > > wrote: > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building > > > > >>>> petsc3.13.4 with > > > > >>>> > > >>> > > matlab and > > > > >>>> > > >>> > > > > >>> also > > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with > > > > >>>> petsc3.17.5 and > > > > >>>> > > >>> matlab. > > > > >>>> > > >>> > > > > >>> Building > > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done > > > successfully. > > > > >>>> But > > > > >>>> > > >>> libmesh is > > > > >>>> > > >>> > > not > > > > >>>> > > >>> > > > > >>> able to > > > > >>>> > > >>> > > > > >>> > find the petsc > > > > >>>> > > >>> > > > > >>> > Please find the attachments. > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish > Balay < > > > > >>>> > > >>> balay at mcs.anl.gov> > > > > >>>> > > >>> > > > > >>> wrote: > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both > > > > >>>> petsc-3.13 and > > > > >>>> > > >>> 3.17 [or > > > > >>>> > > >>> > > 3.19]. > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs > > > friendly to > > > > >>>> mailing > > > > >>>> > > >>> list - > > > > >>>> > > >>> > > or > > > > >>>> > > >>> > > > > >>> send > > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or > > > 3.19?] > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > Satish > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS > > > 20PHD0548 > > > > >>>> via > > > > >>>> > > >>> petsc-users > > > > >>>> > > >>> > > wrote: > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while > > > building > > > > >>>> > > >>> petsc-3.13.4 > > > > >>>> > > >>> > > with > > > > >>>> > > >>> > > > > >>> Matlab. > > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the > > > needful. > > > > >>>> > > >>> > > > > >>> > > > > > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM > INTURU > > > > >>>> SRINIVAS > > > > >>>> > > >>> 20PHD0548 < > > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> > > > wrote: > > > > >>>> > > >>> > > > > >>> > > > > > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During > > > building > > > > >>>> of > > > > >>>> > > >>> libmesh, the > > > > >>>> > > >>> > > error > > > > >>>> > > >>> > > > > >>> shows > > > > >>>> > > >>> > > > > >>> > > > > petsc was not found > > > > >>>> > > >>> > > > > >>> > > > > > > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM > Satish > > > > >>>> Balay < > > > > >>>> > > >>> > > balay at mcs.anl.gov> > > > > >>>> > > >>> > > > > >>> > > wrote: > > > > >>>> > > >>> > > > > >>> > > > > > > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says > > > > >>>> petsc-3.17 > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> Satish > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU > SRINIVAS > > > > >>>> 20PHD0548 via > > > > >>>> > > >>> > > petsc-users > > > > >>>> > > >>> > > > > >>> wrote: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > Hello, > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with > MATLAB for > > > > >>>> working on > > > > >>>> > > >>> the > > > > >>>> > > >>> > > > > >>> simulation > > > > >>>> > > >>> > > > > >>> > > using > > > > >>>> > > >>> > > > > >>> > > > >> IBAMR > > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the > > > PETSc, > > > > >>>> using the > > > > >>>> > > >>> > > following > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>>> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 > > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error > > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEnginePut' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineEvaluate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGet' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEnginePut' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineEvaluate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGet' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGet' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: > in > > > > >>>> > > >>> > > > > >>> > > > >> > function `main': > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineCreate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineEvaluate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineEvaluate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGetArray' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGetArray' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGetArray' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGetArray' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineGetArray' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineEvaluate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineEvaluate' > > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > > > >>>> > > >>> > > > > >>>> > > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > > > > >>>> `PetscMatlabEngineDestroy' > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 > exit > > > > >>>> status > > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >>>> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > > > > >>>> > > >>> > > > > >>> > > > >> Error 1 > > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished > > > jobs.... > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this > issue > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > Thank you > > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > >> > > > > >>>> > > >>> > > > > >>> > > > > > > > >>>> > > >>> > > > > >>> > > > > > > > >>>> > > >>> > > > > >>> > > > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > > >>>> > > >>> > > > > >>> > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> > > > > >>>> > > >>> > > > > >> *Disclaimer:This message 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If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From Pierre.Jolivet at lip6.fr Mon Sep 4 14:30:55 2023 From: Pierre.Jolivet at lip6.fr (Pierre Jolivet) Date: Mon, 4 Sep 2023 21:30:55 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: References: <68909B9F-A693-46FD-97B0-23AA5531E814@lip6.fr> <009EB5B4-E65F-4486-8045-6CA5E20DBD94@lip6.fr> Message-ID: <98308F14-CC1C-4B6B-8082-559D6867E32E@lip6.fr> The branch should now be good to go (https://gitlab.com/petsc/petsc/-/merge_requests/6841). Sorry, I made a mistake before, hence the error on PetscObjectQuery(). I?m not sure the code will be covered by the pipeline, but I have tested this on a Raviart?Thomas discretization with PCFIELDSPLIT. You?ll see in the attached logs that: 1) the numerics match 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} block from the global (symmetric) A and we get the A_{10} block cheaply by just using MatCreateHermitianTranspose(), instead of calling another time MatCreateSubMatrix() Please let me know if you have some time to test the branch and whether it fails or succeeds on your test cases. Also, I do not agree with what Hong said. Sometimes, the assembly of a coefficient can be more expensive than the communication of the said coefficient. So they are instances where SBAIJ would be more efficient than AIJ even if it would require more communication, it is not a black and white picture. Thanks, Pierre ?? > On 28 Aug 2023, at 12:12 PM, Pierre Jolivet wrote: > > >> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore wrote: >> >> I've tried the new files, and with them, PCFIELDSPLIT now gets set up without crashes (but the setup is significantly slower than for MATAIJ) > > I?ll be back from Japan at the end of this week, my schedule is too packed to get anything done in the meantime. > But I?ll let you know when things are working properly (last I checked, I think it was working, but I may have forgotten about a corner case or two). > But yes, though one would except things to be faster and less memory intensive with SBAIJ, it?s unfortunately not always the case. > > Thanks, > Pierre > >> Unfortunately I still get errors later in the process: >> >> [0]PETSC ERROR: Null argument, when expecting valid pointer >> [0]PETSC ERROR: Null Pointer: Parameter # 1 >> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d GIT Date: 2023-08-22 20:32:33 -0400 >> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 --with-cuda --with-cusp --download-scalapack --download-hdf5 --download-zlib --download-mumps --download-parmetis --download-metis --download-ptscotch --download-hypre --download-spai >> [0]PETSC ERROR: #1 PetscObjectQuery() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 >> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 >> [0]PETSC ERROR: #3 MatCreateSubMatrix() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 >> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 >> [0]PETSC ERROR: #5 PCSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 >> [0]PETSC ERROR: #6 KSPSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 >> >> The code I'm running here works without any problems for MATAIJ. To run it with MATSBAIJ I've simply used the command-line option >> -dm_mat_type sbaij >> >> >> Kind regards, >> Carl-Johan >> >> >> On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users > wrote: >>> >>> >>>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore > wrote: >>>> >>>> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue.? >>>> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices from these blocks, or is there >>>> somewhere else in the code that things will go wrong? >>> >>> Ah, no, you are right, in that case it should work. >>> >>>> For the MATNEST I was thinking to get some savings from the block-symmetry at least >>>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for them would just be a >>>> (pretty big) bonus. >>>> >>>> ?I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling >>>> right now so everything gets done more slowly, sorry).? >>>> Sound great, Thanks again! >>> >>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >>> I need to add a new code path in MatCreateRedundantMatrix() to make sure the resulting Mat is indeed SBAIJ, but that is orthogonal to the PCFIELDSPLIT issue. >>> The branch should be usable in its current state. >>> >>> Thanks, >>> Pierre >>> >>>> >>>> From: Pierre Jolivet > >>>> Sent: Saturday, August 26, 2023 4:36 PM >>>> To: Carl-Johan Thore > >>>> Cc: Carl-Johan Thore >; petsc-users at mcs.anl.gov >>>> Subject: Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >>>> >>>> >>>> >>>> >>>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore > wrote: >>>> >>>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get the A01 and A10 blocks in PCFIELDSPLIT. >>>> I have a branch that fixes this, but I haven?t rebased in a while (and I?m AFK right now), would you want me to rebase and give it a go, or must you stick to a release tarball?" >>>> >>>> Ok, would be great if you could look at this! I don't need to stick to any particular branch. >>>> >>>> Do you think MATNEST could be an alternative here? >>>> >>>> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue. >>>> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was crashing but I think it was thoroughly fixed in https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >>>> It is ugly code on top of ugly code, so I didn?t try to get it integrated and just used the branch locally, and then moved to some other stuff. >>>> I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling right now so everything gets done more slowly, sorry). >>>> >>>> Thanks, >>>> Pierre >>>> >>>> >>>> My matrix is >>>> [A00 A01; >>>> A01^t A11] >>>> so perhaps with MATNEST I can make use of the block-symmetry at least, and then use MATSBAIJ for >>>> A00 and A11 if it's possible to combine matrix types which the manual seems to imply. >>>> >>>> Kind regards >>>> Carl-Johan >>>> >>>> >>>> >>>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore > wrote: >>>> ? >>>> Hi, >>>> >>>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >>>> According to the manual "[t]he fieldsplit preconditioner cannot >>>> currently be used with the MATBAIJ or MATSBAIJ data formats if the >>>> blocksize is larger than 1". Since my blocksize is exactly 1 it would seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For symmetric format, iscol must equal isrow" >>>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >>>> fieldsplit.c at >>>> >>>> /* extract the A01 and A10 matrices */ ilink = jac->head; >>>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >>>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >>>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >>>> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >>>> MAT_INITIAL_MATRIX, &jac->B)); } >>>> >>>> This, since my A01 and A10 are not square, seems to explain why iscol is not equal to isrow. >>>> From this I gather that it is in general NOT possible to use >>>> PCFIELDSPLIT with MATSBAIJ even with block size 1? >>>> >>>> Kind regards, >>>> Carl-Johan >>> > -------------- next part -------------- An HTML attachment was scrubbed... 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URL: From inturu.srinivas2020 at vitstudent.ac.in Tue Sep 5 02:39:04 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Tue, 5 Sep 2023 13:09:04 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> Message-ID: Hi Amneeth, I think the errors are different with petsc 3.17.5 *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ The version of PETSc you are using is out-of-date, we recommend updating to the new release Available Version: 3.19.5 Installed Version: 3.17.5 https://petsc.org/release/download/ +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ============================================================================================= Configuring PETSc to compile on your system ============================================================================================= Compilers: C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 Linkers: Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 Libraries linked against: -lquadmath -lstdc++ -ldl BlasLapack: Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads uses 8 byte integers MPI: Version: 3 mpiexec: /usr/bin/mpiexec Implementation: openmpi OMPI_VERSION: 4.0.3 pthread: cmake: Version: 3.16.3 /usr/bin/cmake regex: Matlab: Includes: -I/usr/local/MATLAB/R2020b/extern/include /usr/local/MATLAB/R2020b MatlabEngine: Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c Language used to compile PETSc: C PETSc: PETSC_ARCH: linux-opt PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 Prefix: Scalar type: real Precision: double Support for __float128 Integer size: 4 bytes Single library: yes Shared libraries: yes Memory alignment from malloc(): 16 bytes Using GNU make: /usr/bin/make xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with: make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all xxx=========================================================================xxx *$make* FC linux-opt/obj/tao/f90-mod/petsctaomod.o CLINKER linux-opt/lib/libpetsc.so.3.17.5 BEGINNING TO COMPILE MATLAB INTERFACE Building with 'gcc'. /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. ========================================= ========================================= Now to check if the libraries are working do: make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check *$make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/* /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires CC linux-opt/tests/ksp/ksp/tutorials/ex72.o CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -check_pointer_intensity 0 # [0]PETSC ERROR: -error_output_stdout # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 # [0]PETSC ERROR: -malloc_dump # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab # [0]PETSC ERROR: -pc_type lu # [0]PETSC ERROR: -use_gpu_aware_mpi 0 # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD # with errorcode 85. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff # FAILED ksp_ksp_tutorials-ex72_12 # # To rerun failed tests: # /usr/bin/make -f gmakefile test test-fail=1 To get the info of the error there is no specific probe id reported. How to check error info and proceed further? Thanks and regards Srinivas On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla wrote: > Do you get similar errors with petsc 3.17.5 using the new configure > options that Satish mentioned? > > On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users < > petsc-users at mcs.anl.gov> wrote: > >> Sorry for missing that. >> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >> >> < M A T L A B (R) > >> Copyright 1984-2020 The MathWorks, Inc. >> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >> November 23, 2020 >> >> >> To get started, type doc. >> For product information, visit www.mathworks.com. >> >> Thanks and regards >> Srinivas >> >> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay wrote: >> >>> You are missing one more step: >>> >>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> >>> No run matlab manually on "MB108SMEC028" with the command >>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>> >>> Does this work for you? As the message indicates this command is invoked >>> by "matlab_ls_test" - and that is failing. >>> >>> Satish >>> >>> >>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>> >>> > Hi Sathish, >>> > >>> > I tried the following procedure >>> > >>> > *$make * >>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>> > BEGINNING TO COMPILE MATLAB INTERFACE >>> > Building with 'gcc'. >>> > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> > In function ?PetscBinaryWrite?: >>> > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> > warning: ?err? may be used uninitialized in this function >>> > [-Wmaybe-uninitialized] >>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> > | ^ >>> > >>> > MEX completed successfully. >>> > Building with 'gcc'. >>> > MEX completed successfully. >>> > Building with 'gcc'. >>> > MEX completed successfully. >>> > Building with 'gcc'. >>> > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> > In function ?PetscBinaryWrite?: >>> > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> > warning: ?err? may be used uninitialized in this function >>> > [-Wmaybe-uninitialized] >>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> > | ^ >>> > >>> > MEX completed successfully. >>> > ========================================= >>> > Now to check if the libraries are working do: >>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>> > >>> > *$make test query=requires queryval=matlab >>> > DATAFILESPATH=/home/vit/datafiles/* >>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>> > query=requires >>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>> > # [0]PETSC ERROR: --------------------- Error Message >>> > -------------------------------------------------------------- >>> > # [0]PETSC ERROR: Error in external library >>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > for trouble shooting. >>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon >>> Sep >>> > 4 10:02:32 2023 >>> > # [0]PETSC ERROR: Configure options >>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > # [0]PETSC ERROR: --------------------- Error Message >>> > -------------------------------------------------------------- >>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>> > # [0]PETSC ERROR: >>> > # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > for trouble shooting. >>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon >>> Sep >>> > 4 10:02:32 2023 >>> > # [0]PETSC ERROR: Configure options >>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > # [0]PETSC ERROR: >>> > >>> ------------------------------------------------------------------------ >>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>> > probably memory access out of range >>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>> -on_error_attach_debugger >>> > # [0]PETSC ERROR: or see >>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple >>> Mac OS >>> > X to find memory corruption errors >>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>> link, >>> > and run >>> > # [0]PETSC ERROR: to get more information on the crash. >>> > # [0]PETSC ERROR: --------------------- Error Message >>> > -------------------------------------------------------------- >>> > # [0]PETSC ERROR: Signal received >>> > # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > for trouble shooting. >>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon >>> Sep >>> > 4 10:02:32 2023 >>> > # [0]PETSC ERROR: Configure options >>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>> > # >>> -------------------------------------------------------------------------- >>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> > # with errorcode 50162059. >>> > # >>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> > # You may or may not see output from other processes, depending on >>> > # exactly when Open MPI kills them. >>> > # >>> -------------------------------------------------------------------------- >>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> > CC >>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>> > CLINKER >>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > TEST >>> > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: >>> 124 >>> > # Running problem 5 >>> > # [0]PETSC ERROR: --------------------- Error Message >>> > -------------------------------------------------------------- >>> > # [0]PETSC ERROR: Error in external library >>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > # [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > for trouble shooting. >>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 >>> by >>> > vit Mon Sep 4 10:02:34 2023 >>> > # [0]PETSC ERROR: Configure options >>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > # [0]PETSC ERROR: #2 main() line 126 in >>> > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > # [0]PETSC ERROR: PETSc Option Table entries: >>> > # [0]PETSC ERROR: -prob_id 5 >>> > # [0]PETSC ERROR: -tao_smonitor >>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire >>> > error message to petsc-maint at mcs.anl.gov---------- >>> > # >>> -------------------------------------------------------------------------- >>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> > # with errorcode 126076. >>> > # >>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> > # You may or may not see output from other processes, depending on >>> > # exactly when Open MPI kills them. >>> > # >>> -------------------------------------------------------------------------- >>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>> failed >>> > so no diff >>> > >>> > # ------------- >>> > # Summary >>> > # ------------- >>> > # FAILED ksp_ksp_tutorials-ex72_12 >>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > # success 0/2 tests (0.0%) >>> > # failed 2/2 tests (100.0%) >>> > # todo 0/2 tests (0.0%) >>> > # skip 0/2 tests (0.0%) >>> > # >>> > # Wall clock time for tests: 4 sec >>> > # Approximate CPU time (not incl. build time): 0.03 sec >>> > # >>> > # To rerun failed tests: >>> > # /usr/bin/make -f gmakefile test test-fail=1 >>> > # >>> > # Timing summary (actual test time / total CPU time): >>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 >>> sec >>> > >>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>> > *$make matlab_ls_test* >>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>> -Wno-strict-aliasing >>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>> > -I/home/vit/sfw/petsc/3.13.4/include >>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>> > -I/usr/local/MATLAB/R2020b/extern/include >>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>> -lquadmath >>> > -lstdc++ -ldl -o matlab_ls_test >>> > >>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>> > -tao_smonitor -prob_id 5 -info* >>> > [0] PetscInitialize(): PETSc successfully started: number of >>> processors = 1 >>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>> > MB108SMEC028.(none) >>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>> > Running problem 5 >>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>> > 94202473157392 max tags = 2147483647 >>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> > [0]PETSC ERROR: --------------------- Error Message >>> > -------------------------------------------------------------- >>> > [0]PETSC ERROR: Error in external library >>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>> > [0]PETSC ERROR: See >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > for trouble shooting. >>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by >>> vit >>> > Mon Sep 4 10:09:56 2023 >>> > [0]PETSC ERROR: Configure options >>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>> > [0]PETSC ERROR: PETSc Option Table entries: >>> > [0]PETSC ERROR: -info >>> > [0]PETSC ERROR: -prob_id 5 >>> > [0]PETSC ERROR: -tao_smonitor >>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>> > error message to petsc-maint at mcs.anl.gov---------- >>> > >>> -------------------------------------------------------------------------- >>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> > with errorcode 126076. >>> > >>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> > You may or may not see output from other processes, depending on >>> > exactly when Open MPI kills them. >>> > >>> > Please find the attachment for configure.log and make.log files >>> > >>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay wrote: >>> > >>> > > To use datafiles in the test suite: >>> > > >>> > > cd $HOME >>> > > git clone https://gitlab.com/petsc/datafiles >>> > > >> or set >>> > > manually with make> >>> > > >>> > > make test query=requires queryval=matlab >>> DATAFILESPATH=$HOME/datafiles >>> > > >>> > > Satish >>> > > >>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>> > > >>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> > > > >>> > > > > Hi Matthew, >>> > > > > >>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not >>> have >>> > > any >>> > > > > separate test files to test PETSc alone. Can you please help me >>> how to >>> > > > > define this DATAFILESPATH? >>> > > > > >>> > > > >>> > > > That test you tried uses a certain matrix. On our machine, we >>> point to >>> > > this >>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>> have those >>> > > > matrices, since they are just for testing here. That >>> > > > is why I suggested just using a different matrix, or running a >>> problem >>> > > you >>> > > > care about in IBAMR. >>> > > > >>> > > > Thanks, >>> > > > >>> > > > Matt >>> > > > >>> > > > >>> > > > > Thanks and regards >>> > > > > Srinivas. >>> > > > > >>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>> knepley at gmail.com> >>> > > wrote: >>> > > > > >>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>> > > petsc-users < >>> > > > >> petsc-users at mcs.anl.gov> wrote: >>> > > > >> >>> > > > >>> Hi Sathish, >>> > > > >>> >>> > > > >>> Thank you so much for your efforts and the support you are >>> giving me >>> > > to >>> > > > >>> sort this out. >>> > > > >>> >>> > > > >>> I tried to follow the same procedure which you followed to >>> build >>> > > Petsc >>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>> > > > >>> >>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>> PETSC_ARCH=linux-opt >>> > > > >>> --with-debugging=0 --with-x=0 >>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>> > > > >>> Using python3 for Python >>> > > > >>> >>> > > > >>> >>> > > >>> =============================================================================== >>> > > > >>> Configuring PETSc to compile on your system >>> > > > >>> >>> > > > >>> >>> > > > >>> >>> > > >>> =============================================================================== >>> > > > >>> >>> > > >>> =============================================================================== >>> > > > >>> It appears you do not >>> have >>> > > valgrind >>> > > > >>> installed on your system. >>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>> > > > >>> Or install >>> > > valgrind-devel or >>> > > > >>> equivalent using your package manager. >>> > > > >>> Then rerun ./configure >>> > > > >>> >>> > > > >>> >>> > > >>> =============================================================================== >>> > > > >>> Compilers: >>> > > > >>> >>> > > > >>> C Compiler: >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > -fPIC >>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > > > >>> C++ Compiler: >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>> -Wno-unknown-pragmas >>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>> > > > >>> Fortran Compiler: >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument >>> -O3 >>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > > > >>> Linkers: >>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > -shared >>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>> > > -Wno-unknown-pragmas >>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > -shared >>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>> > > -Wno-unknown-pragmas >>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>> > > > >>> make: >>> > > > >>> Version: 4.2 >>> > > > >>> /usr/bin/make >>> > > > >>> BlasLapack: >>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>> -omp_num_threads >>> > >

to >>> > > > >>> control the number of threads >>> > > > >>> uses 8 byte integers >>> > > > >>> MPI: >>> > > > >>> Version: 3 >>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>> > > --oversubscribe >>> > > > >>> OMPI_VERSION: 4.1.4 >>> > > > >>> pthread: >>> > > > >>> cmake: >>> > > > >>> Version: 3.16.3 >>> > > > >>> /usr/bin/cmake >>> > > > >>> regex: >>> > > > >>> Matlab: >>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> > > > >>> /usr/local/MATLAB/R2020b >>> > > > >>> MatlabEngine: >>> > > > >>> Library: >>> > > > >>> >>> > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx >>> -lmat >>> > > -lut >>> > > > >>> -licudata -licui18n -licuuc >>> > > > >>> Language used to compile PETSc: C >>> > > > >>> PETSc: >>> > > > >>> PETSC_ARCH: linux-opt >>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>> > > > >>> Scalar type: real >>> > > > >>> Precision: double >>> > > > >>> Support for __float128 >>> > > > >>> Integer size: 4 bytes >>> > > > >>> shared libraries: enabled >>> > > > >>> Memory alignment from malloc(): 16 bytes >>> > > > >>> >>> > > > >>> >>> > > >>> xxx=========================================================================xxx >>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>> PETSC_ARCH=linux-opt all >>> > > > >>> >>> > > > >>> >>> > > >>> xxx=========================================================================xxx >>> > > > >>> >>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>> -licuuc as >>> > > > >>> you suggested earlier. >>> > > > >>> >>> > > > >>> *$make* >>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> > > > >>> Building with 'gcc'. >>> > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> > > > >>> In function ?PetscBinaryWrite?: >>> > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> > > > >>> warning: ?err? may be used uninitialized in this function >>> > > > >>> [-Wmaybe-uninitialized] >>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>> socket\n"); >>> > > > >>> | ^ >>> > > > >>> >>> > > > >>> MEX completed successfully. >>> > > > >>> Building with 'gcc'. >>> > > > >>> MEX completed successfully. >>> > > > >>> Building with 'gcc'. >>> > > > >>> MEX completed successfully. >>> > > > >>> Building with 'gcc'. >>> > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> > > > >>> In function ?PetscBinaryWrite?: >>> > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> > > > >>> warning: ?err? may be used uninitialized in this function >>> > > > >>> [-Wmaybe-uninitialized] >>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>> socket\n"); >>> > > > >>> | ^ >>> > > > >>> >>> > > > >>> MEX completed successfully. >>> > > > >>> ========================================= >>> > > > >>> Now to check if the libraries are working do: >>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>> check >>> > > > >>> =============================================== >>> > > > >>> >>> > > > >>> *$make test query=requires queryval=matlab* >>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> > > > >>> TEST >>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>> > > > >>> -------------------------------------------------------------- >>> > > > >>> # [0]PETSC ERROR: Unable to open file >>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>> > > > >>> >>> > > > >> >>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, >>> so it >>> > > > >> cannot find the matrix to test. Try running some test of yours. >>> > > > >> >>> > > > >> Thanks, >>> > > > >> >>> > > > >> Matt >>> > > > >> >>> > > > >> >>> > > > >>> # [0]PETSC ERROR: See >>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>> trouble >>> > > > >>> shooting. >>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>> vit >>> > > Sun >>> > > > >>> Sep 3 11:51:03 2023 >>> > > > >>> # [0]PETSC ERROR: Configure options >>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> --with-debugging=0 >>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line >>> 1444 in >>> > > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>> > > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>> > > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>> -------send >>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> > > > >>> # >>> > > > >>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> > > > >>> # with errorcode 113065. >>> > > > >>> # >>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>> processes. >>> > > > >>> # You may or may not see output from other processes, >>> depending on >>> > > > >>> # exactly when Open MPI kills them. >>> > > > >>> # >>> > > > >>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> > > > >>> CC >>> > > > >>> >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>> > > > >>> CLINKER >>> > > > >>> >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > > > >>> TEST >>> > > > >>> >>> > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>> > > code: 124 >>> > > > >>> # Running problem 5 >>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>> > > > >>> -------------------------------------------------------------- >>> > > > >>> # [0]PETSC ERROR: Error in external library >>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > > >>> # [0]PETSC ERROR: See >>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>> trouble >>> > > > >>> shooting. >>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>> > > MB108SMEC028 by >>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>> > > > >>> # [0]PETSC ERROR: Configure options >>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> --with-debugging=0 >>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > > > >>> >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>> > > > >>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>> -------send >>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> > > > >>> # >>> > > > >>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>> > > > >>> # with errorcode 126076. >>> > > > >>> # >>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>> processes. >>> > > > >>> # You may or may not see output from other processes, >>> depending on >>> > > > >>> # exactly when Open MPI kills them. >>> > > > >>> # >>> > > > >>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>> Command >>> > > > >>> failed so no diff >>> > > > >>> >>> > > > >>> # ------------- >>> > > > >>> # Summary >>> > > > >>> # ------------- >>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > > > >>> # success 0/2 tests (0.0%) >>> > > > >>> # failed 2/2 tests (100.0%) >>> > > > >>> # todo 0/2 tests (0.0%) >>> > > > >>> # skip 0/2 tests (0.0%) >>> > > > >>> # >>> > > > >>> # Wall clock time for tests: 3 sec >>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>> > > > >>> # >>> > > > >>> # To rerun failed tests: >>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> > > > >>> # >>> > > > >>> # Timing summary (actual test time / total CPU time): >>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec >>> / >>> > > 0.02 sec >>> > > > >>> >>> > > > >>> *How to sort out this error?* >>> > > > >>> >>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>> > > > >>> *$make matlab_ls_test* >>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>> > > -Wwrite-strings >>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>> > > -Wno-strict-aliasing >>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>> matlab_ls_test.c >>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> > > > >>> >>> > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>> -lmex >>> > > -lmx >>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>> > > -lmpi_mpifh >>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>> -lpthread >>> > > -lquadmath >>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>> > > > >>> >>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>> > > > >>> I am sharing the configure.log and make.log files. Please find >>> the >>> > > > >>> attachment and do the needful. >>> > > > >>> >>> > > > >>> >>> > > > >>> Thanks and regards >>> > > > >>> Srinivas >>> > > > >>> >>> > > > >>> >>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>> balay at mcs.anl.gov> >>> > > wrote: >>> > > > >>> >>> > > > >>>> Perhaps you can try the following to get additional info - >>> and debug >>> > > > >>>> >>> > > > >>>> Satish >>> > > > >>>> ---------- >>> > > > >>>> >>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>> > > > >>>> balay at compute-386-07 >>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>> > > > >>>> make matlab_ls_test >>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>> -fPIC >>> > > -Wall >>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> > > -fstack-protector >>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>> > > -Wno-strict-aliasing >>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>> > > > >>>> -I/scratch/balay/petsc/include >>> > > -I/scratch/balay/petsc/linux-opt/include >>> > > > >>>> >>> > > >>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>> > > > >>>> matlab_ls_test.c >>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>> > > > >>>> >>> > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> > > > >>>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>> > > > >>>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm >>> -leng >>> > > -lmex >>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>> -lmpifort >>> > > -lmpi >>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>> -ldl -o >>> > > > >>>> matlab_ls_test >>> > > > >>>> balay at compute-386-07 >>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>> ./matlab_ls_test >>> > > > >>>> -tao_smonitor -prob_id 5 -info >>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>> > > processors >>> > > > >>>> = 1 >>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>> > > > >>>> compute-386-07.(none) >>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>> > > > >>>> Running problem 5 >>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>> 1140850689 >>> > > > >>>> -2080374784 max tags = 268435455 >>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>> command >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>> > > > >>>> -glnxa64 -nodisplay -nosplash >>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>> > > > >>>> TestingInitialize >>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>> string: >>> > > > >>>> TestingInitialize >>> > > > >>>> 5 >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> <<<< Now verify if the above matlab command actually works >>> for you >>> > > - on >>> > > > >>>> this machine..>>>>> >>> > > > >>>> >>> > > > >>>> balay at compute-386-07 >>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>> > > > >>>> -glnxa64 -nodisplay -nosplash >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> < M A T L A B (R) > >>> > > > >>>> >>> > > > >>>> Copyright 1984-2021 The MathWorks, >>> Inc. >>> > > > >>>> >>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>> (glnxa64) >>> > > > >>>> >>> > > > >>>> February 17, 2021 >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> To get started, type doc. >>> > > > >>>> For product information, visit www.mathworks.com. >>> > > > >>>> >>> > > > >>>> >> >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>> > > > >>>> >>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>> > > thread >>> > > > >>>> to petsc-users only] >>> > > > >>>> > >>> > > > >>>> > I'm not sure what is happening here. Can you send the >>> > > corresponding >>> > > > >>>> configure.log, make.log [compressed]? >>> > > > >>>> > >>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>> Ubuntu-20.04, >>> > > > >>>> with Matlab-R2021a - and that works: >>> > > > >>>> > >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>> > > > >>>> > main >>> > > > >>>> > release >>> > > > >>>> > * release-3.13 >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>> > > matlab/R2021a >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>> > > > >>>> > >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>> > > > >>>> >>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>> PETSC_ARCH=linux-opt >>> > > > >>>> --with-debugging=0 --with-x=0 >>> > > > >>>> >>> > > >>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>> > > > >>>> >>> > > >>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> > > > >>>> > >>> > > > >>>> > Compilers: >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> > C Compiler: >>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>> -fPIC >>> > > -Wall >>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> > > -fstack-protector >>> > > > >>>> -fvisibility=hidden -O3 >>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > > > >>>> > C++ Compiler: >>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx >>> -Wall >>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>> > > -fstack-protector >>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> > > > >>>> > Fortran Compiler: >>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 >>> -fPIC >>> > > -Wall >>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>> 9.4.0 >>> > > > >>>> > Linkers: >>> > > > >>>> > Shared linker: >>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>> > > -shared -fPIC >>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>> -Wno-unknown-pragmas >>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>> > > > >>>> > Dynamic linker: >>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>> > > -shared -fPIC >>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>> -Wno-unknown-pragmas >>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>> > > > >>>> > make: >>> > > > >>>> > Version: 4.2 >>> > > > >>>> > /usr/bin/make >>> > > > >>>> > BlasLapack: >>> > > > >>>> > Library: >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>> > > > >>>> >>> > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>> > > > >>>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>> > > > >>>> -liomp5 -lpthread >>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>> -omp_num_threads >>> > >

>>> > > > >>>> to control the number of threads >>> > > > >>>> > uses 8 byte integers >>> > > > >>>> > MPI: >>> > > > >>>> > Version: 4 >>> > > > >>>> > Includes: >>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>> > > > >>>> > Mpiexec: >>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>> > > > >>>> > pthread: >>> > > > >>>> > Library: -lpthread >>> > > > >>>> > cmake: >>> > > > >>>> > Version: 3.16.3 >>> > > > >>>> > /usr/bin/cmake >>> > > > >>>> > regex: >>> > > > >>>> > Matlab: >>> > > > >>>> > Includes: >>> > > > >>>> >>> > > >>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>> > > > >>>> > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>> > > > >>>> > MatlabEngine: >>> > > > >>>> > Library: >>> > > > >>>> >>> > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> > > > >>>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>> > > > >>>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>> > > > >>>> > sowing: >>> > > > >>>> > Version: 1.1.25 >>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>> > > > >>>> > valgrind: >>> > > > >>>> > Language used to compile PETSc: C >>> > > > >>>> > PETSc: >>> > > > >>>> > PETSC_ARCH: linux-opt >>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>> > > > >>>> > Scalar type: real >>> > > > >>>> > Precision: double >>> > > > >>>> > Support for __float128 >>> > > > >>>> > Integer size: 4 bytes >>> > > > >>>> > shared libraries: enabled >>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>> > > > >>>> > >>> > > > >>>> >>> > > >>> xxx=========================================================================xxx >>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt >>> all >>> > > > >>>> > >>> > > > >>>> >>> > > >>> xxx=========================================================================xxx >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> >>> > > > >>>> > >>> > > > >>>> > >>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>> > > > >>>> > Building with 'gcc'. >>> > > > >>>> > >>> > > > >>>> >>> > > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>> > > > >>>> function ?PetscBinaryWrite?: >>> > > > >>>> > >>> > > > >>>> >>> > > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> > > > >>>> warning: ?err? may be used uninitialized in this function >>> > > > >>>> [-Wmaybe-uninitialized] >>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>> > > socket\n"); >>> > > > >>>> > | ^ >>> > > > >>>> > >>> > > > >>>> > MEX completed successfully. >>> > > > >>>> > Building with 'gcc'. >>> > > > >>>> > MEX completed successfully. >>> > > > >>>> > Building with 'gcc'. >>> > > > >>>> > MEX completed successfully. >>> > > > >>>> > Building with 'gcc'. >>> > > > >>>> > >>> > > > >>>> >>> > > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>> > > > >>>> function ?PetscBinaryWrite?: >>> > > > >>>> > >>> > > > >>>> >>> > > >>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>> > > > >>>> warning: ?err? may be used uninitialized in this function >>> > > > >>>> [-Wmaybe-uninitialized] >>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>> > > socket\n"); >>> > > > >>>> > | ^ >>> > > > >>>> > >>> > > > >>>> > MEX completed successfully. >>> > > > >>>> > ========================================= >>> > > > >>>> > Now to check if the libraries are working do: >>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt >>> check >>> > > > >>>> > ========================================= >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>> > > query=requires >>> > > > >>>> queryval=matlab >>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> > > > >>>> > TEST >>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>> > > > >>>> > # ../ex72: >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>> > > > >>>> version `GFORTRAN_9' not found (required by >>> > > > >>>> >>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>> diff >>> > > > >>>> > CC >>> > > > >>>> >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>> > > > >>>> > CLINKER >>> > > > >>>> >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > > > >>>> > TEST >>> > > > >>>> >>> > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> Error >>> > > code: >>> > > > >>>> 1 >>> > > > >>>> > # ../matlab_ls_test: >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>> > > > >>>> version `GFORTRAN_9' not found (required by >>> > > > >>>> >>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>> > > Command >>> > > > >>>> failed so no diff >>> > > > >>>> > >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>> > > query=requires >>> > > > >>>> queryval=matlab >>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>> > > > >>>> > TEST >>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>> > > > >>>> > TEST >>> > > > >>>> >>> > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > > > >>>> > >>> > > > >>>> > # ------------- >>> > > > >>>> > # Summary >>> > > > >>>> > # ------------- >>> > > > >>>> > # success 4/4 tests (100.0%) >>> > > > >>>> > # failed 0/4 tests (0.0%) >>> > > > >>>> > # todo 0/4 tests (0.0%) >>> > > > >>>> > # skip 0/4 tests (0.0%) >>> > > > >>>> > # >>> > > > >>>> > # Wall clock time for tests: 27 sec >>> > > > >>>> > # Approximate CPU time (not incl. build time): >>> 15.190000000000001 >>> > > sec >>> > > > >>>> > # >>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 >>> sec / >>> > > 7.54 >>> > > > >>>> sec >>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>> > > > >>>> > >>> > > > >>>> > >>> > > > >>>> > >>> > > > >>>> > >>> > > > >>>> > >>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>> > > > >>>> > >>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>> > > > >>>> configure petsc >>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. >>> After >>> > > > >>>> running make >>> > > > >>>> > > -j 10 test command I have got the following error message. >>> > > > >>>> > > >>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> Error >>> > > > >>>> code: 124 >>> > > > >>>> > > # Running problem 5 >>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>> > > > >>>> > > >>> -------------------------------------------------------------- >>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>> > > > >>>> > > # [0]PETSC ERROR: See >>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > > > >>>> > > for trouble shooting. >>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>> 2020 >>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>> > > > >>>> MB108SMEC028 by >>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>> COPTFLAGS=-O3 >>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>> > > > >>>> --with-debugging=0 >>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > > > >>>> > > --with-matlab-engine=1 >>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>>> > > --known-64-bit-blas-indices=1 >>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>> > > > >>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>> > > > >>>> > > >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>> > > -------send >>> > > > >>>> entire >>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>> > > > >>>> > > # >>> > > > >>>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>> MPI_COMM_SELF >>> > > > >>>> > > # with errorcode 126076. >>> > > > >>>> > > # >>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>> > > > >>>> processes. >>> > > > >>>> > > # You may or may not see output from other processes, >>> depending >>> > > on >>> > > > >>>> > > # exactly when Open MPI kills them. >>> > > > >>>> > > # >>> > > > >>>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>>> > > >>> > > > >>>> > > I request you to help me to sort out this error. >>> > > > >>>> > > >>> > > > >>>> > > Thanks >>> > > > >>>> > > Srinivas >>> > > > >>>> > > >>> > > > >>>> > > >>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>> > > > >>>> mail2amneet at gmail.com> wrote: >>> > > > >>>> > > >>> > > > >>>> > > > I think there should be two hyphens in >>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>>> > > > >>> > > > >>>> > > > i.e.: >>> > > > >>>> > > > >>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>>> > > > >>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>> 20PHD0548 via >>> > > > >>>> petsc-users < >>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>> > > > >>>> > > > >>> > > > >>>> > > >> Thank you Sathish.I will try this >>> > > > >>>> > > >> >>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>> balay at mcs.anl.gov> >>> > > > >>>> wrote: >>> > > > >>>> > > >> >>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will >>> work >>> > > > >>>> here]. >>> > > > >>>> > > >>> >>> > > > >>>> > > >>> i.e: >>> > > > >>>> > > >>> >>> > > > >>>> > > >>> ./configure >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>> > > PETSC_ARCH=linux-opt >>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>> > > > >>>> --with-matlab-engine=1 >>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> > > > >>>> --known-64-bit-blas-indices=1 >>> > > > >>>> > > >>> >>> > > > >>>> > > >>> Satish >>> > > > >>>> > > >>> >>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>> > > petsc-users >>> > > > >>>> wrote: >>> > > > >>>> > > >>> >>> > > > >>>> > > >>> > Hi Satish, >>> > > > >>>> > > >>> > >>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>> > > > >>>> > > >>> > >>> > > > >>>> > > >>> > Is this what you are suggesting? >>> > > > >>>> > > >>> > >>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>> > > balay at mcs.anl.gov> >>> > > > >>>> wrote: >>> > > > >>>> > > >>> > >>> > > > >>>> > > >>> > > Also: >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> > > Note: most externalpackages might not work in >>> this mode. >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> > > [we can't really over come such >>> dependency/conflicts >>> > > across >>> > > > >>>> packages] >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> > > Satish >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users >>> wrote: >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] >>> conflict >>> > > with >>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>> > > > >>>> -known-64-bit-blas-indices=1 >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack >>> with >>> > > > >>>> matlab - to >>> > > > >>>> > > >>> have a >>> > > > >>>> > > >>> > > compatible build >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > Satish >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 >>> via >>> > > > >>>> petsc-users >>> > > > >>>> > > >>> wrote: >>> > > > >>>> > > >>> > > > >>> > > > >>>> > > >>> > > > > Hi Amneet, >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB >>> is not >>> > > > >>>> working. It is >>> > > > >>>> > > >>> > > showing >>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster >>> with >>> > > > >>>> libmesh and >>> > > > >>>> > > >>> this is >>> > > > >>>> > > >>> > > for >>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried >>> without >>> > > > >>>> linking >>> > > > >>>> > > >>> Matlab >>> > > > >>>> > > >>> > > with >>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>> configuring >>> > > > >>>> libmesh 1.6.2 >>> > > > >>>> > > >>> that >>> > > > >>>> > > >>> > > PETSc >>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>> > > specified. >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>> libmesh with >>> > > > >>>> PETSc and >>> > > > >>>> > > >>> Matlab >>> > > > >>>> > > >>> > > is in >>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>> > > geometries >>> > > > >>>> it is >>> > > > >>>> > > >>> > > mentioned to >>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>> > > things >>> > > > >>>> and ended >>> > > > >>>> > > >>> up with >>> > > > >>>> > > >>> > > > > errors. >>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to >>> do my >>> > > > >>>> research work. >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>> possible. >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > Thanks and Regards >>> > > > >>>> > > >>> > > > > Srinivas >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>> > > > >>>> mail2amneet at gmail.com> >>> > > > >>>> > > >>> > > wrote: >>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>> > > > >>>> > > >>> > > > > > >>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh >>> for >>> > > the >>> > > > >>>> WEC >>> > > > >>>> > > >>> application. >>> > > > >>>> > > >>> > > You >>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds >>> with >>> > > > >>>> Matlab. >>> > > > >>>> > > >>> > > > > > >>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting >>> to build >>> > > > >>>> libMesh? >>> > > > >>>> > > >>> > > > > > >>> > > > >>>> > > >>> > > > > > Thanks, >>> > > > >>>> > > >>> > > > > > ?Amneet >>> > > > >>>> > > >>> > > > > > >>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU >>> SRINIVAS >>> > > > >>>> 20PHD0548 via >>> > > > >>>> > > >>> > > petsc-users >>> > > > >>>> > > >>> > > > > > wrote: >>> > > > >>>> > > >>> > > > > > >>> > > > >>>> > > >>> > > > > >> Hi, >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>> removing all >>> > > > >>>> occurrences >>> > > > >>>> > > >>> of >>> > > > >>>> > > >>> > > "-lut >>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran >>> "make >>> > > test" >>> > > > >>>> got the >>> > > > >>>> > > >>> > > following >>> > > > >>>> > > >>> > > > > >> errors >>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>> > > > >>>> > > >>> > > > > >> TEST >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > >>>> > > >>> > > > > >> not ok >>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> > > > >>>> > > >>> Error >>> > > > >>>> > > >>> > > code: 124 >>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>> Error >>> > > Message >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> -------------------------------------------------------------- >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB >>> engine >>> > > on >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>> > > > >>>> > > >>> > > > > >> >>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > > > >>>> for >>> > > > >>>> > > >>> trouble >>> > > > >>>> > > >>> > > > > >> shooting. >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>> 3.13.4, >>> > > Aug >>> > > > >>>> 01, 2020 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>> > > linux-debug >>> > > > >>>> named >>> > > > >>>> > > >>> > > MB108SMEC028 >>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>> > > > >>>> > > >>> > > > > >> >>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > > >>>> > > >>> > > > > >> >>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > > >>>> > > >>> > > > > >> >>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> > > > >>>> > > >>> --with-debugging=1 >>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>> > > > >>>> --with-x=0 >>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > > >>>> > > >>> --with-matlab-engine=1 >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> >>> > > > >>>> >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>> PetscMatlabEngineCreate() >>> > > line >>> > > > >>>> 67 in >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>> entries: >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of >>> Error >>> > > > >>>> Message >>> > > > >>>> > > >>> -------send >>> > > > >>>> > > >>> > > entire >>> > > > >>>> > > >>> > > > > >> error message to >>> > > petsc-maint at mcs.anl.gov---------- >>> > > > >>>> > > >>> > > > > >> # >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>> communicator >>> > > > >>>> > > >>> MPI_COMM_SELF >>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>> > > > >>>> > > >>> > > > > >> # >>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI >>> to >>> > > kill >>> > > > >>>> all MPI >>> > > > >>>> > > >>> > > processes. >>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>> > > processes, >>> > > > >>>> > > >>> depending on >>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>> > > > >>>> > > >>> > > > > >> # >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>>> > > >>> > > > > >> ok >>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > > > >>>> # SKIP >>> > > > >>>> > > >>> Command >>> > > > >>>> > > >>> > > > > >> failed so no diff >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>> > > > >>>> > > >>> > > > > >> TEST >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>> > > > >>>> > > >>> > > > > >> not ok >>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>> > > > >>>> > > >>> Error >>> > > > >>>> > > >>> > > code: 124 >>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>> Error >>> > > Message >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> -------------------------------------------------------------- >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB >>> engine >>> > > on >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>> > > > >>>> > > >>> > > > > >> >>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>> > > > >>>> for >>> > > > >>>> > > >>> trouble >>> > > > >>>> > > >>> > > > > >> shooting. >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>> 3.13.4, >>> > > Aug >>> > > > >>>> 01, 2020 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>> > > linux-opt >>> > > > >>>> named >>> > > > >>>> > > >>> > > MB108SMEC028 by >>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>> > > > >>>> > > >>> > > > > >> >>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>> > > > >>>> > > >>> > > > > >> >>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>> > > > >>>> > > >>> > > > > >> >>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>> > > > >>>> --PETSC_ARCH=linux-opt >>> > > > >>>> > > >>> > > --with-debugging=0 >>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>> > > > >>>> --download-fblaslapack=1 >>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > > >>>> > > >>> --with-matlab-engine=1 >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> >>> > > > >>>> >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>> PetscMatlabEngineCreate() >>> > > line >>> > > > >>>> 67 in >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>> entries: >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of >>> Error >>> > > > >>>> Message >>> > > > >>>> > > >>> -------send >>> > > > >>>> > > >>> > > entire >>> > > > >>>> > > >>> > > > > >> error message to >>> > > petsc-maint at mcs.anl.gov---------- >>> > > > >>>> > > >>> > > > > >> # >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>> communicator >>> > > > >>>> > > >>> MPI_COMM_SELF >>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>> > > > >>>> > > >>> > > > > >> # >>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI >>> to >>> > > kill >>> > > > >>>> all MPI >>> > > > >>>> > > >>> > > processes. >>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>> > > processes, >>> > > > >>>> > > >>> depending on >>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>> > > > >>>> > > >>> > > > > >> # >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -------------------------------------------------------------------------- >>> > > > >>>> > > >>> > > > > >> ok >>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>> > > > >>>> # SKIP >>> > > > >>>> > > >>> Command >>> > > > >>>> > > >>> > > > > >> failed so no diff. >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>> > > version. I >>> > > > >>>> am >>> > > > >>>> > > >>> sharing the >>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc >>> 3.13.4 and >>> > > > >>>> petsc >>> > > > >>>> > > >>> 3.17.5. >>> > > > >>>> > > >>> > > Please find >>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> Thanks and regards >>> > > > >>>> > > >>> > > > > >> Srinivas >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish >>> Balay < >>> > > > >>>> > > >>> balay at mcs.anl.gov> >>> > > > >>>> > > >>> > > wrote: >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>> > > > >>>> > > >>> configure.log/make.log >>> > > > >>>> > > >>> > > for >>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> >>>> >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> Matlab: >>> > > > >>>> > > >>> > > > > >>> Includes: >>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>> > > > >>>> > > >>> > > > > >>> Library: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> > > > >>>> > > >>> > > > > >>> >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> > > -leng >>> > > > >>>> -lmex >>> > > > >>>> > > >>> -lmx >>> > > > >>>> > > >>> > > -lmat -lut >>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>> > > > >>>> > > >>> > > > > >>> <<<<< >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we >>> are >>> > > seeing: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> >>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> >>> >>> > > > >>>> > > >>> > > > > >>> Matlab: >>> > > > >>>> > > >>> > > > > >>> Includes: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>> > > > >>>> > > >>> > > > > >>> Libraries: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>> > > > >>>> > > >>> > > > > >>> Executable: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> >>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>> > > > >>>> > > >>> > > > > >>> mex: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>> > > > >>>> > > >>> > > > > >>> matlab: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>> > > > >>>> > > >>> > > > > >>> <<< >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" >>> are not >>> > > > >>>> preset here. >>> > > > >>>> > > >>> This >>> > > > >>>> > > >>> > > might >>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> You can: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> - edit >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> >>> > > > >>>> >>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>> > > > >>>> > > >>> > > and >>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>> > > -licui18n >>> > > > >>>> -licuuc" >>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>> > > '/home/vit/sfw/petsc/3.13.4' >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> Satish >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS >>> 20PHD0548 >>> > > via >>> > > > >>>> > > >>> petsc-users >>> > > > >>>> > > >>> > > wrote: >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>> building >>> > > > >>>> petsc3.13.4 with >>> > > > >>>> > > >>> > > matlab and >>> > > > >>>> > > >>> > > > > >>> also >>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>> > > > >>>> petsc3.17.5 and >>> > > > >>>> > > >>> matlab. >>> > > > >>>> > > >>> > > > > >>> Building >>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>> > > successfully. >>> > > > >>>> But >>> > > > >>>> > > >>> libmesh is >>> > > > >>>> > > >>> > > not >>> > > > >>>> > > >>> > > > > >>> able to >>> > > > >>>> > > >>> > > > > >>> > find the petsc >>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>> > > > >>>> > > >>> > > > > >>> > >>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish >>> Balay < >>> > > > >>>> > > >>> balay at mcs.anl.gov> >>> > > > >>>> > > >>> > > > > >>> wrote: >>> > > > >>>> > > >>> > > > > >>> > >>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>> > > > >>>> petsc-3.13 and >>> > > > >>>> > > >>> 3.17 [or >>> > > > >>>> > > >>> > > 3.19]. >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>> > > friendly to >>> > > > >>>> mailing >>> > > > >>>> > > >>> list - >>> > > > >>>> > > >>> > > or >>> > > > >>>> > > >>> > > > > >>> send >>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? >>> [or >>> > > 3.19?] >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> > > Satish >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>> > > 20PHD0548 >>> > > > >>>> via >>> > > > >>>> > > >>> petsc-users >>> > > > >>>> > > >>> > > wrote: >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>> > > building >>> > > > >>>> > > >>> petsc-3.13.4 >>> > > > >>>> > > >>> > > with >>> > > > >>>> > > >>> > > > > >>> Matlab. >>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do >>> the >>> > > needful. >>> > > > >>>> > > >>> > > > > >>> > > > >>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM >>> INTURU >>> > > > >>>> SRINIVAS >>> > > > >>>> > > >>> 20PHD0548 < >>> > > > >>>> > > >>> > > > > >>> > > > >>> inturu.srinivas2020 at vitstudent.ac.in> >>> > > wrote: >>> > > > >>>> > > >>> > > > > >>> > > > >>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>> > > building >>> > > > >>>> of >>> > > > >>>> > > >>> libmesh, the >>> > > > >>>> > > >>> > > error >>> > > > >>>> > > >>> > > > > >>> shows >>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>> > > > >>>> > > >>> > > > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM >>> Satish >>> > > > >>>> Balay < >>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>> > > > >>>> > > >>> > > > > >>> > > wrote: >>> > > > >>>> > > >>> > > > > >>> > > > > >>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux >>> says >>> > > > >>>> petsc-3.17 >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU >>> SRINIVAS >>> > > > >>>> 20PHD0548 via >>> > > > >>>> > > >>> > > petsc-users >>> > > > >>>> > > >>> > > > > >>> wrote: >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with >>> MATLAB for >>> > > > >>>> working on >>> > > > >>>> > > >>> the >>> > > > >>>> > > >>> > > > > >>> simulation >>> > > > >>>> > > >>> > > > > >>> > > using >>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building >>> the >>> > > PETSc, >>> > > > >>>> using the >>> > > > >>>> > > >>> > > following >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> >>> > > > >>>> >>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> >>> > > > >>>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEnginePut' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineEvaluate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGet' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEnginePut' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineEvaluate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGet' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGet' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineCreate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineEvaluate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineEvaluate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGetArray' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGetArray' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGetArray' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGetArray' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineGetArray' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineEvaluate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineEvaluate' >>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > >>> > > > >>>> > > >>> >>> > > > >>>> >>> > > >>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>> > > > >>>> `PetscMatlabEngineDestroy' >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 >>> exit >>> > > > >>>> status >>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> >>> > > > >>>> >>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>> unfinished >>> > > jobs.... >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this >>> issue >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> > >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >> >>> > > > >>>> > > >>> > > > > >>> > > > >>> > > > >>>> > > >>> > > > > >>> > > > >>> > > > >>>> > > >>> > > > > >>> > > >>> > > > >>>> > > >>> > > > > >>> > >>> > > > >>>> > > >>> > > > > >>> > >>> > > > >>>> > > >>> > > > > >>> >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> >>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from >>> Vellore >>> > > > >>>> Institute of >>> > > > >>>> > > >>> > > Technology. >>> > > > >>>> > > >>> > > > > >> The contents of this email may contain >>> legally >>> > > > >>>> protected >>> > > > >>>> > > >>> > > confidential or >>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>> Institute of >>> > > > >>>> Technology?. >>> > > > 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If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> > > > -- > --Amneet > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Tue Sep 5 10:35:15 2023 From: bsmith at petsc.dev (Barry Smith) Date: Tue, 5 Sep 2023 11:35:15 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> Message-ID: <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> The error is occuring during e->ep = engOpen(buffer); Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line e->ep = engOpen(buffer); replace it with e->ep = engOpen(""); Now in the PETSc directory do make all (it should recompile one file) and then run the make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ again > On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > > Hi Amneeth, > > I think the errors are different with petsc 3.17.5 > > ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > The version of PETSc you are using is out-of-date, we recommend updating to the new release > Available Version: 3.19.5 Installed Version: 3.17.5 > https://petsc.org/release/download/ > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > ============================================================================================= > Configuring PETSc to compile on your system > ============================================================================================= > Compilers: > C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC > Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > Linkers: > Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 > Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 > Libraries linked against: -lquadmath -lstdc++ -ldl > BlasLapack: > Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads > uses 8 byte integers > MPI: > Version: 3 > mpiexec: /usr/bin/mpiexec > Implementation: openmpi > OMPI_VERSION: 4.0.3 > pthread: > cmake: > Version: 3.16.3 > /usr/bin/cmake > regex: > Matlab: > Includes: -I/usr/local/MATLAB/R2020b/extern/include > /usr/local/MATLAB/R2020b > MatlabEngine: > Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c > Language used to compile PETSc: C > PETSc: > PETSC_ARCH: linux-opt > PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 > Prefix: > Scalar type: real > Precision: double > Support for __float128 > Integer size: 4 bytes > Single library: yes > Shared libraries: yes > Memory alignment from malloc(): 16 bytes > Using GNU make: /usr/bin/make > xxx=========================================================================xxx > Configure stage complete. Now build PETSc libraries with: > make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all > xxx=========================================================================xxx > > $make > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > CLINKER linux-opt/lib/libpetsc.so.3.17.5 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check > > $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ > /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 > # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 > # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 > # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -check_pointer_intensity 0 > # [0]PETSC ERROR: -error_output_stdout > # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > # [0]PETSC ERROR: -malloc_dump > # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > # [0]PETSC ERROR: -pc_type lu > # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > # with errorcode 85. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > # FAILED ksp_ksp_tutorials-ex72_12 > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > > To get the info of the error there is no specific probe id reported. > > How to check error info and proceed further? > > Thanks and regards > Srinivas > > On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: >> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? >> >> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>> Sorry for missing that. >>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> >>> < M A T L A B (R) > >>> Copyright 1984-2020 The MathWorks, Inc. >>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>> November 23, 2020 >>> >>> >>> To get started, type doc. >>> For product information, visit www.mathworks.com . >>> >>> Thanks and regards >>> Srinivas >>> >>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: >>>> You are missing one more step: >>>> >>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> >>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>> >>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. >>>> >>>> Satish >>>> >>>> >>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>> >>>> > Hi Sathish, >>>> > >>>> > I tried the following procedure >>>> > >>>> > *$make * >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>> > Building with 'gcc'. >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > In function ?PetscBinaryWrite?: >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > warning: ?err? may be used uninitialized in this function >>>> > [-Wmaybe-uninitialized] >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > | ^ >>>> > >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > In function ?PetscBinaryWrite?: >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > warning: ?err? may be used uninitialized in this function >>>> > [-Wmaybe-uninitialized] >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > | ^ >>>> > >>>> > MEX completed successfully. >>>> > ========================================= >>>> > Now to check if the libraries are working do: >>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>> > >>>> > *$make test query=requires queryval=matlab >>>> > DATAFILESPATH=/home/vit/datafiles/* >>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>> > query=requires >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Error in external library >>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>> > 4 10:02:32 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>> > # [0]PETSC ERROR: >>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>> > 4 10:02:32 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > # [0]PETSC ERROR: >>>> > ------------------------------------------------------------------------ >>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>> > probably memory access out of range >>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>> > # [0]PETSC ERROR: or see >>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS >>>> > X to find memory corruption errors >>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, >>>> > and run >>>> > # [0]PETSC ERROR: to get more information on the crash. >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Signal received >>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>> > 4 10:02:32 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>> > # -------------------------------------------------------------------------- >>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>> > # with errorcode 50162059. >>>> > # >>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > # You may or may not see output from other processes, depending on >>>> > # exactly when Open MPI kills them. >>>> > # -------------------------------------------------------------------------- >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> > CC >>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > CLINKER >>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > TEST >>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>>> > # Running problem 5 >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Error in external library >>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>>> > vit Mon Sep 4 10:02:34 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>> > # [0]PETSC ERROR: -prob_id 5 >>>> > # [0]PETSC ERROR: -tao_smonitor >>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>> > error message to petsc-maint at mcs.anl.gov---------- >>>> > # -------------------------------------------------------------------------- >>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > # with errorcode 126076. >>>> > # >>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > # You may or may not see output from other processes, depending on >>>> > # exactly when Open MPI kills them. >>>> > # -------------------------------------------------------------------------- >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed >>>> > so no diff >>>> > >>>> > # ------------- >>>> > # Summary >>>> > # ------------- >>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > # success 0/2 tests (0.0%) >>>> > # failed 2/2 tests (100.0%) >>>> > # todo 0/2 tests (0.0%) >>>> > # skip 0/2 tests (0.0%) >>>> > # >>>> > # Wall clock time for tests: 4 sec >>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>> > # >>>> > # To rerun failed tests: >>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>> > # >>>> > # Timing summary (actual test time / total CPU time): >>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec >>>> > >>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>> > *$make matlab_ls_test* >>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>>> > -lstdc++ -ldl -o matlab_ls_test >>>> > >>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>> > -tao_smonitor -prob_id 5 -info* >>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 >>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>> > MB108SMEC028.(none) >>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>> > Running problem 5 >>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>> > 94202473157392 max tags = 2147483647 >>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> > [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > [0]PETSC ERROR: Error in external library >>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit >>>> > Mon Sep 4 10:09:56 2023 >>>> > [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>> > [0]PETSC ERROR: -info >>>> > [0]PETSC ERROR: -prob_id 5 >>>> > [0]PETSC ERROR: -tao_smonitor >>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>> > error message to petsc-maint at mcs.anl.gov---------- >>>> > -------------------------------------------------------------------------- >>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > with errorcode 126076. >>>> > >>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > You may or may not see output from other processes, depending on >>>> > exactly when Open MPI kills them. >>>> > >>>> > Please find the attachment for configure.log and make.log files >>>> > >>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: >>>> > >>>> > > To use datafiles in the test suite: >>>> > > >>>> > > cd $HOME >>>> > > git clone https://gitlab.com/petsc/datafiles >>>> > > >>> > > manually with make> >>>> > > >>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles >>>> > > >>>> > > Satish >>>> > > >>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>> > > >>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: >>>> > > > >>>> > > > > Hi Matthew, >>>> > > > > >>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have >>>> > > any >>>> > > > > separate test files to test PETSc alone. Can you please help me how to >>>> > > > > define this DATAFILESPATH? >>>> > > > > >>>> > > > >>>> > > > That test you tried uses a certain matrix. On our machine, we point to >>>> > > this >>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those >>>> > > > matrices, since they are just for testing here. That >>>> > > > is why I suggested just using a different matrix, or running a problem >>>> > > you >>>> > > > care about in IBAMR. >>>> > > > >>>> > > > Thanks, >>>> > > > >>>> > > > Matt >>>> > > > >>>> > > > >>>> > > > > Thanks and regards >>>> > > > > Srinivas. >>>> > > > > >>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > >>>> > > wrote: >>>> > > > > >>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>> > > petsc-users < >>>> > > > >> petsc-users at mcs.anl.gov > wrote: >>>> > > > >> >>>> > > > >>> Hi Sathish, >>>> > > > >>> >>>> > > > >>> Thank you so much for your efforts and the support you are giving me >>>> > > to >>>> > > > >>> sort this out. >>>> > > > >>> >>>> > > > >>> I tried to follow the same procedure which you followed to build >>>> > > Petsc >>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>> > > > >>> >>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> > > > >>> --with-debugging=0 --with-x=0 >>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>> > > > >>> Using python3 for Python >>>> > > > >>> >>>> > > > >>> >>>> > > =============================================================================== >>>> > > > >>> Configuring PETSc to compile on your system >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> > > =============================================================================== >>>> > > > >>> >>>> > > =============================================================================== >>>> > > > >>> It appears you do not have >>>> > > valgrind >>>> > > > >>> installed on your system. >>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>> > > > >>> Or install >>>> > > valgrind-devel or >>>> > > > >>> equivalent using your package manager. >>>> > > > >>> Then rerun ./configure >>>> > > > >>> >>>> > > > >>> >>>> > > =============================================================================== >>>> > > > >>> Compilers: >>>> > > > >>> >>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > -fPIC >>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>> Linkers: >>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > -shared >>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>> > > -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > -shared >>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>> > > -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>> > > > >>> make: >>>> > > > >>> Version: 4.2 >>>> > > > >>> /usr/bin/make >>>> > > > >>> BlasLapack: >>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>> > >

to >>>> > > > >>> control the number of threads >>>> > > > >>> uses 8 byte integers >>>> > > > >>> MPI: >>>> > > > >>> Version: 3 >>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>> > > --oversubscribe >>>> > > > >>> OMPI_VERSION: 4.1.4 >>>> > > > >>> pthread: >>>> > > > >>> cmake: >>>> > > > >>> Version: 3.16.3 >>>> > > > >>> /usr/bin/cmake >>>> > > > >>> regex: >>>> > > > >>> Matlab: >>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>> > > > >>> /usr/local/MATLAB/R2020b >>>> > > > >>> MatlabEngine: >>>> > > > >>> Library: >>>> > > > >>> >>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>> > > -lut >>>> > > > >>> -licudata -licui18n -licuuc >>>> > > > >>> Language used to compile PETSc: C >>>> > > > >>> PETSc: >>>> > > > >>> PETSC_ARCH: linux-opt >>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>> > > > >>> Scalar type: real >>>> > > > >>> Precision: double >>>> > > > >>> Support for __float128 >>>> > > > >>> Integer size: 4 bytes >>>> > > > >>> shared libraries: enabled >>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>> > > > >>> >>>> > > > >>> >>>> > > xxx=========================================================================xxx >>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>>> > > > >>> >>>> > > > >>> >>>> > > xxx=========================================================================xxx >>>> > > > >>> >>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>>> > > > >>> you suggested earlier. >>>> > > > >>> >>>> > > > >>> *$make* >>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > > > >>> In function ?PetscBinaryWrite?: >>>> > > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>> > > > >>> [-Wmaybe-uninitialized] >>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > > > >>> | ^ >>>> > > > >>> >>>> > > > >>> MEX completed successfully. >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> MEX completed successfully. >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> MEX completed successfully. >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > > > >>> In function ?PetscBinaryWrite?: >>>> > > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>> > > > >>> [-Wmaybe-uninitialized] >>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > > > >>> | ^ >>>> > > > >>> >>>> > > > >>> MEX completed successfully. >>>> > > > >>> ========================================= >>>> > > > >>> Now to check if the libraries are working do: >>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>> > > > >>> =============================================== >>>> > > > >>> >>>> > > > >>> *$make test query=requires queryval=matlab* >>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>> > > > >>> -------------------------------------------------------------- >>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>> > > > >>> >>>> > > > >> >>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it >>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>> > > > >> >>>> > > > >> Thanks, >>>> > > > >> >>>> > > > >> Matt >>>> > > > >> >>>> > > > >> >>>> > > > >>> # [0]PETSC ERROR: See >>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>> > > > >>> shooting. >>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>> > > Sun >>>> > > > >>> Sep 3 11:51:03 2023 >>>> > > > >>> # [0]PETSC ERROR: Configure options >>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> > > > >>> # >>>> > > > >>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > > > >>> # with errorcode 113065. >>>> > > > >>> # >>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > > > >>> # You may or may not see output from other processes, depending on >>>> > > > >>> # exactly when Open MPI kills them. >>>> > > > >>> # >>>> > > > >>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> > > > >>> CC >>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > > > >>> CLINKER >>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > > >>> TEST >>>> > > > >>> >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>> > > code: 124 >>>> > > > >>> # Running problem 5 >>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>> > > > >>> -------------------------------------------------------------- >>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > > >>> # [0]PETSC ERROR: See >>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>> > > > >>> shooting. >>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>> > > MB108SMEC028 by >>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>> > > > >>> # [0]PETSC ERROR: Configure options >>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> > > > >>> # >>>> > > > >>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > > > >>> # with errorcode 126076. >>>> > > > >>> # >>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > > > >>> # You may or may not see output from other processes, depending on >>>> > > > >>> # exactly when Open MPI kills them. >>>> > > > >>> # >>>> > > > >>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>> > > > >>> failed so no diff >>>> > > > >>> >>>> > > > >>> # ------------- >>>> > > > >>> # Summary >>>> > > > >>> # ------------- >>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>> # success 0/2 tests (0.0%) >>>> > > > >>> # failed 2/2 tests (100.0%) >>>> > > > >>> # todo 0/2 tests (0.0%) >>>> > > > >>> # skip 0/2 tests (0.0%) >>>> > > > >>> # >>>> > > > >>> # Wall clock time for tests: 3 sec >>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>> > > > >>> # >>>> > > > >>> # To rerun failed tests: >>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>> > > > >>> # >>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / >>>> > > 0.02 sec >>>> > > > >>> >>>> > > > >>> *How to sort out this error?* >>>> > > > >>> >>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>> > > > >>> *$make matlab_ls_test* >>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>> > > -Wwrite-strings >>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>> > > -Wno-strict-aliasing >>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > > > >>> >>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>> > > -lmx >>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>> > > -lmpi_mpifh >>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>> > > -lquadmath >>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>> > > > >>> >>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>> > > > >>> I am sharing the configure.log and make.log files. Please find the >>>> > > > >>> attachment and do the needful. >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> Thanks and regards >>>> > > > >>> Srinivas >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > >>>> > > wrote: >>>> > > > >>> >>>> > > > >>>> Perhaps you can try the following to get additional info - and debug >>>> > > > >>>> >>>> > > > >>>> Satish >>>> > > > >>>> ---------- >>>> > > > >>>> >>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>> > > > >>>> balay at compute-386-07 >>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> > > > >>>> make matlab_ls_test >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>> > > -Wall >>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > -fstack-protector >>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>> > > -Wno-strict-aliasing >>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>>> -I/scratch/balay/petsc/include >>>> > > -I/scratch/balay/petsc/linux-opt/include >>>> > > > >>>> >>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>> > > > >>>> >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>> > > > >>>> >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng >>>> > > -lmex >>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort >>>> > > -lmpi >>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>> > > > >>>> matlab_ls_test >>>> > > > >>>> balay at compute-386-07 >>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>> > > processors >>>> > > > >>>> = 1 >>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>> > > > >>>> compute-386-07.(none) >>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>> > > > >>>> Running problem 5 >>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>> > > > >>>> -2080374784 max tags = 268435455 >>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>> > > > >>>> TestingInitialize >>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>> > > > >>>> TestingInitialize >>>> > > > >>>> 5 >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you >>>> > > - on >>>> > > > >>>> this machine..>>>>> >>>> > > > >>>> >>>> > > > >>>> balay at compute-386-07 >>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> < M A T L A B (R) > >>>> > > > >>>> >>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. >>>> > > > >>>> >>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>> > > > >>>> >>>> > > > >>>> February 17, 2021 >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> To get started, type doc. >>>> > > > >>>> For product information, visit www.mathworks.com . >>>> > > > >>>> >>>> > > > >>>> >> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>> > > > >>>> >>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>>> > > thread >>>> > > > >>>> to petsc-users only] >>>> > > > >>>> > >>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>> > > corresponding >>>> > > > >>>> configure.log, make.log [compressed]? >>>> > > > >>>> > >>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>> > > > >>>> with Matlab-R2021a - and that works: >>>> > > > >>>> > >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>> > > > >>>> > main >>>> > > > >>>> > release >>>> > > > >>>> > * release-3.13 >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>> > > matlab/R2021a >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>> > > > >>>> > >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> > > > >>>> --with-debugging=0 --with-x=0 >>>> > > > >>>> >>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > > > >>>> >>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > > > >>>> > >>>> > > > >>>> > Compilers: >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> > C Compiler: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>> > > -Wall >>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > -fstack-protector >>>> > > > >>>> -fvisibility=hidden -O3 >>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>>> > C++ Compiler: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > -fstack-protector >>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>>> > Fortran Compiler: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>> > > -Wall >>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>>> > Linkers: >>>> > > > >>>> > Shared linker: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>> > > -shared -fPIC >>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>>> > Dynamic linker: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>> > > -shared -fPIC >>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>> > > > >>>> > make: >>>> > > > >>>> > Version: 4.2 >>>> > > > >>>> > /usr/bin/make >>>> > > > >>>> > BlasLapack: >>>> > > > >>>> > Library: >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>> > > > >>>> >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>> > > > >>>> >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>> > > > >>>> -liomp5 -lpthread >>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>> > >

>>>> > > > >>>> to control the number of threads >>>> > > > >>>> > uses 8 byte integers >>>> > > > >>>> > MPI: >>>> > > > >>>> > Version: 4 >>>> > > > >>>> > Includes: >>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>> > > > >>>> > Mpiexec: >>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>> > > > >>>> > pthread: >>>> > > > >>>> > Library: -lpthread >>>> > > > >>>> > cmake: >>>> > > > >>>> > Version: 3.16.3 >>>> > > > >>>> > /usr/bin/cmake >>>> > > > >>>> > regex: >>>> > > > >>>> > Matlab: >>>> > > > >>>> > Includes: >>>> > > > >>>> >>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > > > >>>> > MatlabEngine: >>>> > > > >>>> > Library: >>>> > > > >>>> >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>> > > > >>>> >>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>> > > > >>>> > sowing: >>>> > > > >>>> > Version: 1.1.25 >>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>> > > > >>>> > valgrind: >>>> > > > >>>> > Language used to compile PETSc: C >>>> > > > >>>> > PETSc: >>>> > > > >>>> > PETSC_ARCH: linux-opt >>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>> > > > >>>> > Scalar type: real >>>> > > > >>>> > Precision: double >>>> > > > >>>> > Support for __float128 >>>> > > > >>>> > Integer size: 4 bytes >>>> > > > >>>> > shared libraries: enabled >>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>> > > > >>>> > >>>> > > > >>>> >>>> > > xxx=========================================================================xxx >>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>> > > > >>>> > >>>> > > > >>>> >>>> > > xxx=========================================================================xxx >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > >>>> > > > >>>> >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>> > > > >>>> function ?PetscBinaryWrite?: >>>> > > > >>>> > >>>> > > > >>>> >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>> > > > >>>> [-Wmaybe-uninitialized] >>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>> > > socket\n"); >>>> > > > >>>> > | ^ >>>> > > > >>>> > >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > >>>> > > > >>>> >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>> > > > >>>> function ?PetscBinaryWrite?: >>>> > > > >>>> > >>>> > > > >>>> >>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>> > > > >>>> [-Wmaybe-uninitialized] >>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>> > > socket\n"); >>>> > > > >>>> > | ^ >>>> > > > >>>> > >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > ========================================= >>>> > > > >>>> > Now to check if the libraries are working do: >>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>> > > > >>>> > ========================================= >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>> > > query=requires >>>> > > > >>>> queryval=matlab >>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > > > >>>> > TEST >>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>> > > > >>>> > # ../ex72: >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>> > > > >>>> >>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> > > > >>>> > CC >>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > > > >>>> > CLINKER >>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > > >>>> > TEST >>>> > > > >>>> >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>> > > code: >>>> > > > >>>> 1 >>>> > > > >>>> > # ../matlab_ls_test: >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>> > > > >>>> >>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>> > > Command >>>> > > > >>>> failed so no diff >>>> > > > >>>> > >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>> > > query=requires >>>> > > > >>>> queryval=matlab >>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > > > >>>> > TEST >>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>> > > > >>>> > TEST >>>> > > > >>>> >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> > >>>> > > > >>>> > # ------------- >>>> > > > >>>> > # Summary >>>> > > > >>>> > # ------------- >>>> > > > >>>> > # success 4/4 tests (100.0%) >>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>> > > > >>>> > # >>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 >>>> > > sec >>>> > > > >>>> > # >>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>> > > 7.54 >>>> > > > >>>> sec >>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>> > > > >>>> > >>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>> > > > >>>> configure petsc >>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>> > > > >>>> running make >>>> > > > >>>> > > -j 10 test command I have got the following error message. >>>> > > > >>>> > > >>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>> > > > >>>> code: 124 >>>> > > > >>>> > > # Running problem 5 >>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>> > > > >>>> > > -------------------------------------------------------------- >>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > > >>>> > > # [0]PETSC ERROR: See >>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > > >>>> > > for trouble shooting. >>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>> > > > >>>> MB108SMEC028 by >>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> > > > >>>> --with-debugging=0 >>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > --with-matlab-engine=1 >>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>>> > > >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>> > > -------send >>>> > > > >>>> entire >>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>> > > > >>>> > > # >>>> > > > >>>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > > > >>>> > > # with errorcode 126076. >>>> > > > >>>> > > # >>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>> > > > >>>> processes. >>>> > > > >>>> > > # You may or may not see output from other processes, depending >>>> > > on >>>> > > > >>>> > > # exactly when Open MPI kills them. >>>> > > > >>>> > > # >>>> > > > >>>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>>> > > >>>> > > > >>>> > > I request you to help me to sort out this error. >>>> > > > >>>> > > >>>> > > > >>>> > > Thanks >>>> > > > >>>> > > Srinivas >>>> > > > >>>> > > >>>> > > > >>>> > > >>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>> > > > >>>> mail2amneet at gmail.com > wrote: >>>> > > > >>>> > > >>>> > > > >>>> > > > I think there should be two hyphens in >>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > > >>>> > > > >>>> > > > i.e.: >>>> > > > >>>> > > > >>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > > >>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>> > > > >>>> petsc-users < >>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: >>>> > > > >>>> > > > >>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>> > > > >>>> > > >> >>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>> > > > >>>> wrote: >>>> > > > >>>> > > >> >>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>> > > > >>>> here]. >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> i.e: >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>> > > PETSC_ARCH=linux-opt >>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> --with-matlab-engine=1 >>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> --known-64-bit-blas-indices=1 >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> Satish >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>> > > petsc-users >>>> > > > >>>> wrote: >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> > Hi Satish, >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>> > > balay at mcs.anl.gov > >>>> > > > >>>> wrote: >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > > Also: >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts >>>> > > across >>>> > > > >>>> packages] >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > Satish >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict >>>> > > with >>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>> > > > >>>> -known-64-bit-blas-indices=1 >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>> > > > >>>> matlab - to >>>> > > > >>>> > > >>> have a >>>> > > > >>>> > > >>> > > compatible build >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > Satish >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>> > > > >>>> petsc-users >>>> > > > >>>> > > >>> wrote: >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>> > > > >>>> working. It is >>>> > > > >>>> > > >>> > > showing >>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>> > > > >>>> libmesh and >>>> > > > >>>> > > >>> this is >>>> > > > >>>> > > >>> > > for >>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>> > > > >>>> linking >>>> > > > >>>> > > >>> Matlab >>>> > > > >>>> > > >>> > > with >>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>> > > > >>>> libmesh 1.6.2 >>>> > > > >>>> > > >>> that >>>> > > > >>>> > > >>> > > PETSc >>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>> > > specified. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>> > > > >>>> PETSc and >>>> > > > >>>> > > >>> Matlab >>>> > > > >>>> > > >>> > > is in >>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>> > > geometries >>>> > > > >>>> it is >>>> > > > >>>> > > >>> > > mentioned to >>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>>> > > things >>>> > > > >>>> and ended >>>> > > > >>>> > > >>> up with >>>> > > > >>>> > > >>> > > > > errors. >>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>> > > > >>>> research work. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>> > > > >>>> > > >>> > > > > Srinivas >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>> > > > >>>> mail2amneet at gmail.com > >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for >>>> > > the >>>> > > > >>>> WEC >>>> > > > >>>> > > >>> application. >>>> > > > >>>> > > >>> > > You >>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>> > > > >>>> Matlab. >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>> > > > >>>> libMesh? >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > Thanks, >>>> > > > >>>> > > >>> > > > > > ?Amneet >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>> > > > >>>> 20PHD0548 via >>>> > > > >>>> > > >>> > > petsc-users >>>> > > > >>>> > > >>> > > > > > > wrote: >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > >> Hi, >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>> > > > >>>> occurrences >>>> > > > >>>> > > >>> of >>>> > > > >>>> > > >>> > > "-lut >>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make >>>> > > test" >>>> > > > >>>> got the >>>> > > > >>>> > > >>> > > following >>>> > > > >>>> > > >>> > > > > >> errors >>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>> > > > >>>> > > >>> > > > > >> TEST >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > > >>> > > > > >> not ok >>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> > > > >>>> > > >>> Error >>>> > > > >>>> > > >>> > > code: 124 >>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>> > > Message >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> -------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>> > > on >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>> > > > >>>> > > >>> > > > > >> >>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > > >>>> for >>>> > > > >>>> > > >>> trouble >>>> > > > >>>> > > >>> > > > > >> shooting. >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>> > > Aug >>>> > > > >>>> 01, 2020 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>> > > linux-debug >>>> > > > >>>> named >>>> > > > >>>> > > >>> > > MB108SMEC028 >>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > > >>>> > > >>> > > > > >> >>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > > >>>> > > >>> --with-debugging=1 >>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>> > > > >>>> --with-x=0 >>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>> > > line >>>> > > > >>>> 67 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>> > > > >>>> Message >>>> > > > >>>> > > >>> -------send >>>> > > > >>>> > > >>> > > entire >>>> > > > >>>> > > >>> > > > > >> error message to >>>> > > petsc-maint at mcs.anl.gov---------- >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>> > > > >>>> > > >>> MPI_COMM_SELF >>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>> > > kill >>>> > > > >>>> all MPI >>>> > > > >>>> > > >>> > > processes. >>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>> > > processes, >>>> > > > >>>> > > >>> depending on >>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> ok >>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> # SKIP >>>> > > > >>>> > > >>> Command >>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>> > > > >>>> > > >>> > > > > >> TEST >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > > >>> > > > > >> not ok >>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> > > > >>>> > > >>> Error >>>> > > > >>>> > > >>> > > code: 124 >>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>> > > Message >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> -------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>> > > on >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>> > > > >>>> > > >>> > > > > >> >>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > > >>>> for >>>> > > > >>>> > > >>> trouble >>>> > > > >>>> > > >>> > > > > >> shooting. >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>> > > Aug >>>> > > > >>>> 01, 2020 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>> > > linux-opt >>>> > > > >>>> named >>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > > >>>> > > >>> > > > > >> >>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>> > > > >>>> --PETSC_ARCH=linux-opt >>>> > > > >>>> > > >>> > > --with-debugging=0 >>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>> > > > >>>> --download-fblaslapack=1 >>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>> > > line >>>> > > > >>>> 67 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>> > > > >>>> Message >>>> > > > >>>> > > >>> -------send >>>> > > > >>>> > > >>> > > entire >>>> > > > >>>> > > >>> > > > > >> error message to >>>> > > petsc-maint at mcs.anl.gov---------- >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>> > > > >>>> > > >>> MPI_COMM_SELF >>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>> > > kill >>>> > > > >>>> all MPI >>>> > > > >>>> > > >>> > > processes. >>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>> > > processes, >>>> > > > >>>> > > >>> depending on >>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> ok >>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> # SKIP >>>> > > > >>>> > > >>> Command >>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>> > > version. I >>>> > > > >>>> am >>>> > > > >>>> > > >>> sharing the >>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>> > > > >>>> petsc >>>> > > > >>>> > > >>> 3.17.5. >>>> > > > >>>> > > >>> > > Please find >>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>> > > > >>>> > > >>> > > > > >> Srinivas >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>> > > > >>>> > > >>> configure.log/make.log >>>> > > > >>>> > > >>> > > for >>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> >>>> >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>> > > > >>>> > > >>> > > > > >>> Includes: >>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>> > > > >>>> > > >>> > > > > >>> Library: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > -leng >>>> > > > >>>> -lmex >>>> > > > >>>> > > >>> -lmx >>>> > > > >>>> > > >>> > > -lmat -lut >>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are >>>> > > seeing: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> >>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> >>> >>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>> > > > >>>> > > >>> > > > > >>> Includes: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>> > > > >>>> > > >>> > > > > >>> Executable: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>> > > > >>>> > > >>> > > > > >>> mex: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>> > > > >>>> > > >>> > > > > >>> matlab: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>> > > > >>>> > > >>> > > > > >>> <<< >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>> > > > >>>> preset here. >>>> > > > >>>> > > >>> This >>>> > > > >>>> > > >>> > > might >>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> You can: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> - edit >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>> > > > >>>> > > >>> > > and >>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>> > > -licui18n >>>> > > > >>>> -licuuc" >>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>> > > '/home/vit/sfw/petsc/3.13.4' >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> Satish >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>> > > via >>>> > > > >>>> > > >>> petsc-users >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>> > > > >>>> petsc3.13.4 with >>>> > > > >>>> > > >>> > > matlab and >>>> > > > >>>> > > >>> > > > > >>> also >>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>> > > > >>>> petsc3.17.5 and >>>> > > > >>>> > > >>> matlab. >>>> > > > >>>> > > >>> > > > > >>> Building >>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>> > > successfully. >>>> > > > >>>> But >>>> > > > >>>> > > >>> libmesh is >>>> > > > >>>> > > >>> > > not >>>> > > > >>>> > > >>> > > > > >>> able to >>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>> > > > >>>> > > >>> > > > > >>> wrote: >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>> > > > >>>> petsc-3.13 and >>>> > > > >>>> > > >>> 3.17 [or >>>> > > > >>>> > > >>> > > 3.19]. >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>> > > friendly to >>>> > > > >>>> mailing >>>> > > > >>>> > > >>> list - >>>> > > > >>>> > > >>> > > or >>>> > > > >>>> > > >>> > > > > >>> send >>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or >>>> > > 3.19?] >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>> > > 20PHD0548 >>>> > > > >>>> via >>>> > > > >>>> > > >>> petsc-users >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>>> > > building >>>> > > > >>>> > > >>> petsc-3.13.4 >>>> > > > >>>> > > >>> > > with >>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the >>>> > > needful. >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>> > > > >>>> SRINIVAS >>>> > > > >>>> > > >>> 20PHD0548 < >>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > >>>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>> > > building >>>> > > > >>>> of >>>> > > > >>>> > > >>> libmesh, the >>>> > > > >>>> > > >>> > > error >>>> > > > >>>> > > >>> > > > > >>> shows >>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>> > > > >>>> Balay < >>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > >>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>> > > > >>>> petsc-3.17 >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>> > > > >>>> 20PHD0548 via >>>> > > > >>>> > > >>> > > petsc-users >>>> > > > >>>> > > >>> > > > > >>> wrote: >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>> > > > >>>> working on >>>> > > > >>>> > > >>> the >>>> > > > >>>> > > >>> > > > > >>> simulation >>>> > > > >>>> > > >>> > > > > >>> > > using >>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the >>>> > > PETSc, >>>> > > > >>>> using the >>>> > > > >>>> > > >>> > > following >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEnginePut' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGet' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEnginePut' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGet' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGet' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineCreate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineDestroy' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>> > > > >>>> status >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished >>>> > > jobs.... >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>>> > > > >>>> Institute of >>>> > > > >>>> > > >>> > > Technology. >>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain legally >>>> > > > >>>> protected >>>> > > > >>>> > > >>> > > confidential or >>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>>> > > > >>>> Technology?. >>>> > > > >>>> > > >>> If >>>> > > > >>>> > > >>> > > you are >>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should not >>>> > > > >>>> disseminate, >>>> > > > >>>> > > >>> distribute >>>> > > > >>>> > > >>> > > or copy >>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately >>>> > > > >>>> and destroy >>>> > > > >>>> > > >>> all >>>> > > > >>>> > > >>> > > copies of >>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you have >>>> > > > >>>> received this >>>> > > > >>>> > > >>> email >>>> > > > >>>> > > >>> > > in error, >>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by reply email >>>> > > and >>>> > > > >>>> delete >>>> > > > >>>> > > >>> the >>>> > > > >>>> > > >>> > > original >>>> > > > >>>> > > >>> > > > > >> email and any backup copies without reading >>>> > > them.* >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >> >>>> > > > >>>> > > >> >>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>>> > > > >>>> Technology. >>>> > > > >>>> > > >> The contents of this email may contain legally protected >>>> > > > >>>> confidential or >>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>> > > Technology?. If >>>> > > > >>>> you are >>>> > > > >>>> > > >> not the intended recipient, you should not disseminate, >>>> > > > >>>> distribute or copy >>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy >>>> > > > >>>> all copies of >>>> > > > >>>> > > >> this message and any attachments. If you have received this >>>> > > > >>>> email in error, >>>> > > > >>>> > > >> please promptly notify the sender by reply email and delete >>>> > > the >>>> > > > >>>> original >>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>> > > > >>>> > > >> >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > -- >>>> > > > >>>> > > > --Amneet >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > >>>> > > > >>>> > > >>>> > > > >>>> >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>> > > Technology. >>>> > > > >>> The contents of this email may contain legally protected >>>> > > confidential or >>>> > > > >>> privileged information of ?Vellore Institute of Technology?. If you >>>> > > are >>>> > > > >>> not the intended recipient, you should not disseminate, distribute >>>> > > or copy >>>> > > > >>> this e-mail. Please notify the sender immediately and destroy all >>>> > > copies of >>>> > > > >>> this message and any attachments. If you have received this email in >>>> > > error, >>>> > > > >>> please promptly notify the sender by reply email and delete the >>>> > > original >>>> > > > >>> email and any backup copies without reading them.* >>>> > > > >>> >>>> > > > >> >>>> > > > >> >>>> > > > >> -- >>>> > > > >> What most experimenters take for granted before they begin their >>>> > > > >> experiments is infinitely more interesting than any results to which >>>> > > their >>>> > > > >> experiments lead. >>>> > > > >> -- Norbert Wiener >>>> > > > >> >>>> > > > >> https://www.cse.buffalo.edu/~knepley/ >>>> > > > >> >>>> > > > >> >>>> > > > > >>>> > > > > >>>> > > > > *Disclaimer:This message was sent from Vellore Institute of Technology. >>>> > > > > The contents of this email may contain legally protected confidential >>>> > > or >>>> > > > > privileged information of ?Vellore Institute of Technology?. If you >>>> > > are >>>> > > > > not the intended recipient, you should not disseminate, distribute or >>>> > > copy >>>> > > > > this e-mail. Please notify the sender immediately and destroy all >>>> > > copies of >>>> > > > > this message and any attachments. If you have received this email in >>>> > > error, >>>> > > > > please promptly notify the sender by reply email and delete the >>>> > > original >>>> > > > > email and any backup copies without reading them.* >>>> > > > > >>>> > > > >>>> > > > >>>> > > > >>>> > > >>>> > >>>> > >>> >>> Disclaimer: >>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >> >> >> -- >> --Amneet >> >> >> > > Disclaimer: > This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Tue Sep 5 11:27:06 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Tue, 5 Sep 2023 21:57:06 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> Message-ID: I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); I got the same errors for petsc 3.17.5 *make all* CC linux-opt/obj/sys/classes/matlabengine/matlab.o CLINKER linux-opt/lib/libpetsc.so.3.17.5 BEGINNING TO COMPILE MATLAB INTERFACE Building with 'gcc'. /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. MEX completed successfully. Building with 'gcc'. /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); | ^ MEX completed successfully. ========================================= ========================================= Now to check if the libraries are working do: make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check *make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/* Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- # [0]PETSC ERROR: Error in external library # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 # [0]PETSC ERROR: PETSc Option Table entries: # [0]PETSC ERROR: -check_pointer_intensity 0 # [0]PETSC ERROR: -error_output_stdout # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 # [0]PETSC ERROR: -malloc_dump # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab # [0]PETSC ERROR: -pc_type lu # [0]PETSC ERROR: -use_gpu_aware_mpi 0 # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- # -------------------------------------------------------------------------- # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD # with errorcode 85. # # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. # You may or may not see output from other processes, depending on # exactly when Open MPI kills them. # -------------------------------------------------------------------------- ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff # FAILED ksp_ksp_tutorials-ex72_12 # # To rerun failed tests: # /usr/bin/make -f gmakefile test test-fail=1 Thanks and regards Srinivas On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: > > The error is occuring during > > e->ep = engOpen(buffer); > > Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 > -nodisplay -nosplash from your terminal shell worked we have to assume the > problem is occuring when engOpen() is attempting to connect the stdout and > stdin from the Matlab session that is launched to the executable. > > You can try the following. In 3.17.5 edit the > file src/sys/classes/matlabengine/matlab.c and locate the line > > e->ep = engOpen(buffer); > > replace it with > > e->ep = engOpen(""); > > Now in the PETSc directory do make all (it should recompile one file) and > then run the > > make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ > > again > > > > > > On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < > petsc-users at mcs.anl.gov> wrote: > > Hi Amneeth, > > I think the errors are different with petsc 3.17.5 > > *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx > --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1* > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > The version of PETSc you are using is out-of-date, we recommend updating > to the new release > Available Version: 3.19.5 Installed Version: 3.17.5 > https://petsc.org/release/download/ > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > ============================================================================================= > Configuring PETSc to compile on your system > > > ============================================================================================= > Compilers: > > C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector > -fvisibility=hidden -O3 > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch > -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC > Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall > -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > Linkers: > Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector > -fvisibility=hidden -O3 > Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector > -fvisibility=hidden -O3 > Libraries linked against: -lquadmath -lstdc++ -ldl > BlasLapack: > Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to > control the number of threads > uses 8 byte integers > MPI: > Version: 3 > mpiexec: /usr/bin/mpiexec > Implementation: openmpi > OMPI_VERSION: 4.0.3 > pthread: > cmake: > Version: 3.16.3 > /usr/bin/cmake > regex: > Matlab: > Includes: -I/usr/local/MATLAB/R2020b/extern/include > /usr/local/MATLAB/R2020b > MatlabEngine: > Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat > -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher > -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c > Language used to compile PETSc: C > PETSc: > PETSC_ARCH: linux-opt > PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 > Prefix: > Scalar type: real > Precision: double > Support for __float128 > Integer size: 4 bytes > Single library: yes > Shared libraries: yes > Memory alignment from malloc(): 16 bytes > Using GNU make: /usr/bin/make > > xxx=========================================================================xxx > Configure stage complete. Now build PETSc libraries with: > make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all > > xxx=========================================================================xxx > > *$make* > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > CLINKER linux-opt/lib/libpetsc.so.3.17.5 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check > > *$make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/* > /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py > --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt > --testdir=./linux-opt/tests > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab > query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine with > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep > 5 10:15:57 2023 > # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc > --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 > FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 > # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 > # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at > /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > # [0]PETSC ERROR: #5 MatLUFactorNumeric() at > /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > # [0]PETSC ERROR: #6 PCSetUp_LU() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > # [0]PETSC ERROR: #7 PCSetUp() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > # [0]PETSC ERROR: #8 KSPSetUp() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > # [0]PETSC ERROR: #9 main() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -check_pointer_intensity 0 > # [0]PETSC ERROR: -error_output_stdout > # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > # [0]PETSC ERROR: -malloc_dump > # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > # [0]PETSC ERROR: -pc_type lu > # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # > -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > # with errorcode 85. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # > -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > # FAILED ksp_ksp_tutorials-ex72_12 > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > > To get the info of the error there is no specific probe id reported. > > How to check error info and proceed further? > > Thanks and regards > Srinivas > > On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: > >> Do you get similar errors with petsc 3.17.5 using the new configure >> options that Satish mentioned? >> >> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users >> wrote: >> >>> Sorry for missing that. >>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>> >>> < M A T L A B (R) > >>> Copyright 1984-2020 The MathWorks, Inc. >>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>> November 23, 2020 >>> >>> >>> To get started, type doc. >>> For product information, visit www.mathworks.com. >>> >>> Thanks and regards >>> Srinivas >>> >>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay wrote: >>> >>>> You are missing one more step: >>>> >>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> >>>> No run matlab manually on "MB108SMEC028" with the command >>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>> >>>> Does this work for you? As the message indicates this command is >>>> invoked by "matlab_ls_test" - and that is failing. >>>> >>>> Satish >>>> >>>> >>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>> >>>> > Hi Sathish, >>>> > >>>> > I tried the following procedure >>>> > >>>> > *$make * >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>> > Building with 'gcc'. >>>> > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > In function ?PetscBinaryWrite?: >>>> > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > warning: ?err? may be used uninitialized in this function >>>> > [-Wmaybe-uninitialized] >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > | ^ >>>> > >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > MEX completed successfully. >>>> > Building with 'gcc'. >>>> > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > In function ?PetscBinaryWrite?: >>>> > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > warning: ?err? may be used uninitialized in this function >>>> > [-Wmaybe-uninitialized] >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> > | ^ >>>> > >>>> > MEX completed successfully. >>>> > ========================================= >>>> > Now to check if the libraries are working do: >>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>> > >>>> > *$make test query=requires queryval=matlab >>>> > DATAFILESPATH=/home/vit/datafiles/* >>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>> > query=requires >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Error in external library >>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > # [0]PETSC ERROR: See >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>> Mon Sep >>>> > 4 10:02:32 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>> > # [0]PETSC ERROR: >>>> > # [0]PETSC ERROR: See >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>> Mon Sep >>>> > 4 10:02:32 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > # [0]PETSC ERROR: >>>> > >>>> ------------------------------------------------------------------------ >>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>> Violation, >>>> > probably memory access out of range >>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>> -on_error_attach_debugger >>>> > # [0]PETSC ERROR: or see >>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple >>>> Mac OS >>>> > X to find memory corruption errors >>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>>> link, >>>> > and run >>>> > # [0]PETSC ERROR: to get more information on the crash. >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Signal received >>>> > # [0]PETSC ERROR: See >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>> Mon Sep >>>> > 4 10:02:32 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>> > # >>>> -------------------------------------------------------------------------- >>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>> > # with errorcode 50162059. >>>> > # >>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > # You may or may not see output from other processes, depending on >>>> > # exactly when Open MPI kills them. >>>> > # >>>> -------------------------------------------------------------------------- >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> > CC >>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > CLINKER >>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > TEST >>>> > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: >>>> 124 >>>> > # Running problem 5 >>>> > # [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > # [0]PETSC ERROR: Error in external library >>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > # [0]PETSC ERROR: See >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 >>>> by >>>> > vit Mon Sep 4 10:02:34 2023 >>>> > # [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>> > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>> > # [0]PETSC ERROR: -prob_id 5 >>>> > # [0]PETSC ERROR: -tao_smonitor >>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> entire >>>> > error message to petsc-maint at mcs.anl.gov---------- >>>> > # >>>> -------------------------------------------------------------------------- >>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > # with errorcode 126076. >>>> > # >>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > # You may or may not see output from other processes, depending on >>>> > # exactly when Open MPI kills them. >>>> > # >>>> -------------------------------------------------------------------------- >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>> failed >>>> > so no diff >>>> > >>>> > # ------------- >>>> > # Summary >>>> > # ------------- >>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > # success 0/2 tests (0.0%) >>>> > # failed 2/2 tests (100.0%) >>>> > # todo 0/2 tests (0.0%) >>>> > # skip 0/2 tests (0.0%) >>>> > # >>>> > # Wall clock time for tests: 4 sec >>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>> > # >>>> > # To rerun failed tests: >>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>> > # >>>> > # Timing summary (actual test time / total CPU time): >>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 >>>> sec >>>> > >>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>> > *$make matlab_ls_test* >>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>> -Wwrite-strings >>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>> -Wno-strict-aliasing >>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>> -lmpi_mpifh >>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>> -lquadmath >>>> > -lstdc++ -ldl -o matlab_ls_test >>>> > >>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>> > -tao_smonitor -prob_id 5 -info* >>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>> processors = 1 >>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>> > MB108SMEC028.(none) >>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>> > Running problem 5 >>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>> > 94202473157392 max tags = 2147483647 >>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> > [0]PETSC ERROR: --------------------- Error Message >>>> > -------------------------------------------------------------- >>>> > [0]PETSC ERROR: Error in external library >>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > [0]PETSC ERROR: See >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > for trouble shooting. >>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by >>>> vit >>>> > Mon Sep 4 10:09:56 2023 >>>> > [0]PETSC ERROR: Configure options >>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>> > [0]PETSC ERROR: -info >>>> > [0]PETSC ERROR: -prob_id 5 >>>> > [0]PETSC ERROR: -tao_smonitor >>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>> entire >>>> > error message to petsc-maint at mcs.anl.gov---------- >>>> > >>>> -------------------------------------------------------------------------- >>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>> > with errorcode 126076. >>>> > >>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> > You may or may not see output from other processes, depending on >>>> > exactly when Open MPI kills them. >>>> > >>>> > Please find the attachment for configure.log and make.log files >>>> > >>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>> wrote: >>>> > >>>> > > To use datafiles in the test suite: >>>> > > >>>> > > cd $HOME >>>> > > git clone https://gitlab.com/petsc/datafiles >>>> > > >>> or set >>>> > > manually with make> >>>> > > >>>> > > make test query=requires queryval=matlab >>>> DATAFILESPATH=$HOME/datafiles >>>> > > >>>> > > Satish >>>> > > >>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>> > > >>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>> > > > >>>> > > > > Hi Matthew, >>>> > > > > >>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not >>>> have >>>> > > any >>>> > > > > separate test files to test PETSc alone. Can you please help me >>>> how to >>>> > > > > define this DATAFILESPATH? >>>> > > > > >>>> > > > >>>> > > > That test you tried uses a certain matrix. On our machine, we >>>> point to >>>> > > this >>>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>>> have those >>>> > > > matrices, since they are just for testing here. That >>>> > > > is why I suggested just using a different matrix, or running a >>>> problem >>>> > > you >>>> > > > care about in IBAMR. >>>> > > > >>>> > > > Thanks, >>>> > > > >>>> > > > Matt >>>> > > > >>>> > > > >>>> > > > > Thanks and regards >>>> > > > > Srinivas. >>>> > > > > >>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>> knepley at gmail.com> >>>> > > wrote: >>>> > > > > >>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>> > > petsc-users < >>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>> > > > >> >>>> > > > >>> Hi Sathish, >>>> > > > >>> >>>> > > > >>> Thank you so much for your efforts and the support you are >>>> giving me >>>> > > to >>>> > > > >>> sort this out. >>>> > > > >>> >>>> > > > >>> I tried to follow the same procedure which you followed to >>>> build >>>> > > Petsc >>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>> > > > >>> >>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>> PETSC_ARCH=linux-opt >>>> > > > >>> --with-debugging=0 --with-x=0 >>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>> > > > >>> Using python3 for Python >>>> > > > >>> >>>> > > > >>> >>>> > > >>>> =============================================================================== >>>> > > > >>> Configuring PETSc to compile on your system >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> >>>> > > >>>> =============================================================================== >>>> > > > >>> >>>> > > >>>> =============================================================================== >>>> > > > >>> It appears you do not >>>> have >>>> > > valgrind >>>> > > > >>> installed on your system. >>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>> > > > >>> Or install >>>> > > valgrind-devel or >>>> > > > >>> equivalent using your package manager. >>>> > > > >>> Then rerun ./configure >>>> > > > >>> >>>> > > > >>> >>>> > > >>>> =============================================================================== >>>> > > > >>> Compilers: >>>> > > > >>> >>>> > > > >>> C Compiler: >>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > -fPIC >>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>> -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>> C++ Compiler: >>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>> -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>> > > > >>> Fortran Compiler: >>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument >>>> -O3 >>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>> Linkers: >>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > -shared >>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>> > > -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> Dynamic linker: >>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > -shared >>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>> > > -Wno-unknown-pragmas >>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>> > > > >>> make: >>>> > > > >>> Version: 4.2 >>>> > > > >>> /usr/bin/make >>>> > > > >>> BlasLapack: >>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>> -omp_num_threads >>>> > >

to >>>> > > > >>> control the number of threads >>>> > > > >>> uses 8 byte integers >>>> > > > >>> MPI: >>>> > > > >>> Version: 3 >>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>> > > --oversubscribe >>>> > > > >>> OMPI_VERSION: 4.1.4 >>>> > > > >>> pthread: >>>> > > > >>> cmake: >>>> > > > >>> Version: 3.16.3 >>>> > > > >>> /usr/bin/cmake >>>> > > > >>> regex: >>>> > > > >>> Matlab: >>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>> > > > >>> /usr/local/MATLAB/R2020b >>>> > > > >>> MatlabEngine: >>>> > > > >>> Library: >>>> > > > >>> >>>> > > >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>> -lmx -lmat >>>> > > -lut >>>> > > > >>> -licudata -licui18n -licuuc >>>> > > > >>> Language used to compile PETSc: C >>>> > > > >>> PETSc: >>>> > > > >>> PETSC_ARCH: linux-opt >>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>> > > > >>> Scalar type: real >>>> > > > >>> Precision: double >>>> > > > >>> Support for __float128 >>>> > > > >>> Integer size: 4 bytes >>>> > > > >>> shared libraries: enabled >>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>> > > > >>> >>>> > > > >>> >>>> > > >>>> xxx=========================================================================xxx >>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>> PETSC_ARCH=linux-opt all >>>> > > > >>> >>>> > > > >>> >>>> > > >>>> xxx=========================================================================xxx >>>> > > > >>> >>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>>> -licuuc as >>>> > > > >>> you suggested earlier. >>>> > > > >>> >>>> > > > >>> *$make* >>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > > > >>> In function ?PetscBinaryWrite?: >>>> > > > >>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>> > > > >>> [-Wmaybe-uninitialized] >>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>> socket\n"); >>>> > > > >>> | ^ >>>> > > > >>> >>>> > > > >>> MEX completed successfully. >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> MEX completed successfully. >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> MEX completed successfully. >>>> > > > >>> Building with 'gcc'. >>>> > > > >>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> > > > >>> In function ?PetscBinaryWrite?: >>>> > > > >>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>> > > > >>> [-Wmaybe-uninitialized] >>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>> socket\n"); >>>> > > > >>> | ^ >>>> > > > >>> >>>> > > > >>> MEX completed successfully. >>>> > > > >>> ========================================= >>>> > > > >>> Now to check if the libraries are working do: >>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>> PETSC_ARCH=linux-opt check >>>> > > > >>> =============================================== >>>> > > > >>> >>>> > > > >>> *$make test query=requires queryval=matlab* >>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > > > >>> TEST >>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>> > > > >>> -------------------------------------------------------------- >>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>> > > > >>> >>>> > > > >> >>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, >>>> so it >>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>> > > > >> >>>> > > > >> Thanks, >>>> > > > >> >>>> > > > >> Matt >>>> > > > >> >>>> > > > >> >>>> > > > >>> # [0]PETSC ERROR: See >>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>> trouble >>>> > > > >>> shooting. >>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 >>>> by vit >>>> > > Sun >>>> > > > >>> Sep 3 11:51:03 2023 >>>> > > > >>> # [0]PETSC ERROR: Configure options >>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> --with-debugging=0 >>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line >>>> 1444 in >>>> > > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>> > > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>> > > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>> -------send >>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> > > > >>> # >>>> > > > >>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>> MPI_COMM_SELF >>>> > > > >>> # with errorcode 113065. >>>> > > > >>> # >>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>> processes. >>>> > > > >>> # You may or may not see output from other processes, >>>> depending on >>>> > > > >>> # exactly when Open MPI kills them. >>>> > > > >>> # >>>> > > > >>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> > > > >>> CC >>>> > > > >>> >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > > > >>> CLINKER >>>> > > > >>> >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > > >>> TEST >>>> > > > >>> >>>> > > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> Error >>>> > > code: 124 >>>> > > > >>> # Running problem 5 >>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>> > > > >>> -------------------------------------------------------------- >>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > > >>> # [0]PETSC ERROR: See >>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>> trouble >>>> > > > >>> shooting. >>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>> > > MB108SMEC028 by >>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>> > > > >>> # [0]PETSC ERROR: Configure options >>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> --with-debugging=0 >>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > > > >>> >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>> -------send >>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> > > > >>> # >>>> > > > >>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>> MPI_COMM_SELF >>>> > > > >>> # with errorcode 126076. >>>> > > > >>> # >>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>> processes. >>>> > > > >>> # You may or may not see output from other processes, >>>> depending on >>>> > > > >>> # exactly when Open MPI kills them. >>>> > > > >>> # >>>> > > > >>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>> Command >>>> > > > >>> failed so no diff >>>> > > > >>> >>>> > > > >>> # ------------- >>>> > > > >>> # Summary >>>> > > > >>> # ------------- >>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>> # success 0/2 tests (0.0%) >>>> > > > >>> # failed 2/2 tests (100.0%) >>>> > > > >>> # todo 0/2 tests (0.0%) >>>> > > > >>> # skip 0/2 tests (0.0%) >>>> > > > >>> # >>>> > > > >>> # Wall clock time for tests: 3 sec >>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>> > > > >>> # >>>> > > > >>> # To rerun failed tests: >>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>> > > > >>> # >>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 >>>> sec / >>>> > > 0.02 sec >>>> > > > >>> >>>> > > > >>> *How to sort out this error?* >>>> > > > >>> >>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>> > > > >>> *$make matlab_ls_test* >>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>> > > -Wwrite-strings >>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>> > > -Wno-strict-aliasing >>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>> matlab_ls_test.c >>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> > > > >>> >>>> > > >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>> -lmex >>>> > > -lmx >>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>> > > -lmpi_mpifh >>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>> -lpthread >>>> > > -lquadmath >>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>> > > > >>> >>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>> find the >>>> > > > >>> attachment and do the needful. >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> Thanks and regards >>>> > > > >>> Srinivas >>>> > > > >>> >>>> > > > >>> >>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>> balay at mcs.anl.gov> >>>> > > wrote: >>>> > > > >>> >>>> > > > >>>> Perhaps you can try the following to get additional info - >>>> and debug >>>> > > > >>>> >>>> > > > >>>> Satish >>>> > > > >>>> ---------- >>>> > > > >>>> >>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>> > > > >>>> balay at compute-386-07 >>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> > > > >>>> make matlab_ls_test >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>> -fPIC >>>> > > -Wall >>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > -fstack-protector >>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>> > > -Wno-strict-aliasing >>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>> -O3 >>>> > > > >>>> -I/scratch/balay/petsc/include >>>> > > -I/scratch/balay/petsc/linux-opt/include >>>> > > > >>>> >>>> > > >>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>> > > > >>>> matlab_ls_test.c >>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>> > > > >>>> >>>> > > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> >>>> > > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>> > > > >>>> >>>> > > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread >>>> -lm -leng >>>> > > -lmex >>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>>> -lmpifort >>>> > > -lmpi >>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>>> -ldl -o >>>> > > > >>>> matlab_ls_test >>>> > > > >>>> balay at compute-386-07 >>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>> ./matlab_ls_test >>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>> > > processors >>>> > > > >>>> = 1 >>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>> > > > >>>> compute-386-07.(none) >>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>> > > > >>>> Running problem 5 >>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>> 1140850689 >>>> > > > >>>> -2080374784 max tags = 268435455 >>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>> command >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>> > > > >>>> TestingInitialize >>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>> string: >>>> > > > >>>> TestingInitialize >>>> > > > >>>> 5 >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> <<<< Now verify if the above matlab command actually works >>>> for you >>>> > > - on >>>> > > > >>>> this machine..>>>>> >>>> > > > >>>> >>>> > > > >>>> balay at compute-386-07 >>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> < M A T L A B (R) > >>>> > > > >>>> >>>> > > > >>>> Copyright 1984-2021 The MathWorks, >>>> Inc. >>>> > > > >>>> >>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>> (glnxa64) >>>> > > > >>>> >>>> > > > >>>> February 17, 2021 >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> To get started, type doc. >>>> > > > >>>> For product information, visit www.mathworks.com. >>>> > > > >>>> >>>> > > > >>>> >> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>> > > > >>>> >>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>> [reverting >>>> > > thread >>>> > > > >>>> to petsc-users only] >>>> > > > >>>> > >>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>> > > corresponding >>>> > > > >>>> configure.log, make.log [compressed]? >>>> > > > >>>> > >>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>> Ubuntu-20.04, >>>> > > > >>>> with Matlab-R2021a - and that works: >>>> > > > >>>> > >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>> > > > >>>> > main >>>> > > > >>>> > release >>>> > > > >>>> > * release-3.13 >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>> > > matlab/R2021a >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>> > > > >>>> >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>> PETSC_ARCH=linux-opt >>>> > > > >>>> --with-debugging=0 --with-x=0 >>>> > > > >>>> >>>> > > >>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > > > >>>> >>>> > > >>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> > > > >>>> > >>>> > > > >>>> > Compilers: >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> > C Compiler: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>> -fPIC >>>> > > -Wall >>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > -fstack-protector >>>> > > > >>>> -fvisibility=hidden -O3 >>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>>> > C++ Compiler: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx >>>> -Wall >>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>> > > -fstack-protector >>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> > > > >>>> > Fortran Compiler: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 >>>> -fPIC >>>> > > -Wall >>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>> 9.4.0 >>>> > > > >>>> > Linkers: >>>> > > > >>>> > Shared linker: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>> > > -shared -fPIC >>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>> -Wno-unknown-pragmas >>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>>> > Dynamic linker: >>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>> > > -shared -fPIC >>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>> -Wno-unknown-pragmas >>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>> > > > >>>> > make: >>>> > > > >>>> > Version: 4.2 >>>> > > > >>>> > /usr/bin/make >>>> > > > >>>> > BlasLapack: >>>> > > > >>>> > Library: >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>> > > > >>>> >>>> > > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>> > > > >>>> >>>> > > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>> > > > >>>> -liomp5 -lpthread >>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>> -omp_num_threads >>>> > >

>>>> > > > >>>> to control the number of threads >>>> > > > >>>> > uses 8 byte integers >>>> > > > >>>> > MPI: >>>> > > > >>>> > Version: 4 >>>> > > > >>>> > Includes: >>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>> > > > >>>> > Mpiexec: >>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>> > > > >>>> > pthread: >>>> > > > >>>> > Library: -lpthread >>>> > > > >>>> > cmake: >>>> > > > >>>> > Version: 3.16.3 >>>> > > > >>>> > /usr/bin/cmake >>>> > > > >>>> > regex: >>>> > > > >>>> > Matlab: >>>> > > > >>>> > Includes: >>>> > > > >>>> >>>> > > >>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>> > > > >>>> > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>> > > > >>>> > MatlabEngine: >>>> > > > >>>> > Library: >>>> > > > >>>> >>>> > > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> >>>> > > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>> > > > >>>> >>>> > > >>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>> > > > >>>> > sowing: >>>> > > > >>>> > Version: 1.1.25 >>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>> > > > >>>> > valgrind: >>>> > > > >>>> > Language used to compile PETSc: C >>>> > > > >>>> > PETSc: >>>> > > > >>>> > PETSC_ARCH: linux-opt >>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>> > > > >>>> > Scalar type: real >>>> > > > >>>> > Precision: double >>>> > > > >>>> > Support for __float128 >>>> > > > >>>> > Integer size: 4 bytes >>>> > > > >>>> > shared libraries: enabled >>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> xxx=========================================================================xxx >>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>> PETSC_ARCH=linux-opt all >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> xxx=========================================================================xxx >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>> > > > >>>> function ?PetscBinaryWrite?: >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>> > > > >>>> [-Wmaybe-uninitialized] >>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>> > > socket\n"); >>>> > > > >>>> > | ^ >>>> > > > >>>> > >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > Building with 'gcc'. >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>> > > > >>>> function ?PetscBinaryWrite?: >>>> > > > >>>> > >>>> > > > >>>> >>>> > > >>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>> > > > >>>> [-Wmaybe-uninitialized] >>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>> > > socket\n"); >>>> > > > >>>> > | ^ >>>> > > > >>>> > >>>> > > > >>>> > MEX completed successfully. >>>> > > > >>>> > ========================================= >>>> > > > >>>> > Now to check if the libraries are working do: >>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt >>>> check >>>> > > > >>>> > ========================================= >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>> > > query=requires >>>> > > > >>>> queryval=matlab >>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> > > > >>>> > TEST >>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>> > > > >>>> > # ../ex72: >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>> > > > >>>> >>>> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>> diff >>>> > > > >>>> > CC >>>> > > > >>>> >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>> > > > >>>> > CLINKER >>>> > > > >>>> >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > > >>>> > TEST >>>> > > > >>>> >>>> > > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> Error >>>> > > code: >>>> > > > >>>> 1 >>>> > > > >>>> > # ../matlab_ls_test: >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>> > > > >>>> >>>> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>> > > Command >>>> > > > >>>> failed so no diff >>>> > > > >>>> > >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>> > > query=requires >>>> > > > >>>> queryval=matlab >>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>> > > > >>>> > TEST >>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>> > > > >>>> > TEST >>>> > > > >>>> >>>> > > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> > >>>> > > > >>>> > # ------------- >>>> > > > >>>> > # Summary >>>> > > > >>>> > # ------------- >>>> > > > >>>> > # success 4/4 tests (100.0%) >>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>> > > > >>>> > # >>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>> 15.190000000000001 >>>> > > sec >>>> > > > >>>> > # >>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 >>>> sec / >>>> > > 7.54 >>>> > > > >>>> sec >>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > >>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>> > > > >>>> > >>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried >>>> to >>>> > > > >>>> configure petsc >>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. >>>> After >>>> > > > >>>> running make >>>> > > > >>>> > > -j 10 test command I have got the following error >>>> message. >>>> > > > >>>> > > >>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> # Error >>>> > > > >>>> code: 124 >>>> > > > >>>> > > # Running problem 5 >>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>> > > > >>>> > > >>>> -------------------------------------------------------------- >>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>> > > > >>>> > > # [0]PETSC ERROR: See >>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > > >>>> > > for trouble shooting. >>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>> 2020 >>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>> > > > >>>> MB108SMEC028 by >>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>> COPTFLAGS=-O3 >>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>> > > > >>>> --with-debugging=0 >>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > --with-matlab-engine=1 >>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>> > > > >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>>> > > >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>> > > -------send >>>> > > > >>>> entire >>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>> > > > >>>> > > # >>>> > > > >>>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>> MPI_COMM_SELF >>>> > > > >>>> > > # with errorcode 126076. >>>> > > > >>>> > > # >>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>> MPI >>>> > > > >>>> processes. >>>> > > > >>>> > > # You may or may not see output from other processes, >>>> depending >>>> > > on >>>> > > > >>>> > > # exactly when Open MPI kills them. >>>> > > > >>>> > > # >>>> > > > >>>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>>> > > >>>> > > > >>>> > > I request you to help me to sort out this error. >>>> > > > >>>> > > >>>> > > > >>>> > > Thanks >>>> > > > >>>> > > Srinivas >>>> > > > >>>> > > >>>> > > > >>>> > > >>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>> > > > >>>> > > >>>> > > > >>>> > > > I think there should be two hyphens in >>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > > >>>> > > > >>>> > > > i.e.: >>>> > > > >>>> > > > >>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> > > > >>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>> 20PHD0548 via >>>> > > > >>>> petsc-users < >>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>> > > > >>>> > > > >>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>> > > > >>>> > > >> >>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>> balay at mcs.anl.gov> >>>> > > > >>>> wrote: >>>> > > > >>>> > > >> >>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>> will work >>>> > > > >>>> here]. >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> i.e: >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> ./configure >>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>> > > PETSC_ARCH=linux-opt >>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> --with-matlab-engine=1 >>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> > > > >>>> --known-64-bit-blas-indices=1 >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> Satish >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>> > > petsc-users >>>> > > > >>>> wrote: >>>> > > > >>>> > > >>> >>>> > > > >>>> > > >>> > Hi Satish, >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>> > > balay at mcs.anl.gov> >>>> > > > >>>> wrote: >>>> > > > >>>> > > >>> > >>>> > > > >>>> > > >>> > > Also: >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in >>>> this mode. >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > [we can't really over come such >>>> dependency/conflicts >>>> > > across >>>> > > > >>>> packages] >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > Satish >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users >>>> wrote: >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > >>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] >>>> conflict >>>> > > with >>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>> > > > >>>> -known-64-bit-blas-indices=1 >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack >>>> with >>>> > > > >>>> matlab - to >>>> > > > >>>> > > >>> have a >>>> > > > >>>> > > >>> > > compatible build >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > Satish >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 >>>> via >>>> > > > >>>> petsc-users >>>> > > > >>>> > > >>> wrote: >>>> > > > >>>> > > >>> > > > >>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB >>>> is not >>>> > > > >>>> working. It is >>>> > > > >>>> > > >>> > > showing >>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster >>>> with >>>> > > > >>>> libmesh and >>>> > > > >>>> > > >>> this is >>>> > > > >>>> > > >>> > > for >>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried >>>> without >>>> > > > >>>> linking >>>> > > > >>>> > > >>> Matlab >>>> > > > >>>> > > >>> > > with >>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>> configuring >>>> > > > >>>> libmesh 1.6.2 >>>> > > > >>>> > > >>> that >>>> > > > >>>> > > >>> > > PETSc >>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>> > > specified. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>> libmesh with >>>> > > > >>>> PETSc and >>>> > > > >>>> > > >>> Matlab >>>> > > > >>>> > > >>> > > is in >>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>> > > geometries >>>> > > > >>>> it is >>>> > > > >>>> > > >>> > > mentioned to >>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>> various >>>> > > things >>>> > > > >>>> and ended >>>> > > > >>>> > > >>> up with >>>> > > > >>>> > > >>> > > > > errors. >>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to >>>> do my >>>> > > > >>>> research work. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>>> possible. >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>> > > > >>>> > > >>> > > > > Srinivas >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>> > > > >>>> mail2amneet at gmail.com> >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>> libMesh for >>>> > > the >>>> > > > >>>> WEC >>>> > > > >>>> > > >>> application. >>>> > > > >>>> > > >>> > > You >>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>> builds with >>>> > > > >>>> Matlab. >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting >>>> to build >>>> > > > >>>> libMesh? >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > Thanks, >>>> > > > >>>> > > >>> > > > > > ?Amneet >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU >>>> SRINIVAS >>>> > > > >>>> 20PHD0548 via >>>> > > > >>>> > > >>> > > petsc-users >>>> > > > >>>> > > >>> > > > > > wrote: >>>> > > > >>>> > > >>> > > > > > >>>> > > > >>>> > > >>> > > > > >> Hi, >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>>> removing all >>>> > > > >>>> occurrences >>>> > > > >>>> > > >>> of >>>> > > > >>>> > > >>> > > "-lut >>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran >>>> "make >>>> > > test" >>>> > > > >>>> got the >>>> > > > >>>> > > >>> > > following >>>> > > > >>>> > > >>> > > > > >> errors >>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>> > > > >>>> > > >>> > > > > >> TEST >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > > >>> > > > > >> not ok >>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> > > > >>>> > > >>> Error >>>> > > > >>>> > > >>> > > code: 124 >>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>>> Error >>>> > > Message >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> >>>> -------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>> library >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB >>>> engine >>>> > > on >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>> > > > >>>> > > >>> > > > > >> >>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > > >>>> for >>>> > > > >>>> > > >>> trouble >>>> > > > >>>> > > >>> > > > > >> shooting. >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>>> 3.13.4, >>>> > > Aug >>>> > > > >>>> 01, 2020 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>> > > linux-debug >>>> > > > >>>> named >>>> > > > >>>> > > >>> > > MB108SMEC028 >>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>> > > > >>>> > > >>> > > > > >> >>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > > >>>> > > >>> > > > > >> >>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > > >>>> > > >>> > > > > >> >>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > > >>>> > > >>> --with-debugging=1 >>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>> --download-fblaslapack=1 >>>> > > > >>>> --with-x=0 >>>> > > > >>>> > > >>> > > > > >> >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>> PetscMatlabEngineCreate() >>>> > > line >>>> > > > >>>> 67 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>> entries: >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of >>>> Error >>>> > > > >>>> Message >>>> > > > >>>> > > >>> -------send >>>> > > > >>>> > > >>> > > entire >>>> > > > >>>> > > >>> > > > > >> error message to >>>> > > petsc-maint at mcs.anl.gov---------- >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>> communicator >>>> > > > >>>> > > >>> MPI_COMM_SELF >>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>> MPI to >>>> > > kill >>>> > > > >>>> all MPI >>>> > > > >>>> > > >>> > > processes. >>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>> > > processes, >>>> > > > >>>> > > >>> depending on >>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> ok >>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> # SKIP >>>> > > > >>>> > > >>> Command >>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>> > > > >>>> > > >>> > > > > >> TEST >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>> > > > >>>> > > >>> > > > > >> not ok >>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>> > > > >>>> > > >>> Error >>>> > > > >>>> > > >>> > > code: 124 >>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>>> Error >>>> > > Message >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> >>>> -------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>> library >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB >>>> engine >>>> > > on >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>> > > > >>>> > > >>> > > > > >> >>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>> > > > >>>> for >>>> > > > >>>> > > >>> trouble >>>> > > > >>>> > > >>> > > > > >> shooting. >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>>> 3.13.4, >>>> > > Aug >>>> > > > >>>> 01, 2020 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>> > > linux-opt >>>> > > > >>>> named >>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>> > > > >>>> > > >>> > > > > >> >>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>> > > > >>>> > > >>> > > > > >> >>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>> > > > >>>> > > >>> > > > > >> >>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>> > > > >>>> --PETSC_ARCH=linux-opt >>>> > > > >>>> > > >>> > > --with-debugging=0 >>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>> > > > >>>> --download-fblaslapack=1 >>>> > > > >>>> > > >>> > > > > >> >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>> PetscMatlabEngineCreate() >>>> > > line >>>> > > > >>>> 67 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>> entries: >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of >>>> Error >>>> > > > >>>> Message >>>> > > > >>>> > > >>> -------send >>>> > > > >>>> > > >>> > > entire >>>> > > > >>>> > > >>> > > > > >> error message to >>>> > > petsc-maint at mcs.anl.gov---------- >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>> communicator >>>> > > > >>>> > > >>> MPI_COMM_SELF >>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>> MPI to >>>> > > kill >>>> > > > >>>> all MPI >>>> > > > >>>> > > >>> > > processes. >>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>> > > processes, >>>> > > > >>>> > > >>> depending on >>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>> > > > >>>> > > >>> > > > > >> # >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -------------------------------------------------------------------------- >>>> > > > >>>> > > >>> > > > > >> ok >>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>> > > > >>>> # SKIP >>>> > > > >>>> > > >>> Command >>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>> > > version. I >>>> > > > >>>> am >>>> > > > >>>> > > >>> sharing the >>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc >>>> 3.13.4 and >>>> > > > >>>> petsc >>>> > > > >>>> > > >>> 3.17.5. >>>> > > > >>>> > > >>> > > Please find >>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>> > > > >>>> > > >>> > > > > >> Srinivas >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish >>>> Balay < >>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>> petsc's >>>> > > > >>>> > > >>> configure.log/make.log >>>> > > > >>>> > > >>> > > for >>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> >>>> >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>> > > > >>>> > > >>> > > > > >>> Includes: >>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>> > > > >>>> > > >>> > > > > >>> Library: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> >>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> > > -leng >>>> > > > >>>> -lmex >>>> > > > >>>> > > >>> -lmx >>>> > > > >>>> > > >>> > > -lmat -lut >>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we >>>> are >>>> > > seeing: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> >>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> >>> >>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>> > > > >>>> > > >>> > > > > >>> Includes: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>> > > > >>>> > > >>> > > > > >>> Executable: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>> > > > >>>> > > >>> > > > > >>> mex: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>> > > > >>>> > > >>> > > > > >>> matlab: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>> > > > >>>> > > >>> > > > > >>> <<< >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" >>>> are not >>>> > > > >>>> preset here. >>>> > > > >>>> > > >>> This >>>> > > > >>>> > > >>> > > might >>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> You can: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> - edit >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>> > > > >>>> > > >>> > > and >>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>> > > -licui18n >>>> > > > >>>> -licuuc" >>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>> > > '/home/vit/sfw/petsc/3.13.4' >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> Satish >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS >>>> 20PHD0548 >>>> > > via >>>> > > > >>>> > > >>> petsc-users >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>> building >>>> > > > >>>> petsc3.13.4 with >>>> > > > >>>> > > >>> > > matlab and >>>> > > > >>>> > > >>> > > > > >>> also >>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh >>>> with >>>> > > > >>>> petsc3.17.5 and >>>> > > > >>>> > > >>> matlab. >>>> > > > >>>> > > >>> > > > > >>> Building >>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>> > > successfully. >>>> > > > >>>> But >>>> > > > >>>> > > >>> libmesh is >>>> > > > >>>> > > >>> > > not >>>> > > > >>>> > > >>> > > > > >>> able to >>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish >>>> Balay < >>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>> > > > >>>> > > >>> > > > > >>> wrote: >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from >>>> both >>>> > > > >>>> petsc-3.13 and >>>> > > > >>>> > > >>> 3.17 [or >>>> > > > >>>> > > >>> > > 3.19]. >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>> > > friendly to >>>> > > > >>>> mailing >>>> > > > >>>> > > >>> list - >>>> > > > >>>> > > >>> > > or >>>> > > > >>>> > > >>> > > > > >>> send >>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? >>>> [or >>>> > > 3.19?] >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>> > > 20PHD0548 >>>> > > > >>>> via >>>> > > > >>>> > > >>> petsc-users >>>> > > > >>>> > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file >>>> while >>>> > > building >>>> > > > >>>> > > >>> petsc-3.13.4 >>>> > > > >>>> > > >>> > > with >>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do >>>> the >>>> > > needful. >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM >>>> INTURU >>>> > > > >>>> SRINIVAS >>>> > > > >>>> > > >>> 20PHD0548 < >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> inturu.srinivas2020 at vitstudent.ac.in> >>>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>> > > building >>>> > > > >>>> of >>>> > > > >>>> > > >>> libmesh, the >>>> > > > >>>> > > >>> > > error >>>> > > > >>>> > > >>> > > > > >>> shows >>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM >>>> Satish >>>> > > > >>>> Balay < >>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>> > > > >>>> > > >>> > > > > >>> > > > > >>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux >>>> says >>>> > > > >>>> petsc-3.17 >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU >>>> SRINIVAS >>>> > > > >>>> 20PHD0548 via >>>> > > > >>>> > > >>> > > petsc-users >>>> > > > >>>> > > >>> > > > > >>> wrote: >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with >>>> MATLAB for >>>> > > > >>>> working on >>>> > > > >>>> > > >>> the >>>> > > > >>>> > > >>> > > > > >>> simulation >>>> > > > >>>> > > >>> > > > > >>> > > using >>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building >>>> the >>>> > > PETSc, >>>> > > > >>>> using the >>>> > > > >>>> > > >>> > > following >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEnginePut' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGet' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEnginePut' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGet' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGet' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineCreate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineGetArray' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> > > >>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>> > > > >>>> `PetscMatlabEngineDestroy' >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned >>>> 1 exit >>>> > > > >>>> status >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> >>>> > > > >>>> >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>> unfinished >>>> > > jobs.... >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this >>>> issue >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > > >>>> > > > >>>> > > >>> > > > > >>> > > >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> > >>>> > > > >>>> > > >>> > > > > >>> >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> >>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from >>>> Vellore >>>> > > > >>>> Institute of >>>> > > > >>>> > > >>> > > Technology. >>>> > > > >>>> > > >>> > > > > >> The contents 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Please notify the sender >>>> immediately >>>> > > > >>>> and destroy >>>> > > > >>>> > > >>> all >>>> > > > >>>> > > >>> > > copies of >>>> > > > >>>> > > >>> > > > > >> this message and any attachments. 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URL: From bsmith at petsc.dev Tue Sep 5 12:37:18 2023 From: bsmith at petsc.dev (Barry Smith) Date: Tue, 5 Sep 2023 13:37:18 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> Message-ID: <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Ok, I have no suggestions. It seems to be more an issue with the Matlab than PETSc. You could find a pure Matlab example of using the engine (in the Matlab documentation) and try it to see if it works. Barry > On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 wrote: > > I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); > I got the same errors for petsc 3.17.5 > > make all > CC linux-opt/obj/sys/classes/matlabengine/matlab.o > CLINKER linux-opt/lib/libpetsc.so.3.17.5 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check > > make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 > # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 > # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 > # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -check_pointer_intensity 0 > # [0]PETSC ERROR: -error_output_stdout > # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > # [0]PETSC ERROR: -malloc_dump > # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > # [0]PETSC ERROR: -pc_type lu > # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > # with errorcode 85. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > # FAILED ksp_ksp_tutorials-ex72_12 > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > > Thanks and regards > Srinivas > > On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: >> >> The error is occuring during >> >> e->ep = engOpen(buffer); >> >> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. >> >> You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line >> >> e->ep = engOpen(buffer); >> >> replace it with >> >> e->ep = engOpen(""); >> >> Now in the PETSc directory do make all (it should recompile one file) and then run the >> >> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >> >> again >> >> >> >> >> >>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>> >>> Hi Amneeth, >>> >>> I think the errors are different with petsc 3.17.5 >>> >>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> The version of PETSc you are using is out-of-date, we recommend updating to the new release >>> Available Version: 3.19.5 Installed Version: 3.17.5 >>> https://petsc.org/release/download/ >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> ============================================================================================= >>> Configuring PETSc to compile on your system >>> ============================================================================================= >>> Compilers: >>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> Linkers: >>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>> BlasLapack: >>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads >>> uses 8 byte integers >>> MPI: >>> Version: 3 >>> mpiexec: /usr/bin/mpiexec >>> Implementation: openmpi >>> OMPI_VERSION: 4.0.3 >>> pthread: >>> cmake: >>> Version: 3.16.3 >>> /usr/bin/cmake >>> regex: >>> Matlab: >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> /usr/local/MATLAB/R2020b >>> MatlabEngine: >>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>> Language used to compile PETSc: C >>> PETSc: >>> PETSC_ARCH: linux-opt >>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>> Prefix: >>> Scalar type: real >>> Precision: double >>> Support for __float128 >>> Integer size: 4 bytes >>> Single library: yes >>> Shared libraries: yes >>> Memory alignment from malloc(): 16 bytes >>> Using GNU make: /usr/bin/make >>> xxx=========================================================================xxx >>> Configure stage complete. Now build PETSc libraries with: >>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all >>> xxx=========================================================================xxx >>> >>> $make >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> Building with 'gcc'. >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> ========================================= >>> ========================================= >>> Now to check if the libraries are working do: >>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>> >>> $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests >>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>> # [0]PETSC ERROR: Error in external library >>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 >>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>> # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>> # [0]PETSC ERROR: -error_output_stdout >>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>> # [0]PETSC ERROR: -malloc_dump >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> # [0]PETSC ERROR: -pc_type lu >>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>> # -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> # with errorcode 85. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # -------------------------------------------------------------------------- >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> >>> >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> # >>> # To rerun failed tests: >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> >>> To get the info of the error there is no specific probe id reported. >>> >>> How to check error info and proceed further? >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: >>>> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? >>>> >>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>> Sorry for missing that. >>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>> >>>>> < M A T L A B (R) > >>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>> November 23, 2020 >>>>> >>>>> >>>>> To get started, type doc. >>>>> For product information, visit www.mathworks.com . >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: >>>>>> You are missing one more step: >>>>>> >>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> >>>>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>> >>>>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. >>>>>> >>>>>> Satish >>>>>> >>>>>> >>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>> >>>>>> > Hi Sathish, >>>>>> > >>>>>> > I tried the following procedure >>>>>> > >>>>>> > *$make * >>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > Building with 'gcc'. >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > In function ?PetscBinaryWrite?: >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > warning: ?err? may be used uninitialized in this function >>>>>> > [-Wmaybe-uninitialized] >>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > | ^ >>>>>> > >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > In function ?PetscBinaryWrite?: >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > warning: ?err? may be used uninitialized in this function >>>>>> > [-Wmaybe-uninitialized] >>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > | ^ >>>>>> > >>>>>> > MEX completed successfully. >>>>>> > ========================================= >>>>>> > Now to check if the libraries are working do: >>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>> > >>>>>> > *$make test query=requires queryval=matlab >>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>>> > query=requires >>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Error in external library >>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>> > # [0]PETSC ERROR: >>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: >>>>>> > ------------------------------------------------------------------------ >>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>>>> > probably memory access out of range >>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>>>> > # [0]PETSC ERROR: or see >>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS >>>>>> > X to find memory corruption errors >>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, >>>>>> > and run >>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Signal received >>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>>>> > # -------------------------------------------------------------------------- >>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> > # with errorcode 50162059. >>>>>> > # >>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > # You may or may not see output from other processes, depending on >>>>>> > # exactly when Open MPI kills them. >>>>>> > # -------------------------------------------------------------------------- >>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> > CC >>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > CLINKER >>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > TEST >>>>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>>>>> > # Running problem 5 >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Error in external library >>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > # -------------------------------------------------------------------------- >>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > # with errorcode 126076. >>>>>> > # >>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > # You may or may not see output from other processes, depending on >>>>>> > # exactly when Open MPI kills them. >>>>>> > # -------------------------------------------------------------------------- >>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed >>>>>> > so no diff >>>>>> > >>>>>> > # ------------- >>>>>> > # Summary >>>>>> > # ------------- >>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > # success 0/2 tests (0.0%) >>>>>> > # failed 2/2 tests (100.0%) >>>>>> > # todo 0/2 tests (0.0%) >>>>>> > # skip 0/2 tests (0.0%) >>>>>> > # >>>>>> > # Wall clock time for tests: 4 sec >>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>> > # >>>>>> > # To rerun failed tests: >>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> > # >>>>>> > # Timing summary (actual test time / total CPU time): >>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec >>>>>> > >>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>> > *$make matlab_ls_test* >>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>> > >>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 >>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>> > MB108SMEC028.(none) >>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>> > Running problem 5 >>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>> > 94202473157392 max tags = 2147483647 >>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > [0]PETSC ERROR: Error in external library >>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit >>>>>> > Mon Sep 4 10:09:56 2023 >>>>>> > [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > [0]PETSC ERROR: -info >>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > -------------------------------------------------------------------------- >>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > with errorcode 126076. >>>>>> > >>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > You may or may not see output from other processes, depending on >>>>>> > exactly when Open MPI kills them. >>>>>> > >>>>>> > Please find the attachment for configure.log and make.log files >>>>>> > >>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: >>>>>> > >>>>>> > > To use datafiles in the test suite: >>>>>> > > >>>>>> > > cd $HOME >>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>> > > >>>>> > > manually with make> >>>>>> > > >>>>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles >>>>>> > > >>>>>> > > Satish >>>>>> > > >>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>> > > >>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: >>>>>> > > > >>>>>> > > > > Hi Matthew, >>>>>> > > > > >>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have >>>>>> > > any >>>>>> > > > > separate test files to test PETSc alone. Can you please help me how to >>>>>> > > > > define this DATAFILESPATH? >>>>>> > > > > >>>>>> > > > >>>>>> > > > That test you tried uses a certain matrix. On our machine, we point to >>>>>> > > this >>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those >>>>>> > > > matrices, since they are just for testing here. That >>>>>> > > > is why I suggested just using a different matrix, or running a problem >>>>>> > > you >>>>>> > > > care about in IBAMR. >>>>>> > > > >>>>>> > > > Thanks, >>>>>> > > > >>>>>> > > > Matt >>>>>> > > > >>>>>> > > > >>>>>> > > > > Thanks and regards >>>>>> > > > > Srinivas. >>>>>> > > > > >>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > >>>>>> > > wrote: >>>>>> > > > > >>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>> > > petsc-users < >>>>>> > > > >> petsc-users at mcs.anl.gov > wrote: >>>>>> > > > >> >>>>>> > > > >>> Hi Sathish, >>>>>> > > > >>> >>>>>> > > > >>> Thank you so much for your efforts and the support you are giving me >>>>>> > > to >>>>>> > > > >>> sort this out. >>>>>> > > > >>> >>>>>> > > > >>> I tried to follow the same procedure which you followed to build >>>>>> > > Petsc >>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>> > > > >>> >>>>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>> > > > >>> Using python3 for Python >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > =============================================================================== >>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > =============================================================================== >>>>>> > > > >>> >>>>>> > > =============================================================================== >>>>>> > > > >>> It appears you do not have >>>>>> > > valgrind >>>>>> > > > >>> installed on your system. >>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>> > > > >>> Or install >>>>>> > > valgrind-devel or >>>>>> > > > >>> equivalent using your package manager. >>>>>> > > > >>> Then rerun ./configure >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > =============================================================================== >>>>>> > > > >>> Compilers: >>>>>> > > > >>> >>>>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -fPIC >>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>> Linkers: >>>>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -shared >>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > > -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -shared >>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > > -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> > > > >>> make: >>>>>> > > > >>> Version: 4.2 >>>>>> > > > >>> /usr/bin/make >>>>>> > > > >>> BlasLapack: >>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>> > >

to >>>>>> > > > >>> control the number of threads >>>>>> > > > >>> uses 8 byte integers >>>>>> > > > >>> MPI: >>>>>> > > > >>> Version: 3 >>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>> > > --oversubscribe >>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>> > > > >>> pthread: >>>>>> > > > >>> cmake: >>>>>> > > > >>> Version: 3.16.3 >>>>>> > > > >>> /usr/bin/cmake >>>>>> > > > >>> regex: >>>>>> > > > >>> Matlab: >>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>> > > > >>> MatlabEngine: >>>>>> > > > >>> Library: >>>>>> > > > >>> >>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>> > > -lut >>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>> > > > >>> Language used to compile PETSc: C >>>>>> > > > >>> PETSc: >>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>> > > > >>> Scalar type: real >>>>>> > > > >>> Precision: double >>>>>> > > > >>> Support for __float128 >>>>>> > > > >>> Integer size: 4 bytes >>>>>> > > > >>> shared libraries: enabled >>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > xxx=========================================================================xxx >>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > xxx=========================================================================xxx >>>>>> > > > >>> >>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>>>>> > > > >>> you suggested earlier. >>>>>> > > > >>> >>>>>> > > > >>> *$make* >>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>> > > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > > > >>> | ^ >>>>>> > > > >>> >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>> > > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > > > >>> | ^ >>>>>> > > > >>> >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> ========================================= >>>>>> > > > >>> Now to check if the libraries are working do: >>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>> > > > >>> =============================================== >>>>>> > > > >>> >>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>> -------------------------------------------------------------- >>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>> > > > >>> >>>>>> > > > >> >>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it >>>>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>>>> > > > >> >>>>>> > > > >> Thanks, >>>>>> > > > >> >>>>>> > > > >> Matt >>>>>> > > > >> >>>>>> > > > >> >>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>> > > > >>> shooting. >>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> > > Sun >>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > > > >>> # with errorcode 113065. >>>>>> > > > >>> # >>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> > > > >>> CC >>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > > > >>> CLINKER >>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>> TEST >>>>>> > > > >>> >>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> > > code: 124 >>>>>> > > > >>> # Running problem 5 >>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>> -------------------------------------------------------------- >>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>> > > > >>> shooting. >>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>> > > MB108SMEC028 by >>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > > > >>> # with errorcode 126076. >>>>>> > > > >>> # >>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>> > > > >>> failed so no diff >>>>>> > > > >>> >>>>>> > > > >>> # ------------- >>>>>> > > > >>> # Summary >>>>>> > > > >>> # ------------- >>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>> > > > >>> # >>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>> > > > >>> # >>>>>> > > > >>> # To rerun failed tests: >>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> > > > >>> # >>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / >>>>>> > > 0.02 sec >>>>>> > > > >>> >>>>>> > > > >>> *How to sort out this error?* >>>>>> > > > >>> >>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>> > > > >>> *$make matlab_ls_test* >>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>> > > -Wwrite-strings >>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> > > -Wno-strict-aliasing >>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> >>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>> > > -lmx >>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>> > > -lmpi_mpifh >>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>> > > -lquadmath >>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>> > > > >>> >>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>> > > > >>> I am sharing the configure.log and make.log files. Please find the >>>>>> > > > >>> attachment and do the needful. >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> Thanks and regards >>>>>> > > > >>> Srinivas >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > >>>>>> > > wrote: >>>>>> > > > >>> >>>>>> > > > >>>> Perhaps you can try the following to get additional info - and debug >>>>>> > > > >>>> >>>>>> > > > >>>> Satish >>>>>> > > > >>>> ---------- >>>>>> > > > >>>> >>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> make matlab_ls_test >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> > > -Wno-strict-aliasing >>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>> > > > >>>> >>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>> > > > >>>> >>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>> > > > >>>> >>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng >>>>>> > > -lmex >>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort >>>>>> > > -lmpi >>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>>>> > > > >>>> matlab_ls_test >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>>>> > > processors >>>>>> > > > >>>> = 1 >>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>> > > > >>>> compute-386-07.(none) >>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>> > > > >>>> Running problem 5 >>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>> > > > >>>> TestingInitialize >>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>>>> > > > >>>> TestingInitialize >>>>>> > > > >>>> 5 >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you >>>>>> > > - on >>>>>> > > > >>>> this machine..>>>>> >>>>>> > > > >>>> >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> < M A T L A B (R) > >>>>>> > > > >>>> >>>>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. >>>>>> > > > >>>> >>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>>>> > > > >>>> >>>>>> > > > >>>> February 17, 2021 >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> To get started, type doc. >>>>>> > > > >>>> For product information, visit www.mathworks.com . >>>>>> > > > >>>> >>>>>> > > > >>>> >> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>> > > > >>>> >>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>>>>> > > thread >>>>>> > > > >>>> to petsc-users only] >>>>>> > > > >>>> > >>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>> > > corresponding >>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>> > > > >>>> > >>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>> > > > >>>> > >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>> > > > >>>> > main >>>>>> > > > >>>> > release >>>>>> > > > >>>> > * release-3.13 >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>> > > matlab/R2021a >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>> > > > >>>> >>>>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> >>>>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>>> > >>>>>> > > > >>>> > Compilers: >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> > C Compiler: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > C++ Compiler: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > Fortran Compiler: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > Linkers: >>>>>> > > > >>>> > Shared linker: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> > > -shared -fPIC >>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> > Dynamic linker: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> > > -shared -fPIC >>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> > > > >>>> > make: >>>>>> > > > >>>> > Version: 4.2 >>>>>> > > > >>>> > /usr/bin/make >>>>>> > > > >>>> > BlasLapack: >>>>>> > > > >>>> > Library: >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>> > > > >>>> >>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>> > > > >>>> >>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>> > > > >>>> -liomp5 -lpthread >>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>> > >

>>>>>> > > > >>>> to control the number of threads >>>>>> > > > >>>> > uses 8 byte integers >>>>>> > > > >>>> > MPI: >>>>>> > > > >>>> > Version: 4 >>>>>> > > > >>>> > Includes: >>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>> > > > >>>> > Mpiexec: >>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>> > > > >>>> > pthread: >>>>>> > > > >>>> > Library: -lpthread >>>>>> > > > >>>> > cmake: >>>>>> > > > >>>> > Version: 3.16.3 >>>>>> > > > >>>> > /usr/bin/cmake >>>>>> > > > >>>> > regex: >>>>>> > > > >>>> > Matlab: >>>>>> > > > >>>> > Includes: >>>>>> > > > >>>> >>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> > MatlabEngine: >>>>>> > > > >>>> > Library: >>>>>> > > > >>>> >>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>> > > > >>>> >>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>> > > > >>>> > sowing: >>>>>> > > > >>>> > Version: 1.1.25 >>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>> > > > >>>> > valgrind: >>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>> > > > >>>> > PETSc: >>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>> > > > >>>> > Scalar type: real >>>>>> > > > >>>> > Precision: double >>>>>> > > > >>>> > Support for __float128 >>>>>> > > > >>>> > Integer size: 4 bytes >>>>>> > > > >>>> > shared libraries: enabled >>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > xxx=========================================================================xxx >>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > xxx=========================================================================xxx >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> > > socket\n"); >>>>>> > > > >>>> > | ^ >>>>>> > > > >>>> > >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> > > socket\n"); >>>>>> > > > >>>> > | ^ >>>>>> > > > >>>> > >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > ========================================= >>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>>>> > > > >>>> > ========================================= >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>> > > query=requires >>>>>> > > > >>>> queryval=matlab >>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > > > >>>> > TEST >>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>> > > > >>>> > # ../ex72: >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>> > > > >>>> >>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> > > > >>>> > CC >>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > > > >>>> > CLINKER >>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>>> > TEST >>>>>> > > > >>>> >>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> > > code: >>>>>> > > > >>>> 1 >>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>> > > > >>>> >>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>> > > Command >>>>>> > > > >>>> failed so no diff >>>>>> > > > >>>> > >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>> > > query=requires >>>>>> > > > >>>> queryval=matlab >>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>>> > TEST >>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>>> > TEST >>>>>> > > > >>>> >>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> > >>>>>> > > > >>>> > # ------------- >>>>>> > > > >>>> > # Summary >>>>>> > > > >>>> > # ------------- >>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>> > > > >>>> > # >>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 >>>>>> > > sec >>>>>> > > > >>>> > # >>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>> > > 7.54 >>>>>> > > > >>>> sec >>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>> > > > >>>> > >>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>>>> > > > >>>> configure petsc >>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>>>> > > > >>>> running make >>>>>> > > > >>>> > > -j 10 test command I have got the following error message. >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> > > > >>>> code: 124 >>>>>> > > > >>>> > > # Running problem 5 >>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>>> > > -------------------------------------------------------------- >>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> > > for trouble shooting. >>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>> > > > >>>> MB108SMEC028 by >>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> > > > >>>> --with-debugging=0 >>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>> > > -------send >>>>>> > > > >>>> entire >>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > # >>>>>> > > > >>>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > > > >>>> > > # with errorcode 126076. >>>>>> > > > >>>> > > # >>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> > > > >>>> processes. >>>>>> > > > >>>> > > # You may or may not see output from other processes, depending >>>>>> > > on >>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>> > > > >>>> > > # >>>>>> > > > >>>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > Thanks >>>>>> > > > >>>> > > Srinivas >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>> > > > >>>> mail2amneet at gmail.com > wrote: >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > i.e.: >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>>>> > > > >>>> petsc-users < >>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>>>> > > > >>>> here]. >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> i.e: >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> > > PETSC_ARCH=linux-opt >>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> Satish >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>> > > petsc-users >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>> > > balay at mcs.anl.gov > >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > > Also: >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts >>>>>> > > across >>>>>> > > > >>>> packages] >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > Satish >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict >>>>>> > > with >>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>>>> > > > >>>> matlab - to >>>>>> > > > >>>> > > >>> have a >>>>>> > > > >>>> > > >>> > > compatible build >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > Satish >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>> > > > >>>> petsc-users >>>>>> > > > >>>> > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>>>> > > > >>>> working. It is >>>>>> > > > >>>> > > >>> > > showing >>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>>>> > > > >>>> libmesh and >>>>>> > > > >>>> > > >>> this is >>>>>> > > > >>>> > > >>> > > for >>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>>>> > > > >>>> linking >>>>>> > > > >>>> > > >>> Matlab >>>>>> > > > >>>> > > >>> > > with >>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>>>> > > > >>>> libmesh 1.6.2 >>>>>> > > > >>>> > > >>> that >>>>>> > > > >>>> > > >>> > > PETSc >>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>>>> > > specified. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>>>> > > > >>>> PETSc and >>>>>> > > > >>>> > > >>> Matlab >>>>>> > > > >>>> > > >>> > > is in >>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>>>> > > geometries >>>>>> > > > >>>> it is >>>>>> > > > >>>> > > >>> > > mentioned to >>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>>>>> > > things >>>>>> > > > >>>> and ended >>>>>> > > > >>>> > > >>> up with >>>>>> > > > >>>> > > >>> > > > > errors. >>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>>>> > > > >>>> research work. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>> > > > >>>> mail2amneet at gmail.com > >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for >>>>>> > > the >>>>>> > > > >>>> WEC >>>>>> > > > >>>> > > >>> application. >>>>>> > > > >>>> > > >>> > > You >>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>>>> > > > >>>> Matlab. >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>>>> > > > >>>> libMesh? >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>>>> > > > >>>> 20PHD0548 via >>>>>> > > > >>>> > > >>> > > petsc-users >>>>>> > > > >>>> > > >>> > > > > > > wrote: >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>>>> > > > >>>> occurrences >>>>>> > > > >>>> > > >>> of >>>>>> > > > >>>> > > >>> > > "-lut >>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make >>>>>> > > test" >>>>>> > > > >>>> got the >>>>>> > > > >>>> > > >>> > > following >>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> > > > >>>> > > >>> Error >>>>>> > > > >>>> > > >>> > > code: 124 >>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>> > > Message >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> -------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>> > > on >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> for >>>>>> > > > >>>> > > >>> trouble >>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>> > > Aug >>>>>> > > > >>>> 01, 2020 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>> > > linux-debug >>>>>> > > > >>>> named >>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>>>> > > > >>>> --with-x=0 >>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>> > > line >>>>>> > > > >>>> 67 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>> > > > >>>> Message >>>>>> > > > >>>> > > >>> -------send >>>>>> > > > >>>> > > >>> > > entire >>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>> > > kill >>>>>> > > > >>>> all MPI >>>>>> > > > >>>> > > >>> > > processes. >>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>> > > processes, >>>>>> > > > >>>> > > >>> depending on >>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> # SKIP >>>>>> > > > >>>> > > >>> Command >>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> > > > >>>> > > >>> Error >>>>>> > > > >>>> > > >>> > > code: 124 >>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>> > > Message >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> -------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>> > > on >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> for >>>>>> > > > >>>> > > >>> trouble >>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>> > > Aug >>>>>> > > > >>>> 01, 2020 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>> > > linux-opt >>>>>> > > > >>>> named >>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>> > > > >>>> --download-fblaslapack=1 >>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>> > > line >>>>>> > > > >>>> 67 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>> > > > >>>> Message >>>>>> > > > >>>> > > >>> -------send >>>>>> > > > >>>> > > >>> > > entire >>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>> > > kill >>>>>> > > > >>>> all MPI >>>>>> > > > >>>> > > >>> > > processes. >>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>> > > processes, >>>>>> > > > >>>> > > >>> depending on >>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> # SKIP >>>>>> > > > >>>> > > >>> Command >>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>>>> > > version. I >>>>>> > > > >>>> am >>>>>> > > > >>>> > > >>> sharing the >>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>>>> > > > >>>> petsc >>>>>> > > > >>>> > > >>> 3.17.5. >>>>>> > > > >>>> > > >>> > > Please find >>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>> > > > >>>> > > >>> > > for >>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > -leng >>>>>> > > > >>>> -lmex >>>>>> > > > >>>> > > >>> -lmx >>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are >>>>>> > > seeing: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>>>> > > > >>>> preset here. >>>>>> > > > >>>> > > >>> This >>>>>> > > > >>>> > > >>> > > might >>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>> > > > >>>> > > >>> > > and >>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>>>> > > -licui18n >>>>>> > > > >>>> -licuuc" >>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>>>> > > via >>>>>> > > > >>>> > > >>> petsc-users >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>>>> > > > >>>> petsc3.13.4 with >>>>>> > > > >>>> > > >>> > > matlab and >>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>>>> > > > >>>> petsc3.17.5 and >>>>>> > > > >>>> > > >>> matlab. >>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>> > > successfully. >>>>>> > > > >>>> But >>>>>> > > > >>>> > > >>> libmesh is >>>>>> > > > >>>> > > >>> > > not >>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>>>> > > > >>>> petsc-3.13 and >>>>>> > > > >>>> > > >>> 3.17 [or >>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>>> > > friendly to >>>>>> > > > >>>> mailing >>>>>> > > > >>>> > > >>> list - >>>>>> > > > >>>> > > >>> > > or >>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or >>>>>> > > 3.19?] >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>> > > 20PHD0548 >>>>>> > > > >>>> via >>>>>> > > > >>>> > > >>> petsc-users >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>>>>> > > building >>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>> > > > >>>> > > >>> > > with >>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the >>>>>> > > needful. >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>>>> > > > >>>> SRINIVAS >>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > >>>>>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>>>> > > building >>>>>> > > > >>>> of >>>>>> > > > >>>> > > >>> libmesh, the >>>>>> > > > >>>> > > >>> > > error >>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>>>> > > > >>>> Balay < >>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > >>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>>>> > > > >>>> petsc-3.17 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>>>> > > > >>>> 20PHD0548 via >>>>>> > > > >>>> > > >>> > > petsc-users >>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>>>> > > > >>>> working on >>>>>> > > > >>>> > > >>> the >>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the >>>>>> > > PETSc, >>>>>> > > > >>>> using the >>>>>> > > > >>>> > > >>> > > following >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>>>> > > > >>>> status >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished >>>>>> > > jobs.... >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>>>>> > > > >>>> Institute of >>>>>> > > > >>>> > > >>> > > Technology. >>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain legally >>>>>> > > > >>>> protected >>>>>> > > > >>>> > > >>> > > confidential or >>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>>>>> > > > >>>> Technology?. >>>>>> > > > >>>> > > >>> If >>>>>> > > > >>>> > > >>> > > you are >>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should not >>>>>> > > > >>>> disseminate, >>>>>> > > > >>>> > > >>> distribute >>>>>> > > > >>>> > > >>> > > or copy >>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately >>>>>> > > > >>>> and destroy >>>>>> > > > >>>> > > >>> all >>>>>> > > > >>>> > > >>> > > copies of >>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you have >>>>>> > > > >>>> received this >>>>>> > > > >>>> > > >>> email >>>>>> > > > >>>> > > >>> > > in error, >>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by reply email >>>>>> > > and >>>>>> > > > >>>> delete >>>>>> > > > >>>> > > >>> the >>>>>> > > > >>>> > > >>> > > original >>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without reading >>>>>> > > them.* >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>>>>> > > > >>>> Technology. >>>>>> > > > >>>> > > >> The contents of this email may contain legally protected >>>>>> > > > >>>> confidential or >>>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>>> > > Technology?. If >>>>>> > > > >>>> you are >>>>>> > > > >>>> > > >> not the intended recipient, you should not disseminate, >>>>>> > > > >>>> distribute or copy >>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy >>>>>> > > > >>>> all copies of >>>>>> > > > >>>> > > >> this message and any attachments. If you have received this >>>>>> > > > >>>> email in error, >>>>>> > > > >>>> > > >> please promptly notify the sender by reply email and delete >>>>>> > > the >>>>>> > > > >>>> original >>>>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > -- >>>>>> > > > >>>> > > > --Amneet >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > >>>>>> > > > >>>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>>>> > > Technology. >>>>>> > > > >>> The contents of this email may contain legally protected >>>>>> > > confidential or >>>>>> > > > >>> privileged information of ?Vellore Institute of Technology?. If you >>>>>> > > are >>>>>> > > > >>> not the intended recipient, you should not disseminate, distribute >>>>>> > > or copy >>>>>> > > > >>> this e-mail. Please notify the sender immediately and destroy all >>>>>> > > copies of >>>>>> > > > >>> this message and any attachments. If you have received this email in >>>>>> > > error, >>>>>> > > > >>> please promptly notify the sender by reply email and delete the >>>>>> > > original >>>>>> > > > >>> email and any backup copies without reading them.* >>>>>> > > > >>> >>>>>> > > > >> >>>>>> > > > >> >>>>>> > > > >> -- >>>>>> > > > >> What most experimenters take for granted before they begin their >>>>>> > > > >> experiments is infinitely more interesting than any results to which >>>>>> > > their >>>>>> > > > >> experiments lead. >>>>>> > > > >> -- Norbert Wiener >>>>>> > > > >> >>>>>> > > > >> https://www.cse.buffalo.edu/~knepley/ >>>>>> > > > >> >>>>>> > > > >> >>>>>> > > > > >>>>>> > > > > >>>>>> > > > > *Disclaimer:This message was sent from Vellore Institute of Technology. >>>>>> > > > > The contents of this email may contain legally protected confidential >>>>>> > > or >>>>>> > > > > privileged information of ?Vellore Institute of Technology?. If you >>>>>> > > are >>>>>> > > > > not the intended recipient, you should not disseminate, distribute or >>>>>> > > copy >>>>>> > > > > this e-mail. Please notify the sender immediately and destroy all >>>>>> > > copies of >>>>>> > > > > this message and any attachments. If you have received this email in >>>>>> > > error, >>>>>> > > > > please promptly notify the sender by reply email and delete the >>>>>> > > original >>>>>> > > > > email and any backup copies without reading them.* >>>>>> > > > > >>>>>> > > > >>>>>> > > > >>>>>> > > > >>>>>> > > >>>>>> > >>>>>> > >>>>> >>>>> Disclaimer: >>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>> >>>> >>>> -- >>>> --Amneet >>>> >>>> >>>> >>> >>> Disclaimer: >>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >> > > Disclaimer: > This message was sent from Vellore Institute of Technology. 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URL: From mail2amneet at gmail.com Tue Sep 5 13:02:32 2023 From: mail2amneet at gmail.com (Amneet Bhalla) Date: Tue, 5 Sep 2023 11:02:32 -0700 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: Srinivas --- Do you have a different version of MATLAB that you can install? If your organization has a MATLAB license, you can install recent versions of MATLAB from mathworks.com On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: > > Ok, I have no suggestions. It seems to be more an issue with the Matlab > than PETSc. You could find a pure Matlab example of using the engine (in > the Matlab documentation) and try it to see if it works. > > Barry > > > On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); > I got the same errors for petsc 3.17.5 > > > *make all* > CC linux-opt/obj/sys/classes/matlabengine/matlab.o > CLINKER linux-opt/lib/libpetsc.so.3.17.5 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check > > *make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/* > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab > query=requires > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine with > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep > 5 21:39:22 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 > # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 > # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at > /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > # [0]PETSC ERROR: #5 MatLUFactorNumeric() at > /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > # [0]PETSC ERROR: #6 PCSetUp_LU() at > /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > # [0]PETSC ERROR: #7 PCSetUp() at > /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > # [0]PETSC ERROR: #8 KSPSetUp() at > /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > # [0]PETSC ERROR: #9 main() at > /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -check_pointer_intensity 0 > # [0]PETSC ERROR: -error_output_stdout > # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > # [0]PETSC ERROR: -malloc_dump > # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > # [0]PETSC ERROR: -pc_type lu > # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-maint at mcs.anl.gov---------- > # > -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > # with errorcode 85. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # > -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > # FAILED ksp_ksp_tutorials-ex72_12 > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > > Thanks and regards > Srinivas > > On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: > >> >> The error is occuring during >> >> e->ep = engOpen(buffer); >> >> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 >> -nodisplay -nosplash from your terminal shell worked we have to assume the >> problem is occuring when engOpen() is attempting to connect the stdout and >> stdin from the Matlab session that is launched to the executable. >> >> You can try the following. In 3.17.5 edit the >> file src/sys/classes/matlabengine/matlab.c and locate the line >> >> e->ep = engOpen(buffer); >> >> replace it with >> >> e->ep = engOpen(""); >> >> Now in the PETSc directory do make all (it should recompile one file) and >> then run the >> >> make test query=requires queryval=matlab >> DATAFILESPATH=/home/vit/datafiles/ >> >> again >> >> >> >> >> >> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < >> petsc-users at mcs.anl.gov> wrote: >> >> Hi Amneeth, >> >> I think the errors are different with petsc 3.17.5 >> >> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >> --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> The version of PETSc you are using is out-of-date, we recommend updating >> to the new release >> Available Version: 3.19.5 Installed Version: 3.17.5 >> https://petsc.org/release/download/ >> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >> ============================================================================================= >> Configuring PETSc to compile on your system >> >> >> ============================================================================================= >> Compilers: >> >> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >> -fvisibility=hidden -O3 >> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >> Linkers: >> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >> -fvisibility=hidden -O3 >> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >> -fvisibility=hidden -O3 >> Libraries linked against: -lquadmath -lstdc++ -ldl >> BlasLapack: >> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to >> control the number of threads >> uses 8 byte integers >> MPI: >> Version: 3 >> mpiexec: /usr/bin/mpiexec >> Implementation: openmpi >> OMPI_VERSION: 4.0.3 >> pthread: >> cmake: >> Version: 3.16.3 >> /usr/bin/cmake >> regex: >> Matlab: >> Includes: -I/usr/local/MATLAB/R2020b/extern/include >> /usr/local/MATLAB/R2020b >> MatlabEngine: >> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >> Language used to compile PETSc: C >> PETSc: >> PETSC_ARCH: linux-opt >> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >> Prefix: >> Scalar type: real >> Precision: double >> Support for __float128 >> Integer size: 4 bytes >> Single library: yes >> Shared libraries: yes >> Memory alignment from malloc(): 16 bytes >> Using GNU make: /usr/bin/make >> >> xxx=========================================================================xxx >> Configure stage complete. Now build PETSc libraries with: >> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all >> >> xxx=========================================================================xxx >> >> *$make* >> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >> BEGINNING TO COMPILE MATLAB INTERFACE >> Building with 'gcc'. >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> ========================================= >> ========================================= >> Now to check if the libraries are working do: >> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >> >> *$make test query=requires queryval=matlab >> DATAFILESPATH=/home/vit/datafiles/* >> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >> --testdir=./linux-opt/tests >> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >> query=requires >> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Error in external library >> # [0]PETSC ERROR: Unable to start MATLAB engine with >> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >> Sep 5 10:15:57 2023 >> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >> --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >> # [0]PETSC ERROR: #6 PCSetUp_LU() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >> # [0]PETSC ERROR: #7 PCSetUp() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >> # [0]PETSC ERROR: #8 KSPSetUp() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >> # [0]PETSC ERROR: #9 main() at >> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -check_pointer_intensity 0 >> # [0]PETSC ERROR: -error_output_stdout >> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >> # [0]PETSC ERROR: -malloc_dump >> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >> # [0]PETSC ERROR: -pc_type lu >> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >> # with errorcode 85. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >> >> >> # FAILED ksp_ksp_tutorials-ex72_12 >> # >> # To rerun failed tests: >> # /usr/bin/make -f gmakefile test test-fail=1 >> >> To get the info of the error there is no specific probe id reported. >> >> How to check error info and proceed further? >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >> wrote: >> >>> Do you get similar errors with petsc 3.17.5 using the new configure >>> options that Satish mentioned? >>> >>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>> petsc-users wrote: >>> >>>> Sorry for missing that. >>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>> >>>> < M A T L A B (R) > >>>> Copyright 1984-2020 The MathWorks, Inc. >>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>> November 23, 2020 >>>> >>>> >>>> To get started, type doc. >>>> For product information, visit www.mathworks.com. >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay wrote: >>>> >>>>> You are missing one more step: >>>>> >>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>> >>>>> No run matlab manually on "MB108SMEC028" with the command >>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>> >>>>> Does this work for you? As the message indicates this command is >>>>> invoked by "matlab_ls_test" - and that is failing. >>>>> >>>>> Satish >>>>> >>>>> >>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>> >>>>> > Hi Sathish, >>>>> > >>>>> > I tried the following procedure >>>>> > >>>>> > *$make * >>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>> > Building with 'gcc'. >>>>> > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> > In function ?PetscBinaryWrite?: >>>>> > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>> > warning: ?err? may be used uninitialized in this function >>>>> > [-Wmaybe-uninitialized] >>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> > | ^ >>>>> > >>>>> > MEX completed successfully. >>>>> > Building with 'gcc'. >>>>> > MEX completed successfully. >>>>> > Building with 'gcc'. >>>>> > MEX completed successfully. >>>>> > Building with 'gcc'. >>>>> > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> > In function ?PetscBinaryWrite?: >>>>> > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>> > warning: ?err? may be used uninitialized in this function >>>>> > [-Wmaybe-uninitialized] >>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> > | ^ >>>>> > >>>>> > MEX completed successfully. >>>>> > ========================================= >>>>> > Now to check if the libraries are working do: >>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>> > >>>>> > *$make test query=requires queryval=matlab >>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>> queryval=matlab >>>>> > query=requires >>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>> > -------------------------------------------------------------- >>>>> > # [0]PETSC ERROR: Error in external library >>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>> > # [0]PETSC ERROR: See >>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > for trouble shooting. >>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>> Mon Sep >>>>> > 4 10:02:32 2023 >>>>> > # [0]PETSC ERROR: Configure options >>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>> > -------------------------------------------------------------- >>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>> > # [0]PETSC ERROR: >>>>> > # [0]PETSC ERROR: See >>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > for trouble shooting. >>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>> Mon Sep >>>>> > 4 10:02:32 2023 >>>>> > # [0]PETSC ERROR: Configure options >>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > # [0]PETSC ERROR: >>>>> > >>>>> ------------------------------------------------------------------------ >>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>> Violation, >>>>> > probably memory access out of range >>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>> -on_error_attach_debugger >>>>> > # [0]PETSC ERROR: or see >>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple >>>>> Mac OS >>>>> > X to find memory corruption errors >>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>>>> link, >>>>> > and run >>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>> > -------------------------------------------------------------- >>>>> > # [0]PETSC ERROR: Signal received >>>>> > # [0]PETSC ERROR: See >>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > for trouble shooting. >>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>> Mon Sep >>>>> > 4 10:02:32 2023 >>>>> > # [0]PETSC ERROR: Configure options >>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>>> > # >>>>> -------------------------------------------------------------------------- >>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>> > # with errorcode 50162059. >>>>> > # >>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> > # You may or may not see output from other processes, depending on >>>>> > # exactly when Open MPI kills them. >>>>> > # >>>>> -------------------------------------------------------------------------- >>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>> > CC >>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>> > CLINKER >>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>> > TEST >>>>> > >>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>> code: 124 >>>>> > # Running problem 5 >>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>> > -------------------------------------------------------------- >>>>> > # [0]PETSC ERROR: Error in external library >>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>> > # [0]PETSC ERROR: See >>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > for trouble shooting. >>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>> MB108SMEC028 by >>>>> > vit Mon Sep 4 10:02:34 2023 >>>>> > # [0]PETSC ERROR: Configure options >>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>> > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>> entire >>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>> > # >>>>> -------------------------------------------------------------------------- >>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>> > # with errorcode 126076. >>>>> > # >>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> > # You may or may not see output from other processes, depending on >>>>> > # exactly when Open MPI kills them. >>>>> > # >>>>> -------------------------------------------------------------------------- >>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>> failed >>>>> > so no diff >>>>> > >>>>> > # ------------- >>>>> > # Summary >>>>> > # ------------- >>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> > # success 0/2 tests (0.0%) >>>>> > # failed 2/2 tests (100.0%) >>>>> > # todo 0/2 tests (0.0%) >>>>> > # skip 0/2 tests (0.0%) >>>>> > # >>>>> > # Wall clock time for tests: 4 sec >>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>> > # >>>>> > # To rerun failed tests: >>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>> > # >>>>> > # Timing summary (actual test time / total CPU time): >>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>> 0.01 sec >>>>> > >>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>> > *$make matlab_ls_test* >>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>> -Wwrite-strings >>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>> -Wno-strict-aliasing >>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> > >>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>> -lmx >>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>> -lmpi_mpifh >>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>> -lquadmath >>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>> > >>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>> > -tao_smonitor -prob_id 5 -info* >>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>> processors = 1 >>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>> > MB108SMEC028.(none) >>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>> > Running problem 5 >>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>> > 94202473157392 max tags = 2147483647 >>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>> > -------------------------------------------------------------- >>>>> > [0]PETSC ERROR: Error in external library >>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>> > [0]PETSC ERROR: See >>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > for trouble shooting. >>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 >>>>> by vit >>>>> > Mon Sep 4 10:09:56 2023 >>>>> > [0]PETSC ERROR: Configure options >>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>> > [0]PETSC ERROR: -info >>>>> > [0]PETSC ERROR: -prob_id 5 >>>>> > [0]PETSC ERROR: -tao_smonitor >>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>> entire >>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>> > >>>>> -------------------------------------------------------------------------- >>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>> > with errorcode 126076. >>>>> > >>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> > You may or may not see output from other processes, depending on >>>>> > exactly when Open MPI kills them. >>>>> > >>>>> > Please find the attachment for configure.log and make.log files >>>>> > >>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>> wrote: >>>>> > >>>>> > > To use datafiles in the test suite: >>>>> > > >>>>> > > cd $HOME >>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>> > > >>>> - or set >>>>> > > manually with make> >>>>> > > >>>>> > > make test query=requires queryval=matlab >>>>> DATAFILESPATH=$HOME/datafiles >>>>> > > >>>>> > > Satish >>>>> > > >>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>> > > >>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>> > > > >>>>> > > > > Hi Matthew, >>>>> > > > > >>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do >>>>> not have >>>>> > > any >>>>> > > > > separate test files to test PETSc alone. Can you please help >>>>> me how to >>>>> > > > > define this DATAFILESPATH? >>>>> > > > > >>>>> > > > >>>>> > > > That test you tried uses a certain matrix. On our machine, we >>>>> point to >>>>> > > this >>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>>>> have those >>>>> > > > matrices, since they are just for testing here. That >>>>> > > > is why I suggested just using a different matrix, or running a >>>>> problem >>>>> > > you >>>>> > > > care about in IBAMR. >>>>> > > > >>>>> > > > Thanks, >>>>> > > > >>>>> > > > Matt >>>>> > > > >>>>> > > > >>>>> > > > > Thanks and regards >>>>> > > > > Srinivas. >>>>> > > > > >>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>> knepley at gmail.com> >>>>> > > wrote: >>>>> > > > > >>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>> > > petsc-users < >>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>> > > > >> >>>>> > > > >>> Hi Sathish, >>>>> > > > >>> >>>>> > > > >>> Thank you so much for your efforts and the support you are >>>>> giving me >>>>> > > to >>>>> > > > >>> sort this out. >>>>> > > > >>> >>>>> > > > >>> I tried to follow the same procedure which you followed to >>>>> build >>>>> > > Petsc >>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>> > > > >>> >>>>> > > > >>> *$./configure >>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>> PETSC_ARCH=linux-opt >>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>> > > > >>> Using python3 for Python >>>>> > > > >>> >>>>> > > > >>> >>>>> > > >>>>> =============================================================================== >>>>> > > > >>> Configuring PETSc to compile on your system >>>>> > > > >>> >>>>> > > > >>> >>>>> > > > >>> >>>>> > > >>>>> =============================================================================== >>>>> > > > >>> >>>>> > > >>>>> =============================================================================== >>>>> > > > >>> It appears you do >>>>> not have >>>>> > > valgrind >>>>> > > > >>> installed on your system. >>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>> > > > >>> Or install >>>>> > > valgrind-devel or >>>>> > > > >>> equivalent using your package manager. >>>>> > > > >>> Then rerun ./configure >>>>> > > > >>> >>>>> > > > >>> >>>>> > > >>>>> =============================================================================== >>>>> > > > >>> Compilers: >>>>> > > > >>> >>>>> > > > >>> C Compiler: >>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>> > > -fPIC >>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>> -Wno-unknown-pragmas >>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>> > > > >>> C++ Compiler: >>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>> -Wno-unknown-pragmas >>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>> > > > >>> Fortran Compiler: >>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument >>>>> -O3 >>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>> 9.4.0 >>>>> > > > >>> Linkers: >>>>> > > > >>> Shared linker: >>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>> > > -shared >>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>> > > -Wno-unknown-pragmas >>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>> > > > >>> Dynamic linker: >>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>> > > -shared >>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>> > > -Wno-unknown-pragmas >>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>> > > > >>> make: >>>>> > > > >>> Version: 4.2 >>>>> > > > >>> /usr/bin/make >>>>> > > > >>> BlasLapack: >>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>> -omp_num_threads >>>>> > >

to >>>>> > > > >>> control the number of threads >>>>> > > > >>> uses 8 byte integers >>>>> > > > >>> MPI: >>>>> > > > >>> Version: 3 >>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>> > > --oversubscribe >>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>> > > > >>> pthread: >>>>> > > > >>> cmake: >>>>> > > > >>> Version: 3.16.3 >>>>> > > > >>> /usr/bin/cmake >>>>> > > > >>> regex: >>>>> > > > >>> Matlab: >>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>> > > > >>> MatlabEngine: >>>>> > > > >>> Library: >>>>> > > > >>> >>>>> > > >>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>>> -lmx -lmat >>>>> > > -lut >>>>> > > > >>> -licudata -licui18n -licuuc >>>>> > > > >>> Language used to compile PETSc: C >>>>> > > > >>> PETSc: >>>>> > > > >>> PETSC_ARCH: linux-opt >>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>> > > > >>> Scalar type: real >>>>> > > > >>> Precision: double >>>>> > > > >>> Support for __float128 >>>>> > > > >>> Integer size: 4 bytes >>>>> > > > >>> shared libraries: enabled >>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>> > > > >>> >>>>> > > > >>> >>>>> > > >>>>> xxx=========================================================================xxx >>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>> PETSC_ARCH=linux-opt all >>>>> > > > >>> >>>>> > > > >>> >>>>> > > >>>>> xxx=========================================================================xxx >>>>> > > > >>> >>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>>>> -licuuc as >>>>> > > > >>> you suggested earlier. >>>>> > > > >>> >>>>> > > > >>> *$make* >>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>> > > > >>> Building with 'gcc'. >>>>> > > > >>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>> > > > >>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>> > > > >>> [-Wmaybe-uninitialized] >>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>> socket\n"); >>>>> > > > >>> | ^ >>>>> > > > >>> >>>>> > > > >>> MEX completed successfully. >>>>> > > > >>> Building with 'gcc'. >>>>> > > > >>> MEX completed successfully. >>>>> > > > >>> Building with 'gcc'. >>>>> > > > >>> MEX completed successfully. >>>>> > > > >>> Building with 'gcc'. >>>>> > > > >>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>> > > > >>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>> > > > >>> [-Wmaybe-uninitialized] >>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>> socket\n"); >>>>> > > > >>> | ^ >>>>> > > > >>> >>>>> > > > >>> MEX completed successfully. >>>>> > > > >>> ========================================= >>>>> > > > >>> Now to check if the libraries are working do: >>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>> PETSC_ARCH=linux-opt check >>>>> > > > >>> =============================================== >>>>> > > > >>> >>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>> > > > >>> TEST >>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>> > > > >>> >>>>> -------------------------------------------------------------- >>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>> > > > >>> >>>>> > > > >> >>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>> defined, so it >>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>> yours. >>>>> > > > >> >>>>> > > > >> Thanks, >>>>> > > > >> >>>>> > > > >> Matt >>>>> > > > >> >>>>> > > > >> >>>>> > > > >>> # [0]PETSC ERROR: See >>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>> trouble >>>>> > > > >>> shooting. >>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 >>>>> by vit >>>>> > > Sun >>>>> > > > >>> Sep 3 11:51:03 2023 >>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>> COPTFLAGS=-O3 >>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>> --with-debugging=0 >>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line >>>>> 1444 in >>>>> > > > >>> >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>> > > > >>> >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>> > > > >>> >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>> -------send >>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>> > > > >>> # >>>>> > > > >>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>> MPI_COMM_SELF >>>>> > > > >>> # with errorcode 113065. >>>>> > > > >>> # >>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>> processes. >>>>> > > > >>> # You may or may not see output from other processes, >>>>> depending on >>>>> > > > >>> # exactly when Open MPI kills them. >>>>> > > > >>> # >>>>> > > > >>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>> diff >>>>> > > > >>> CC >>>>> > > > >>> >>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>> > > > >>> CLINKER >>>>> > > > >>> >>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>> > > > >>> TEST >>>>> > > > >>> >>>>> > > >>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>> Error >>>>> > > code: 124 >>>>> > > > >>> # Running problem 5 >>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>> > > > >>> >>>>> -------------------------------------------------------------- >>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>> > > > >>> # [0]PETSC ERROR: See >>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>> trouble >>>>> > > > >>> shooting. >>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>> > > MB108SMEC028 by >>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>> COPTFLAGS=-O3 >>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>> --with-debugging=0 >>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>> > > > >>> >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>> > > > >>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>> -------send >>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>> > > > >>> # >>>>> > > > >>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>> MPI_COMM_SELF >>>>> > > > >>> # with errorcode 126076. >>>>> > > > >>> # >>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>> processes. >>>>> > > > >>> # You may or may not see output from other processes, >>>>> depending on >>>>> > > > >>> # exactly when Open MPI kills them. >>>>> > > > >>> # >>>>> > > > >>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>> Command >>>>> > > > >>> failed so no diff >>>>> > > > >>> >>>>> > > > >>> # ------------- >>>>> > > > >>> # Summary >>>>> > > > >>> # ------------- >>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> > > > >>> # success 0/2 tests (0.0%) >>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>> > > > >>> # >>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>> > > > >>> # >>>>> > > > >>> # To rerun failed tests: >>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>> > > > >>> # >>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 >>>>> sec / >>>>> > > 0.02 sec >>>>> > > > >>> >>>>> > > > >>> *How to sort out this error?* >>>>> > > > >>> >>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>> > > > >>> *$make matlab_ls_test* >>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>> > > -Wwrite-strings >>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>> > > -Wno-strict-aliasing >>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>> -O3 >>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>> matlab_ls_test.c >>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> > > > >>> >>>>> > > >>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>> -lmex >>>>> > > -lmx >>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>> > > -lmpi_mpifh >>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>> -lpthread >>>>> > > -lquadmath >>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>> > > > >>> >>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>>> find the >>>>> > > > >>> attachment and do the needful. >>>>> > > > >>> >>>>> > > > >>> >>>>> > > > >>> Thanks and regards >>>>> > > > >>> Srinivas >>>>> > > > >>> >>>>> > > > >>> >>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>> balay at mcs.anl.gov> >>>>> > > wrote: >>>>> > > > >>> >>>>> > > > >>>> Perhaps you can try the following to get additional info - >>>>> and debug >>>>> > > > >>>> >>>>> > > > >>>> Satish >>>>> > > > >>>> ---------- >>>>> > > > >>>> >>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>> > > > >>>> balay at compute-386-07 >>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>> > > > >>>> make matlab_ls_test >>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>> -fPIC >>>>> > > -Wall >>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>> > > -fstack-protector >>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>> > > -Wno-strict-aliasing >>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>> -O3 >>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>> > > > >>>> >>>>> > > >>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>> > > > >>>> matlab_ls_test.c >>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>> > > > >>>> >>>>> > > >>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>> > > > >>>> >>>>> > > >>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>> > > > >>>> >>>>> > > >>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>> > > > >>>> >>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread >>>>> -lm -leng >>>>> > > -lmex >>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>>>> -lmpifort >>>>> > > -lmpi >>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>>>> -ldl -o >>>>> > > > >>>> matlab_ls_test >>>>> > > > >>>> balay at compute-386-07 >>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>> ./matlab_ls_test >>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>>> > > processors >>>>> > > > >>>> = 1 >>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>> > > > >>>> compute-386-07.(none) >>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>> > > > >>>> Running problem 5 >>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>> 1140850689 >>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>> command >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>> > > > >>>> TestingInitialize >>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>> string: >>>>> > > > >>>> TestingInitialize >>>>> > > > >>>> 5 >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> <<<< Now verify if the above matlab command actually works >>>>> for you >>>>> > > - on >>>>> > > > >>>> this machine..>>>>> >>>>> > > > >>>> >>>>> > > > >>>> balay at compute-386-07 >>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> < M A T L A B (R) > >>>>> > > > >>>> >>>>> > > > >>>> Copyright 1984-2021 The MathWorks, >>>>> Inc. >>>>> > > > >>>> >>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>> (glnxa64) >>>>> > > > >>>> >>>>> > > > >>>> February 17, 2021 >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> To get started, type doc. >>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>> > > > >>>> >>>>> > > > >>>> >> >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>> > > > >>>> >>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>> [reverting >>>>> > > thread >>>>> > > > >>>> to petsc-users only] >>>>> > > > >>>> > >>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>> > > corresponding >>>>> > > > >>>> configure.log, make.log [compressed]? >>>>> > > > >>>> > >>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>> Ubuntu-20.04, >>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>> > > > >>>> > >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>> > > > >>>> > main >>>>> > > > >>>> > release >>>>> > > > >>>> > * release-3.13 >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>> > > matlab/R2021a >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>> > > > >>>> >>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>> PETSC_ARCH=linux-opt >>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>> > > > >>>> >>>>> > > >>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>> > > > >>>> >>>>> > > >>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> > > > >>>> > >>>>> > > > >>>> > Compilers: >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> > C Compiler: >>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>> -fPIC >>>>> > > -Wall >>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>> > > -fstack-protector >>>>> > > > >>>> -fvisibility=hidden -O3 >>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>> > > > >>>> > C++ Compiler: >>>>> > > > >>>> >>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>> > > -fstack-protector >>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>> > > > >>>> > Fortran Compiler: >>>>> > > > >>>> >>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>> > > -Wall >>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>> 9.4.0 >>>>> > > > >>>> > Linkers: >>>>> > > > >>>> > Shared linker: >>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>> > > -shared -fPIC >>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>> -Wno-unknown-pragmas >>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>> > > > >>>> > Dynamic linker: >>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>> > > -shared -fPIC >>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>> -Wno-unknown-pragmas >>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>> > > > >>>> > make: >>>>> > > > >>>> > Version: 4.2 >>>>> > > > >>>> > /usr/bin/make >>>>> > > > >>>> > BlasLapack: >>>>> > > > >>>> > Library: >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>> > > > >>>> >>>>> > > >>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>> > > > >>>> >>>>> > > >>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>> > > > >>>> -liomp5 -lpthread >>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>> -omp_num_threads >>>>> > >

>>>>> > > > >>>> to control the number of threads >>>>> > > > >>>> > uses 8 byte integers >>>>> > > > >>>> > MPI: >>>>> > > > >>>> > Version: 4 >>>>> > > > >>>> > Includes: >>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>> > > > >>>> > Mpiexec: >>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>> > > > >>>> > pthread: >>>>> > > > >>>> > Library: -lpthread >>>>> > > > >>>> > cmake: >>>>> > > > >>>> > Version: 3.16.3 >>>>> > > > >>>> > /usr/bin/cmake >>>>> > > > >>>> > regex: >>>>> > > > >>>> > Matlab: >>>>> > > > >>>> > Includes: >>>>> > > > >>>> >>>>> > > >>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>> > > > >>>> > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>> > > > >>>> > MatlabEngine: >>>>> > > > >>>> > Library: >>>>> > > > >>>> >>>>> > > >>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>> > > > >>>> >>>>> > > >>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>> > > > >>>> >>>>> > > >>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>> > > > >>>> > sowing: >>>>> > > > >>>> > Version: 1.1.25 >>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>> > > > >>>> > valgrind: >>>>> > > > >>>> > Language used to compile PETSc: C >>>>> > > > >>>> > PETSc: >>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>> > > > >>>> > Scalar type: real >>>>> > > > >>>> > Precision: double >>>>> > > > >>>> > Support for __float128 >>>>> > > > >>>> > Integer size: 4 bytes >>>>> > > > >>>> > shared libraries: enabled >>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> xxx=========================================================================xxx >>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>> PETSC_ARCH=linux-opt all >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> xxx=========================================================================xxx >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> >>>>> > > > >>>> > >>>>> > > > >>>> > >>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>> > > > >>>> > Building with 'gcc'. >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>> > > socket\n"); >>>>> > > > >>>> > | ^ >>>>> > > > >>>> > >>>>> > > > >>>> > MEX completed successfully. >>>>> > > > >>>> > Building with 'gcc'. >>>>> > > > >>>> > MEX completed successfully. >>>>> > > > >>>> > Building with 'gcc'. >>>>> > > > >>>> > MEX completed successfully. >>>>> > > > >>>> > Building with 'gcc'. >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>> > > > >>>> > >>>>> > > > >>>> >>>>> > > >>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>> > > socket\n"); >>>>> > > > >>>> > | ^ >>>>> > > > >>>> > >>>>> > > > >>>> > MEX completed successfully. >>>>> > > > >>>> > ========================================= >>>>> > > > >>>> > Now to check if the libraries are working do: >>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt >>>>> check >>>>> > > > >>>> > ========================================= >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>> > > query=requires >>>>> > > > >>>> queryval=matlab >>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>> > > > >>>> > TEST >>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>> > > > >>>> > # ../ex72: >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>> diff >>>>> > > > >>>> > CC >>>>> > > > >>>> >>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>> > > > >>>> > CLINKER >>>>> > > > >>>> >>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>> > > > >>>> > TEST >>>>> > > > >>>> >>>>> > > >>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>> Error >>>>> > > code: >>>>> > > > >>>> 1 >>>>> > > > >>>> > # ../matlab_ls_test: >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>> SKIP >>>>> > > Command >>>>> > > > >>>> failed so no diff >>>>> > > > >>>> > >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>> > > query=requires >>>>> > > > >>>> queryval=matlab >>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>> > > > >>>> > TEST >>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>> > > > >>>> > TEST >>>>> > > > >>>> >>>>> > > >>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> > > > >>>> > >>>>> > > > >>>> > # ------------- >>>>> > > > >>>> > # Summary >>>>> > > > >>>> > # ------------- >>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>> > > > >>>> > # >>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>> 15.190000000000001 >>>>> > > sec >>>>> > > > >>>> > # >>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>> 6.47 sec / >>>>> > > 7.54 >>>>> > > > >>>> sec >>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>> > > > >>>> > >>>>> > > > >>>> > >>>>> > > > >>>> > >>>>> > > > >>>> > >>>>> > > > >>>> > >>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>> > > > >>>> > >>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried >>>>> to >>>>> > > > >>>> configure petsc >>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. >>>>> After >>>>> > > > >>>> running make >>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>> message. >>>>> > > > >>>> > > >>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> # Error >>>>> > > > >>>> code: 124 >>>>> > > > >>>> > > # Running problem 5 >>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>> > > > >>>> > > >>>>> -------------------------------------------------------------- >>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > > > >>>> > > for trouble shooting. >>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>> 2020 >>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>> > > > >>>> MB108SMEC028 by >>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>> COPTFLAGS=-O3 >>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>> > > > >>>> --with-debugging=0 >>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>>> > > --with-matlab-engine=1 >>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>> in >>>>> > > > >>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>> > > > >>>> > > >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>> > > -------send >>>>> > > > >>>> entire >>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>> > > > >>>> > > # >>>>> > > > >>>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>> MPI_COMM_SELF >>>>> > > > >>>> > > # with errorcode 126076. >>>>> > > > >>>> > > # >>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>> MPI >>>>> > > > >>>> processes. >>>>> > > > >>>> > > # You may or may not see output from other processes, >>>>> depending >>>>> > > on >>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>> > > > >>>> > > # >>>>> > > > >>>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>>> > > >>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>> > > > >>>> > > >>>>> > > > >>>> > > Thanks >>>>> > > > >>>> > > Srinivas >>>>> > > > >>>> > > >>>>> > > > >>>> > > >>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>> > > > >>>> > > >>>>> > > > >>>> > > > I think there should be two hyphens in >>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > i.e.: >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>> 20PHD0548 via >>>>> > > > >>>> petsc-users < >>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>> > > > >>>> > > > >>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>> > > > >>>> > > >> >>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>> balay at mcs.anl.gov> >>>>> > > > >>>> wrote: >>>>> > > > >>>> > > >> >>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>>> will work >>>>> > > > >>>> here]. >>>>> > > > >>>> > > >>> >>>>> > > > >>>> > > >>> i.e: >>>>> > > > >>>> > > >>> >>>>> > > > >>>> > > >>> ./configure >>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>> > > PETSC_ARCH=linux-opt >>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>>> --with-matlab-engine=1 >>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>> > > > >>>> > > >>> >>>>> > > > >>>> > > >>> Satish >>>>> > > > >>>> > > >>> >>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>> > > petsc-users >>>>> > > > >>>> wrote: >>>>> > > > >>>> > > >>> >>>>> > > > >>>> > > >>> > Hi Satish, >>>>> > > > >>>> > > >>> > >>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>> > > > >>>> > > >>> > >>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>> > > > >>>> > > >>> > >>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>> > > balay at mcs.anl.gov> >>>>> > > > >>>> wrote: >>>>> > > > >>>> > > >>> > >>>>> > > > >>>> > > >>> > > Also: >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in >>>>> this mode. >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>> dependency/conflicts >>>>> > > across >>>>> > > > >>>> packages] >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > > Satish >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>> petsc-users wrote: >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > >>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] >>>>> conflict >>>>> > > with >>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack >>>>> with >>>>> > > > >>>> matlab - to >>>>> > > > >>>> > > >>> have a >>>>> > > > >>>> > > >>> > > compatible build >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > Satish >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 >>>>> via >>>>> > > > >>>> petsc-users >>>>> > > > >>>> > > >>> wrote: >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB >>>>> is not >>>>> > > > >>>> working. It is >>>>> > > > >>>> > > >>> > > showing >>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster >>>>> with >>>>> > > > >>>> libmesh and >>>>> > > > >>>> > > >>> this is >>>>> > > > >>>> > > >>> > > for >>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I >>>>> tried without >>>>> > > > >>>> linking >>>>> > > > >>>> > > >>> Matlab >>>>> > > > >>>> > > >>> > > with >>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>>> configuring >>>>> > > > >>>> libmesh 1.6.2 >>>>> > > > >>>> > > >>> that >>>>> > > > >>>> > > >>> > > PETSc >>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>>> > > specified. >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>>> libmesh with >>>>> > > > >>>> PETSc and >>>>> > > > >>>> > > >>> Matlab >>>>> > > > >>>> > > >>> > > is in >>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>>> > > geometries >>>>> > > > >>>> it is >>>>> > > > >>>> > > >>> > > mentioned to >>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>>> various >>>>> > > things >>>>> > > > >>>> and ended >>>>> > > > >>>> > > >>> up with >>>>> > > > >>>> > > >>> > > > > errors. >>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to >>>>> do my >>>>> > > > >>>> research work. >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>>>> possible. >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>> > > > >>>> > > >>> > > > > Srinivas >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>> > > > >>>> mail2amneet at gmail.com> >>>>> > > > >>>> > > >>> > > wrote: >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>> > > > >>>> > > >>> > > > > > >>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>> libMesh for >>>>> > > the >>>>> > > > >>>> WEC >>>>> > > > >>>> > > >>> application. >>>>> > > > >>>> > > >>> > > You >>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>>> builds with >>>>> > > > >>>> Matlab. >>>>> > > > >>>> > > >>> > > > > > >>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting >>>>> to build >>>>> > > > >>>> libMesh? >>>>> > > > >>>> > > >>> > > > > > >>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>> > > > >>>> > > >>> > > > > > >>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU >>>>> SRINIVAS >>>>> > > > >>>> 20PHD0548 via >>>>> > > > >>>> > > >>> > > petsc-users >>>>> > > > >>>> > > >>> > > > > > wrote: >>>>> > > > >>>> > > >>> > > > > > >>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>>>> removing all >>>>> > > > >>>> occurrences >>>>> > > > >>>> > > >>> of >>>>> > > > >>>> > > >>> > > "-lut >>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran >>>>> "make >>>>> > > test" >>>>> > > > >>>> got the >>>>> > > > >>>> > > >>> > > following >>>>> > > > >>>> > > >>> > > > > >> errors >>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>> > > > >>>> > > >>> > > > > >> TEST >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>> > > > >>>> > > >>> > > > > >> not ok >>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>> > > > >>>> > > >>> Error >>>>> > > > >>>> > > >>> > > code: 124 >>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>>>> Error >>>>> > > Message >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> >>>>> -------------------------------------------------------------- >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>> library >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB >>>>> engine >>>>> > > on >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > > > >>>> for >>>>> > > > >>>> > > >>> trouble >>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>>>> 3.13.4, >>>>> > > Aug >>>>> > > > >>>> 01, 2020 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>> > > linux-debug >>>>> > > > >>>> named >>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>> > > > >>>> > > >>> > > > > >> >>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>> > > > >>>> > > >>> > > > > >> >>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>> > > > >>>> > > >>> --with-debugging=1 >>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>> --download-fblaslapack=1 >>>>> > > > >>>> --with-x=0 >>>>> > > > >>>> > > >>> > > > > >> >>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>> PetscMatlabEngineCreate() >>>>> > > line >>>>> > > > >>>> 67 in >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> >>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>> entries: >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of >>>>> Error >>>>> > > > >>>> Message >>>>> > > > >>>> > > >>> -------send >>>>> > > > >>>> > > >>> > > entire >>>>> > > > >>>> > > >>> > > > > >> error message to >>>>> > > petsc-maint at mcs.anl.gov---------- >>>>> > > > >>>> > > >>> > > > > >> # >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>> communicator >>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>> > > > >>>> > > >>> > > > > >> # >>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>>> MPI to >>>>> > > kill >>>>> > > > >>>> all MPI >>>>> > > > >>>> > > >>> > > processes. >>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>> other >>>>> > > processes, >>>>> > > > >>>> > > >>> depending on >>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>> > > > >>>> > > >>> > > > > >> # >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>>> > > >>> > > > > >> ok >>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> > > > >>>> # SKIP >>>>> > > > >>>> > > >>> Command >>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>> > > > >>>> > > >>> > > > > >> TEST >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>> > > > >>>> > > >>> > > > > >> not ok >>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>> > > > >>>> > > >>> Error >>>>> > > > >>>> > > >>> > > code: 124 >>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>>>> Error >>>>> > > Message >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> >>>>> -------------------------------------------------------------- >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>> library >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB >>>>> engine >>>>> > > on >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>> > > > >>>> for >>>>> > > > >>>> > > >>> trouble >>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>>>> 3.13.4, >>>>> > > Aug >>>>> > > > >>>> 01, 2020 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>> > > linux-opt >>>>> > > > >>>> named >>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>> > > > >>>> > > >>> > > > > >> >>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>> > > > >>>> > > >>> > > > > >> >>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>> > > > >>>> --download-fblaslapack=1 >>>>> > > > >>>> > > >>> > > > > >> >>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>> PetscMatlabEngineCreate() >>>>> > > line >>>>> > > > >>>> 67 in >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> >>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>> entries: >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of >>>>> Error >>>>> > > > >>>> Message >>>>> > > > >>>> > > >>> -------send >>>>> > > > >>>> > > >>> > > entire >>>>> > > > >>>> > > >>> > > > > >> error message to >>>>> > > petsc-maint at mcs.anl.gov---------- >>>>> > > > >>>> > > >>> > > > > >> # >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>> communicator >>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>> > > > >>>> > > >>> > > > > >> # >>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>>> MPI to >>>>> > > kill >>>>> > > > >>>> all MPI >>>>> > > > >>>> > > >>> > > processes. >>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>> other >>>>> > > processes, >>>>> > > > >>>> > > >>> depending on >>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>> > > > >>>> > > >>> > > > > >> # >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -------------------------------------------------------------------------- >>>>> > > > >>>> > > >>> > > > > >> ok >>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>> > > > >>>> # SKIP >>>>> > > > >>>> > > >>> Command >>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>>> > > version. I >>>>> > > > >>>> am >>>>> > > > >>>> > > >>> sharing the >>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc >>>>> 3.13.4 and >>>>> > > > >>>> petsc >>>>> > > > >>>> > > >>> 3.17.5. >>>>> > > > >>>> > > >>> > > Please find >>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish >>>>> Balay < >>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>> > > > >>>> > > >>> > > wrote: >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>>> petsc's >>>>> > > > >>>> > > >>> configure.log/make.log >>>>> > > > >>>> > > >>> > > for >>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>> > > > >>>> > > >>> > > > > >>> >>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> > > -leng >>>>> > > > >>>> -lmex >>>>> > > > >>>> > > >>> -lmx >>>>> > > > >>>> > > >>> > > -lmat -lut >>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - >>>>> we are >>>>> > > seeing: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> >>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" >>>>> are not >>>>> > > > >>>> preset here. >>>>> > > > >>>> > > >>> This >>>>> > > > >>>> > > >>> > > might >>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>> > > > >>>> > > >>> > > and >>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>> -licudata >>>>> > > -licui18n >>>>> > > > >>>> -licuuc" >>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>> 20PHD0548 >>>>> > > via >>>>> > > > >>>> > > >>> petsc-users >>>>> > > > >>>> > > >>> > > wrote: >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>>> building >>>>> > > > >>>> petsc3.13.4 with >>>>> > > > >>>> > > >>> > > matlab and >>>>> > > > >>>> > > >>> > > > > >>> also >>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh >>>>> with >>>>> > > > >>>> petsc3.17.5 and >>>>> > > > >>>> > > >>> matlab. >>>>> > > > >>>> > > >>> > > > > >>> Building >>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>> > > successfully. >>>>> > > > >>>> But >>>>> > > > >>>> > > >>> libmesh is >>>>> > > > >>>> > > >>> > > not >>>>> > > > >>>> > > >>> > > > > >>> able to >>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>> > > > >>>> > > >>> > > > > >>> > >>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>> Satish Balay < >>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>> > > > >>>> > > >>> > > > > >>> > >>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from >>>>> both >>>>> > > > >>>> petsc-3.13 and >>>>> > > > >>>> > > >>> 3.17 [or >>>>> > > > >>>> > > >>> > > 3.19]. >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>> > > friendly to >>>>> > > > >>>> mailing >>>>> > > > >>>> > > >>> list - >>>>> > > > >>>> > > >>> > > or >>>>> > > > >>>> > > >>> > > > > >>> send >>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? >>>>> [or >>>>> > > 3.19?] >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>> > > 20PHD0548 >>>>> > > > >>>> via >>>>> > > > >>>> > > >>> petsc-users >>>>> > > > >>>> > > >>> > > wrote: >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file >>>>> while >>>>> > > building >>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>> > > > >>>> > > >>> > > with >>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do >>>>> the >>>>> > > needful. >>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM >>>>> INTURU >>>>> > > > >>>> SRINIVAS >>>>> > > > >>>> > > >>> 20PHD0548 < >>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>> > > wrote: >>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. >>>>> During >>>>> > > building >>>>> > > > >>>> of >>>>> > > > >>>> > > >>> libmesh, the >>>>> > > > >>>> > > >>> > > error >>>>> > > > >>>> > > >>> > > > > >>> shows >>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM >>>>> Satish >>>>> > > > >>>> Balay < >>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux >>>>> says >>>>> > > > >>>> petsc-3.17 >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>> petsc-3.17.5? >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU >>>>> SRINIVAS >>>>> > > > >>>> 20PHD0548 via >>>>> > > > >>>> > > >>> > > petsc-users >>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with >>>>> MATLAB for >>>>> > > > >>>> working on >>>>> > > > >>>> > > >>> the >>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>> building the >>>>> > > PETSc, >>>>> > > > >>>> using the >>>>> > > > >>>> > > >>> > > following >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEnginePut' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGet' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEnginePut' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGet' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGet' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> > > >>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned >>>>> 1 exit >>>>> > > > >>>> status >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>> [gmakefile.test:185: >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> >>>>> > > > >>>> >>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>> unfinished >>>>> > > jobs.... >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this >>>>> issue >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>> > > > >>>> > > >>> > > > > >>> > > >>>>> > > > >>>> > > >>> > > > > >>> > >>>>> > > > >>>> > > >>> > > > > >>> > >>>>> > > > >>>> > > >>> > > > > >>> >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from >>>>> Vellore >>>>> > > > >>>> Institute of >>>>> > > > >>>> > > >>> > > Technology. >>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain >>>>> legally >>>>> > > > >>>> protected >>>>> > > > >>>> > > >>> > > confidential or >>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>> Institute of >>>>> > > > >>>> Technology?. >>>>> > > > >>>> > > >>> If >>>>> > > > >>>> > > >>> > > you are >>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should >>>>> not >>>>> > > > >>>> disseminate, >>>>> > > > >>>> > > >>> distribute >>>>> > > > >>>> > > >>> > > or copy >>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender >>>>> immediately >>>>> > > > >>>> and destroy >>>>> > > > >>>> > > >>> all >>>>> > > > >>>> > > >>> > > copies of >>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you >>>>> have >>>>> > > > >>>> received this >>>>> > > > >>>> > > >>> email >>>>> > > > >>>> > > >>> > > in error, >>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by >>>>> reply email >>>>> > > and >>>>> > > > >>>> delete >>>>> > > > >>>> > > >>> the >>>>> > > > >>>> > > >>> > > original >>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without >>>>> reading >>>>> > > them.* >>>>> > > > >>>> > > >>> > > > > >> >>>>> > > > >>>> > > >>> > > > > > >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > > >>>>> > > > >>>> > > >>> > > > >>>>> > > > >>>> > > >>> > > >>>>> > > > >>>> > > >>> > >>>>> > > > >>>> > > >>> > >>>>> > > > >>>> > > >>> >>>>> > > > >>>> > > >> >>>>> > > > >>>> > > >> >>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore >>>>> Institute of >>>>> > > > >>>> Technology. >>>>> > > > >>>> > > >> The contents of this email may contain legally >>>>> protected >>>>> > > > >>>> confidential or >>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>> > > Technology?. If >>>>> > > > >>>> you are >>>>> > > > >>>> > > >> not the intended recipient, you should not >>>>> disseminate, >>>>> > > > >>>> distribute or copy >>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately >>>>> and destroy >>>>> > > > >>>> all copies of >>>>> > > > >>>> > > >> this message and any attachments. If you have >>>>> received this >>>>> > > > >>>> email in error, >>>>> > > > >>>> > > >> please promptly notify the sender by reply email and >>>>> delete >>>>> > > the >>>>> > > > >>>> original >>>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>>> > > > >>>> > > >> >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > -- >>>>> > > > >>>> > > > --Amneet >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > >>>>> > > > >>>> > > > >>>>> > > > >>>> > > >>>>> > > > >>>> > > >>>>> > > > >>>> >>>>> > > > >>> >>>>> > > > >>> >>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>>> > > Technology. >>>>> > > > >>> The contents of this email may contain legally protected >>>>> > > confidential or >>>>> > > > >>> privileged information of ?Vellore Institute of >>>>> Technology?. If you >>>>> > > are >>>>> > > > >>> not the intended recipient, you should not disseminate, >>>>> distribute >>>>> > > or copy >>>>> > > > >>> this e-mail. Please notify the sender immediately and >>>>> destroy all >>>>> > > copies of >>>>> > > > >>> this message and any attachments. If you have received this >>>>> email in >>>>> > > error, >>>>> > > > >>> please promptly notify the sender by reply email and delete >>>>> the >>>>> > > original >>>>> > > > >>> email and any backup copies without reading them.* >>>>> > > > >>> >>>>> > > > >> >>>>> > > > >> >>>>> > > > >> -- >>>>> > > > >> What most experimenters take for granted before they begin >>>>> their >>>>> > > > >> experiments is infinitely more interesting than any results >>>>> to which >>>>> > > their >>>>> > > > >> experiments lead. >>>>> > > > >> -- Norbert Wiener >>>>> > > > >> >>>>> > > > >> https://www.cse.buffalo.edu/~knepley/ >>>>> > > > >> >>>>> > > > >> >>>>> > > > > >>>>> > > > > >>>>> > > > > *Disclaimer:This message was sent from Vellore Institute of >>>>> Technology. >>>>> > > > > The contents of this email may contain legally protected >>>>> confidential >>>>> > > or >>>>> > > > > privileged information of ?Vellore Institute of Technology?. >>>>> If you >>>>> > > are >>>>> > > > > not the intended recipient, you should not disseminate, >>>>> distribute or >>>>> > > copy >>>>> > > > > this e-mail. Please notify the sender immediately and destroy >>>>> all >>>>> > > copies of >>>>> > > > > this message and any attachments. If you have received this >>>>> email in >>>>> > > error, >>>>> > > > > please promptly notify the sender by reply email and delete the >>>>> > > original >>>>> > > > > email and any backup copies without reading them.* >>>>> > > > > >>>>> > > > >>>>> > > > >>>>> > > > >>>>> > > >>>>> > >>>>> > >>>> >>>> >>>> >>>> *Disclaimer:This message was sent from Vellore Institute of >>>> Technology. The contents of this email may contain legally protected >>>> confidential or privileged information of ?Vellore Institute of >>>> Technology?. If you are not the intended recipient, you should not >>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>> immediately and destroy all copies of this message and any attachments. If >>>> you have received this email in error, please promptly notify the sender by >>>> reply email and delete the original email and any backup copies without >>>> reading them.* >>>> >>> >>> >>> -- >>> --Amneet >>> >>> >>> >>> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> >> >> > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > > > -- --Amneet -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Tue Sep 5 13:07:05 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Tue, 5 Sep 2023 23:37:05 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: I will try with new version of MATLAB and let you know the status. Thanks and regards Srinivas On Tue, Sep 5, 2023, 23:33 Amneet Bhalla wrote: > Srinivas --- Do you have a different version of MATLAB that you can > install? If your organization has a MATLAB license, you can install recent > versions of MATLAB from mathworks.com > > On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: > >> >> Ok, I have no suggestions. It seems to be more an issue with the >> Matlab than PETSc. You could find a pure Matlab example of using the engine >> (in the Matlab documentation) and try it to see if it works. >> >> Barry >> >> >> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >> I got the same errors for petsc 3.17.5 >> >> >> *make all* >> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >> BEGINNING TO COMPILE MATLAB INTERFACE >> Building with 'gcc'. >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> ========================================= >> ========================================= >> Now to check if the libraries are working do: >> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >> >> *make test query=requires queryval=matlab >> DATAFILESPATH=/home/vit/datafiles/* >> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >> query=requires >> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Error in external library >> # [0]PETSC ERROR: Unable to start MATLAB engine with >> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >> Sep 5 21:39:22 2023 >> # [0]PETSC ERROR: Configure options >> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >> # [0]PETSC ERROR: #6 PCSetUp_LU() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >> # [0]PETSC ERROR: #7 PCSetUp() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >> # [0]PETSC ERROR: #8 KSPSetUp() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >> # [0]PETSC ERROR: #9 main() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -check_pointer_intensity 0 >> # [0]PETSC ERROR: -error_output_stdout >> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >> # [0]PETSC ERROR: -malloc_dump >> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >> # [0]PETSC ERROR: -pc_type lu >> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >> # with errorcode 85. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >> >> >> # FAILED ksp_ksp_tutorials-ex72_12 >> # >> # To rerun failed tests: >> # /usr/bin/make -f gmakefile test test-fail=1 >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >> >>> >>> The error is occuring during >>> >>> e->ep = engOpen(buffer); >>> >>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 >>> -nodisplay -nosplash from your terminal shell worked we have to assume the >>> problem is occuring when engOpen() is attempting to connect the stdout and >>> stdin from the Matlab session that is launched to the executable. >>> >>> You can try the following. In 3.17.5 edit the >>> file src/sys/classes/matlabengine/matlab.c and locate the line >>> >>> e->ep = engOpen(buffer); >>> >>> replace it with >>> >>> e->ep = engOpen(""); >>> >>> Now in the PETSc directory do make all (it should recompile one file) >>> and then run the >>> >>> make test query=requires queryval=matlab >>> DATAFILESPATH=/home/vit/datafiles/ >>> >>> again >>> >>> >>> >>> >>> >>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < >>> petsc-users at mcs.anl.gov> wrote: >>> >>> Hi Amneeth, >>> >>> I think the errors are different with petsc 3.17.5 >>> >>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> The version of PETSc you are using is out-of-date, we recommend updating >>> to the new release >>> Available Version: 3.19.5 Installed Version: 3.17.5 >>> https://petsc.org/release/download/ >>> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> >>> ============================================================================================= >>> Configuring PETSc to compile on your system >>> >>> >>> ============================================================================================= >>> Compilers: >>> >>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>> -fvisibility=hidden -O3 >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> Linkers: >>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>> -fvisibility=hidden -O3 >>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>> -fvisibility=hidden -O3 >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>> BlasLapack: >>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to >>> control the number of threads >>> uses 8 byte integers >>> MPI: >>> Version: 3 >>> mpiexec: /usr/bin/mpiexec >>> Implementation: openmpi >>> OMPI_VERSION: 4.0.3 >>> pthread: >>> cmake: >>> Version: 3.16.3 >>> /usr/bin/cmake >>> regex: >>> Matlab: >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> /usr/local/MATLAB/R2020b >>> MatlabEngine: >>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>> Language used to compile PETSc: C >>> PETSc: >>> PETSC_ARCH: linux-opt >>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>> Prefix: >>> Scalar type: real >>> Precision: double >>> Support for __float128 >>> Integer size: 4 bytes >>> Single library: yes >>> Shared libraries: yes >>> Memory alignment from malloc(): 16 bytes >>> Using GNU make: /usr/bin/make >>> >>> xxx=========================================================================xxx >>> Configure stage complete. Now build PETSc libraries with: >>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>> all >>> >>> xxx=========================================================================xxx >>> >>> *$make* >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> Building with 'gcc'. >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> ========================================= >>> ========================================= >>> Now to check if the libraries are working do: >>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>> >>> *$make test query=requires queryval=matlab >>> DATAFILESPATH=/home/vit/datafiles/* >>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>> --testdir=./linux-opt/tests >>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>> query=requires >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>> # [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> # [0]PETSC ERROR: Error in external library >>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>> shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>> Sep 5 10:15:57 2023 >>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>> # [0]PETSC ERROR: #7 PCSetUp() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>> # [0]PETSC ERROR: #8 KSPSetUp() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>> # [0]PETSC ERROR: #9 main() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>> # [0]PETSC ERROR: -error_output_stdout >>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>> # [0]PETSC ERROR: -malloc_dump >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> # [0]PETSC ERROR: -pc_type lu >>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> # >>> -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> # with errorcode 85. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # >>> -------------------------------------------------------------------------- >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> >>> >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> # >>> # To rerun failed tests: >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> >>> To get the info of the error there is no specific probe id reported. >>> >>> How to check error info and proceed further? >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>> wrote: >>> >>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>> options that Satish mentioned? >>>> >>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>> petsc-users wrote: >>>> >>>>> Sorry for missing that. >>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>> >>>>> < M A T L A B (R) > >>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>> November 23, 2020 >>>>> >>>>> >>>>> To get started, type doc. >>>>> For product information, visit www.mathworks.com. >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>> wrote: >>>>> >>>>>> You are missing one more step: >>>>>> >>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> >>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>> >>>>>> Does this work for you? As the message indicates this command is >>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>> >>>>>> Satish >>>>>> >>>>>> >>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>> >>>>>> > Hi Sathish, >>>>>> > >>>>>> > I tried the following procedure >>>>>> > >>>>>> > *$make * >>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > Building with 'gcc'. >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > In function ?PetscBinaryWrite?: >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > warning: ?err? may be used uninitialized in this function >>>>>> > [-Wmaybe-uninitialized] >>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > | ^ >>>>>> > >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > In function ?PetscBinaryWrite?: >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > warning: ?err? may be used uninitialized in this function >>>>>> > [-Wmaybe-uninitialized] >>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > | ^ >>>>>> > >>>>>> > MEX completed successfully. >>>>>> > ========================================= >>>>>> > Now to check if the libraries are working do: >>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>> > >>>>>> > *$make test query=requires queryval=matlab >>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>> queryval=matlab >>>>>> > query=requires >>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Error in external library >>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>> > # [0]PETSC ERROR: >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: >>>>>> > >>>>>> ------------------------------------------------------------------------ >>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>> Violation, >>>>>> > probably memory access out of range >>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>> -on_error_attach_debugger >>>>>> > # [0]PETSC ERROR: or see >>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>> Apple Mac OS >>>>>> > X to find memory corruption errors >>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>>>>> link, >>>>>> > and run >>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Signal received >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>> file >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> > # with errorcode 50162059. >>>>>> > # >>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > # You may or may not see output from other processes, depending on >>>>>> > # exactly when Open MPI kills them. >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> > CC >>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > CLINKER >>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > TEST >>>>>> > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> code: 124 >>>>>> > # Running problem 5 >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Error in external library >>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>> MB108SMEC028 by >>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire >>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > # with errorcode 126076. >>>>>> > # >>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > # You may or may not see output from other processes, depending on >>>>>> > # exactly when Open MPI kills them. >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>> failed >>>>>> > so no diff >>>>>> > >>>>>> > # ------------- >>>>>> > # Summary >>>>>> > # ------------- >>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > # success 0/2 tests (0.0%) >>>>>> > # failed 2/2 tests (100.0%) >>>>>> > # todo 0/2 tests (0.0%) >>>>>> > # skip 0/2 tests (0.0%) >>>>>> > # >>>>>> > # Wall clock time for tests: 4 sec >>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>> > # >>>>>> > # To rerun failed tests: >>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> > # >>>>>> > # Timing summary (actual test time / total CPU time): >>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>> 0.01 sec >>>>>> > >>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>> > *$make matlab_ls_test* >>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>> -Wwrite-strings >>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> -Wno-strict-aliasing >>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>> -lmx >>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>> -lmpi_mpifh >>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>> -lquadmath >>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>> > >>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>> processors = 1 >>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>> > MB108SMEC028.(none) >>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>> > Running problem 5 >>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>> > 94202473157392 max tags = 2147483647 >>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > [0]PETSC ERROR: Error in external library >>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 >>>>>> by vit >>>>>> > Mon Sep 4 10:09:56 2023 >>>>>> > [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > [0]PETSC ERROR: -info >>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire >>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > >>>>>> -------------------------------------------------------------------------- >>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > with errorcode 126076. >>>>>> > >>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > You may or may not see output from other processes, depending on >>>>>> > exactly when Open MPI kills them. >>>>>> > >>>>>> > Please find the attachment for configure.log and make.log files >>>>>> > >>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>> wrote: >>>>>> > >>>>>> > > To use datafiles in the test suite: >>>>>> > > >>>>>> > > cd $HOME >>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>> > > >>>>> - or set >>>>>> > > manually with make> >>>>>> > > >>>>>> > > make test query=requires queryval=matlab >>>>>> DATAFILESPATH=$HOME/datafiles >>>>>> > > >>>>>> > > Satish >>>>>> > > >>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>> > > >>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>> > > > >>>>>> > > > > Hi Matthew, >>>>>> > > > > >>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do >>>>>> not have >>>>>> > > any >>>>>> > > > > separate test files to test PETSc alone. Can you please help >>>>>> me how to >>>>>> > > > > define this DATAFILESPATH? >>>>>> > > > > >>>>>> > > > >>>>>> > > > That test you tried uses a certain matrix. On our machine, we >>>>>> point to >>>>>> > > this >>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>>>>> have those >>>>>> > > > matrices, since they are just for testing here. That >>>>>> > > > is why I suggested just using a different matrix, or running a >>>>>> problem >>>>>> > > you >>>>>> > > > care about in IBAMR. >>>>>> > > > >>>>>> > > > Thanks, >>>>>> > > > >>>>>> > > > Matt >>>>>> > > > >>>>>> > > > >>>>>> > > > > Thanks and regards >>>>>> > > > > Srinivas. >>>>>> > > > > >>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>> knepley at gmail.com> >>>>>> > > wrote: >>>>>> > > > > >>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>> > > petsc-users < >>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>> > > > >> >>>>>> > > > >>> Hi Sathish, >>>>>> > > > >>> >>>>>> > > > >>> Thank you so much for your efforts and the support you are >>>>>> giving me >>>>>> > > to >>>>>> > > > >>> sort this out. >>>>>> > > > >>> >>>>>> > > > >>> I tried to follow the same procedure which you followed to >>>>>> build >>>>>> > > Petsc >>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>> > > > >>> >>>>>> > > > >>> *$./configure >>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> PETSC_ARCH=linux-opt >>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>> > > > >>> Using python3 for Python >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> It appears you do >>>>>> not have >>>>>> > > valgrind >>>>>> > > > >>> installed on your system. >>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>> > > > >>> Or install >>>>>> > > valgrind-devel or >>>>>> > > > >>> equivalent using your package manager. >>>>>> > > > >>> Then rerun ./configure >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> Compilers: >>>>>> > > > >>> >>>>>> > > > >>> C Compiler: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -fPIC >>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>> C++ Compiler: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>> > > > >>> Fortran Compiler: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>> -Wno-unused-dummy-argument -O3 >>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>> 9.4.0 >>>>>> > > > >>> Linkers: >>>>>> > > > >>> Shared linker: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -shared >>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > > -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Dynamic linker: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -shared >>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > > -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> > > > >>> make: >>>>>> > > > >>> Version: 4.2 >>>>>> > > > >>> /usr/bin/make >>>>>> > > > >>> BlasLapack: >>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>> -omp_num_threads >>>>>> > >

to >>>>>> > > > >>> control the number of threads >>>>>> > > > >>> uses 8 byte integers >>>>>> > > > >>> MPI: >>>>>> > > > >>> Version: 3 >>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>> > > --oversubscribe >>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>> > > > >>> pthread: >>>>>> > > > >>> cmake: >>>>>> > > > >>> Version: 3.16.3 >>>>>> > > > >>> /usr/bin/cmake >>>>>> > > > >>> regex: >>>>>> > > > >>> Matlab: >>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>> > > > >>> MatlabEngine: >>>>>> > > > >>> Library: >>>>>> > > > >>> >>>>>> > > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>>>> -lmx -lmat >>>>>> > > -lut >>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>> > > > >>> Language used to compile PETSc: C >>>>>> > > > >>> PETSc: >>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>> > > > >>> Scalar type: real >>>>>> > > > >>> Precision: double >>>>>> > > > >>> Support for __float128 >>>>>> > > > >>> Integer size: 4 bytes >>>>>> > > > >>> shared libraries: enabled >>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>> PETSC_ARCH=linux-opt all >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>> >>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>>>>> -licuuc as >>>>>> > > > >>> you suggested earlier. >>>>>> > > > >>> >>>>>> > > > >>> *$make* >>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> socket\n"); >>>>>> > > > >>> | ^ >>>>>> > > > >>> >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> socket\n"); >>>>>> > > > >>> | ^ >>>>>> > > > >>> >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> ========================================= >>>>>> > > > >>> Now to check if the libraries are working do: >>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>> PETSC_ARCH=linux-opt check >>>>>> > > > >>> =============================================== >>>>>> > > > >>> >>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > > > >>> TEST >>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>> >>>>>> -------------------------------------------------------------- >>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>> > > > >>> >>>>>> > > > >> >>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>> defined, so it >>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>> yours. >>>>>> > > > >> >>>>>> > > > >> Thanks, >>>>>> > > > >> >>>>>> > > > >> Matt >>>>>> > > > >> >>>>>> > > > >> >>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>> trouble >>>>>> > > > >>> shooting. >>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 >>>>>> by vit >>>>>> > > Sun >>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> COPTFLAGS=-O3 >>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>> line 1444 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>> -------send >>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>> MPI_COMM_SELF >>>>>> > > > >>> # with errorcode 113065. >>>>>> > > > >>> # >>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > > > >>> # You may or may not see output from other processes, >>>>>> depending on >>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>>> diff >>>>>> > > > >>> CC >>>>>> > > > >>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > > > >>> CLINKER >>>>>> > > > >>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>> TEST >>>>>> > > > >>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> Error >>>>>> > > code: 124 >>>>>> > > > >>> # Running problem 5 >>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>> >>>>>> -------------------------------------------------------------- >>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>> trouble >>>>>> > > > >>> shooting. >>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>> > > MB108SMEC028 by >>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> COPTFLAGS=-O3 >>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>> -------send >>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>> MPI_COMM_SELF >>>>>> > > > >>> # with errorcode 126076. >>>>>> > > > >>> # >>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > > > >>> # You may or may not see output from other processes, >>>>>> depending on >>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>> Command >>>>>> > > > >>> failed so no diff >>>>>> > > > >>> >>>>>> > > > >>> # ------------- >>>>>> > > > >>> # Summary >>>>>> > > > >>> # ------------- >>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>> > > > >>> # >>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>> > > > >>> # >>>>>> > > > >>> # To rerun failed tests: >>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> > > > >>> # >>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 >>>>>> sec / >>>>>> > > 0.02 sec >>>>>> > > > >>> >>>>>> > > > >>> *How to sort out this error?* >>>>>> > > > >>> >>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>> > > > >>> *$make matlab_ls_test* >>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>> > > -Wwrite-strings >>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> > > -Wno-strict-aliasing >>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>>> -O3 >>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>> matlab_ls_test.c >>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> >>>>>> > > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>> -lmex >>>>>> > > -lmx >>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>> > > -lmpi_mpifh >>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>> -lpthread >>>>>> > > -lquadmath >>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>> > > > >>> >>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>>>> find the >>>>>> > > > >>> attachment and do the needful. >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> Thanks and regards >>>>>> > > > >>> Srinivas >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>> balay at mcs.anl.gov> >>>>>> > > wrote: >>>>>> > > > >>> >>>>>> > > > >>>> Perhaps you can try the following to get additional info - >>>>>> and debug >>>>>> > > > >>>> >>>>>> > > > >>>> Satish >>>>>> > > > >>>> ---------- >>>>>> > > > >>>> >>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> make matlab_ls_test >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> > > -Wno-strict-aliasing >>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>>> -O3 >>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>> > > > >>>> >>>>>> > > >>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>> > > > >>>> matlab_ls_test.c >>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread >>>>>> -lm -leng >>>>>> > > -lmex >>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>>>>> -lmpifort >>>>>> > > -lmpi >>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>>>>> -ldl -o >>>>>> > > > >>>> matlab_ls_test >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>> ./matlab_ls_test >>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number >>>>>> of >>>>>> > > processors >>>>>> > > > >>>> = 1 >>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>> > > > >>>> compute-386-07.(none) >>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>> > > > >>>> Running problem 5 >>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>> 1140850689 >>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>> command >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>> > > > >>>> TestingInitialize >>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>> string: >>>>>> > > > >>>> TestingInitialize >>>>>> > > > >>>> 5 >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works >>>>>> for you >>>>>> > > - on >>>>>> > > > >>>> this machine..>>>>> >>>>>> > > > >>>> >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> < M A T L A B (R) > >>>>>> > > > >>>> >>>>>> > > > >>>> Copyright 1984-2021 The >>>>>> MathWorks, Inc. >>>>>> > > > >>>> >>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>> (glnxa64) >>>>>> > > > >>>> >>>>>> > > > >>>> February 17, 2021 >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> To get started, type doc. >>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>> > > > >>>> >>>>>> > > > >>>> >> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>> > > > >>>> >>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>> [reverting >>>>>> > > thread >>>>>> > > > >>>> to petsc-users only] >>>>>> > > > >>>> > >>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>> > > corresponding >>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>> > > > >>>> > >>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>> Ubuntu-20.04, >>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>> > > > >>>> > >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>> > > > >>>> > main >>>>>> > > > >>>> > release >>>>>> > > > >>>> > * release-3.13 >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>> > > matlab/R2021a >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>> > > > >>>> >>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> PETSC_ARCH=linux-opt >>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>> > > > >>>> >>>>>> > > >>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> >>>>>> > > >>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>>> > >>>>>> > > > >>>> > Compilers: >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> > C Compiler: >>>>>> > > > >>>> >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > C++ Compiler: >>>>>> > > > >>>> >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > Fortran Compiler: >>>>>> > > > >>>> >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>> 9.4.0 >>>>>> > > > >>>> > Linkers: >>>>>> > > > >>>> > Shared linker: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> > > -shared -fPIC >>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> > Dynamic linker: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> > > -shared -fPIC >>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> > > > >>>> > make: >>>>>> > > > >>>> > Version: 4.2 >>>>>> > > > >>>> > /usr/bin/make >>>>>> > > > >>>> > BlasLapack: >>>>>> > > > >>>> > Library: >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>> > > > >>>> -liomp5 -lpthread >>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>> -omp_num_threads >>>>>> > >

>>>>>> > > > >>>> to control the number of threads >>>>>> > > > >>>> > uses 8 byte integers >>>>>> > > > >>>> > MPI: >>>>>> > > > >>>> > Version: 4 >>>>>> > > > >>>> > Includes: >>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>> > > > >>>> > Mpiexec: >>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>> > > > >>>> > pthread: >>>>>> > > > >>>> > Library: -lpthread >>>>>> > > > >>>> > cmake: >>>>>> > > > >>>> > Version: 3.16.3 >>>>>> > > > >>>> > /usr/bin/cmake >>>>>> > > > >>>> > regex: >>>>>> > > > >>>> > Matlab: >>>>>> > > > >>>> > Includes: >>>>>> > > > >>>> >>>>>> > > >>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>> > > > >>>> > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> > MatlabEngine: >>>>>> > > > >>>> > Library: >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>> > > > >>>> > sowing: >>>>>> > > > >>>> > Version: 1.1.25 >>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>> > > > >>>> > valgrind: >>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>> > > > >>>> > PETSc: >>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>> > > > >>>> > Scalar type: real >>>>>> > > > >>>> > Precision: double >>>>>> > > > >>>> > Support for __float128 >>>>>> > > > >>>> > Integer size: 4 bytes >>>>>> > > > >>>> > shared libraries: enabled >>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>> with: >>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>> PETSC_ARCH=linux-opt all >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> > > socket\n"); >>>>>> > > > >>>> > | ^ >>>>>> > > > >>>> > >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> > > socket\n"); >>>>>> > > > >>>> > | ^ >>>>>> > > > >>>> > >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > ========================================= >>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt >>>>>> check >>>>>> > > > >>>> > ========================================= >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>> > > query=requires >>>>>> > > > >>>> queryval=matlab >>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > > > >>>> > TEST >>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>> > > > >>>> > # ../ex72: >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>> no diff >>>>>> > > > >>>> > CC >>>>>> > > > >>>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > > > >>>> > CLINKER >>>>>> > > > >>>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>>> > TEST >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> # Error >>>>>> > > code: >>>>>> > > > >>>> 1 >>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> SKIP >>>>>> > > Command >>>>>> > > > >>>> failed so no diff >>>>>> > > > >>>> > >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>> > > query=requires >>>>>> > > > >>>> queryval=matlab >>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>>> > TEST >>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>>> > TEST >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> > >>>>>> > > > >>>> > # ------------- >>>>>> > > > >>>> > # Summary >>>>>> > > > >>>> > # ------------- >>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>> > > > >>>> > # >>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>> 15.190000000000001 >>>>>> > > sec >>>>>> > > > >>>> > # >>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>> 6.47 sec / >>>>>> > > 7.54 >>>>>> > > > >>>> sec >>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>> > > > >>>> > >>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>> tried to >>>>>> > > > >>>> configure petsc >>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. >>>>>> After >>>>>> > > > >>>> running make >>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>> message. >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > not ok >>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> > > > >>>> code: 124 >>>>>> > > > >>>> > > # Running problem 5 >>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>>> > > >>>>>> -------------------------------------------------------------- >>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> > > for trouble shooting. >>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>> 01, 2020 >>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>> named >>>>>> > > > >>>> MB108SMEC028 by >>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> COPTFLAGS=-O3 >>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> > > > >>>> --with-debugging=0 >>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>>> in >>>>>> > > > >>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>> > > -------send >>>>>> > > > >>>> entire >>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > # >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>> MPI_COMM_SELF >>>>>> > > > >>>> > > # with errorcode 126076. >>>>>> > > > >>>> > > # >>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>> MPI >>>>>> > > > >>>> processes. >>>>>> > > > >>>> > > # You may or may not see output from other processes, >>>>>> depending >>>>>> > > on >>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>> > > > >>>> > > # >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > Thanks >>>>>> > > > >>>> > > Srinivas >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > i.e.: >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>> 20PHD0548 via >>>>>> > > > >>>> petsc-users < >>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>> balay at mcs.anl.gov> >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>>>> will work >>>>>> > > > >>>> here]. >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> i.e: >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> ./configure >>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> > > PETSC_ARCH=linux-opt >>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> Satish >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>> > > petsc-users >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>> > > balay at mcs.anl.gov> >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > > Also: >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in >>>>>> this mode. >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>> dependency/conflicts >>>>>> > > across >>>>>> > > > >>>> packages] >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > Satish >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>> petsc-users wrote: >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > >>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] >>>>>> conflict >>>>>> > > with >>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>> blas/lapack with >>>>>> > > > >>>> matlab - to >>>>>> > > > >>>> > > >>> have a >>>>>> > > > >>>> > > >>> > > compatible build >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > Satish >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>> 20PHD0548 via >>>>>> > > > >>>> petsc-users >>>>>> > > > >>>> > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>> MATLAB is not >>>>>> > > > >>>> working. It is >>>>>> > > > >>>> > > >>> > > showing >>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>> cluster with >>>>>> > > > >>>> libmesh and >>>>>> > > > >>>> > > >>> this is >>>>>> > > > >>>>> >>>>> -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail2amneet at gmail.com Tue Sep 5 13:09:20 2023 From: mail2amneet at gmail.com (Amneet Bhalla) Date: Tue, 5 Sep 2023 11:09:20 -0700 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: BTW, what Barry is suggesting is the following: Compile a sample code with a command line this: g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine This command is provided here: https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html A sample MATLAB code is here: https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html (You can just pick a few lines of code from here to create a barebone example) On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla wrote: > Srinivas --- Do you have a different version of MATLAB that you can > install? If your organization has a MATLAB license, you can install recent > versions of MATLAB from mathworks.com > > On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: > >> >> Ok, I have no suggestions. It seems to be more an issue with the >> Matlab than PETSc. You could find a pure Matlab example of using the engine >> (in the Matlab documentation) and try it to see if it works. >> >> Barry >> >> >> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >> I got the same errors for petsc 3.17.5 >> >> >> *make all* >> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >> BEGINNING TO COMPILE MATLAB INTERFACE >> Building with 'gcc'. >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> MEX completed successfully. >> Building with 'gcc'. >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >> In function ?PetscBinaryWrite?: >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >> warning: ?err? may be used uninitialized in this function >> [-Wmaybe-uninitialized] >> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >> | ^ >> >> MEX completed successfully. >> ========================================= >> ========================================= >> Now to check if the libraries are working do: >> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >> >> *make test query=requires queryval=matlab >> DATAFILESPATH=/home/vit/datafiles/* >> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >> query=requires >> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >> # [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> # [0]PETSC ERROR: Error in external library >> # [0]PETSC ERROR: Unable to start MATLAB engine with >> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >> shooting. >> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >> Sep 5 21:39:22 2023 >> # [0]PETSC ERROR: Configure options >> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >> --known-64-bit-blas-indices=1 >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >> # [0]PETSC ERROR: #6 PCSetUp_LU() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >> # [0]PETSC ERROR: #7 PCSetUp() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >> # [0]PETSC ERROR: #8 KSPSetUp() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >> # [0]PETSC ERROR: #9 main() at >> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >> # [0]PETSC ERROR: PETSc Option Table entries: >> # [0]PETSC ERROR: -check_pointer_intensity 0 >> # [0]PETSC ERROR: -error_output_stdout >> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >> # [0]PETSC ERROR: -malloc_dump >> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >> # [0]PETSC ERROR: -pc_type lu >> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >> # [0]PETSC ERROR: ----------------End of Error Message -------send entire >> error message to petsc-maint at mcs.anl.gov---------- >> # >> -------------------------------------------------------------------------- >> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >> # with errorcode 85. >> # >> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >> # You may or may not see output from other processes, depending on >> # exactly when Open MPI kills them. >> # >> -------------------------------------------------------------------------- >> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >> >> >> # FAILED ksp_ksp_tutorials-ex72_12 >> # >> # To rerun failed tests: >> # /usr/bin/make -f gmakefile test test-fail=1 >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >> >>> >>> The error is occuring during >>> >>> e->ep = engOpen(buffer); >>> >>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 >>> -nodisplay -nosplash from your terminal shell worked we have to assume the >>> problem is occuring when engOpen() is attempting to connect the stdout and >>> stdin from the Matlab session that is launched to the executable. >>> >>> You can try the following. In 3.17.5 edit the >>> file src/sys/classes/matlabengine/matlab.c and locate the line >>> >>> e->ep = engOpen(buffer); >>> >>> replace it with >>> >>> e->ep = engOpen(""); >>> >>> Now in the PETSc directory do make all (it should recompile one file) >>> and then run the >>> >>> make test query=requires queryval=matlab >>> DATAFILESPATH=/home/vit/datafiles/ >>> >>> again >>> >>> >>> >>> >>> >>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < >>> petsc-users at mcs.anl.gov> wrote: >>> >>> Hi Amneeth, >>> >>> I think the errors are different with petsc 3.17.5 >>> >>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> The version of PETSc you are using is out-of-date, we recommend updating >>> to the new release >>> Available Version: 3.19.5 Installed Version: 3.17.5 >>> https://petsc.org/release/download/ >>> >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> >>> ============================================================================================= >>> Configuring PETSc to compile on your system >>> >>> >>> ============================================================================================= >>> Compilers: >>> >>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>> -fvisibility=hidden -O3 >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>> Linkers: >>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>> -fvisibility=hidden -O3 >>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>> -fvisibility=hidden -O3 >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>> BlasLapack: >>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to >>> control the number of threads >>> uses 8 byte integers >>> MPI: >>> Version: 3 >>> mpiexec: /usr/bin/mpiexec >>> Implementation: openmpi >>> OMPI_VERSION: 4.0.3 >>> pthread: >>> cmake: >>> Version: 3.16.3 >>> /usr/bin/cmake >>> regex: >>> Matlab: >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>> /usr/local/MATLAB/R2020b >>> MatlabEngine: >>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>> Language used to compile PETSc: C >>> PETSc: >>> PETSC_ARCH: linux-opt >>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>> Prefix: >>> Scalar type: real >>> Precision: double >>> Support for __float128 >>> Integer size: 4 bytes >>> Single library: yes >>> Shared libraries: yes >>> Memory alignment from malloc(): 16 bytes >>> Using GNU make: /usr/bin/make >>> >>> xxx=========================================================================xxx >>> Configure stage complete. Now build PETSc libraries with: >>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>> all >>> >>> xxx=========================================================================xxx >>> >>> *$make* >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> Building with 'gcc'. >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> ========================================= >>> ========================================= >>> Now to check if the libraries are working do: >>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>> >>> *$make test query=requires queryval=matlab >>> DATAFILESPATH=/home/vit/datafiles/* >>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>> --testdir=./linux-opt/tests >>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>> query=requires >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>> # [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> # [0]PETSC ERROR: Error in external library >>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>> shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>> Sep 5 10:15:57 2023 >>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>> # [0]PETSC ERROR: #7 PCSetUp() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>> # [0]PETSC ERROR: #8 KSPSetUp() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>> # [0]PETSC ERROR: #9 main() at >>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>> # [0]PETSC ERROR: -error_output_stdout >>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>> # [0]PETSC ERROR: -malloc_dump >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> # [0]PETSC ERROR: -pc_type lu >>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> # >>> -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> # with errorcode 85. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # >>> -------------------------------------------------------------------------- >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> >>> >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> # >>> # To rerun failed tests: >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> >>> To get the info of the error there is no specific probe id reported. >>> >>> How to check error info and proceed further? >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>> wrote: >>> >>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>> options that Satish mentioned? >>>> >>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>> petsc-users wrote: >>>> >>>>> Sorry for missing that. >>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>> >>>>> < M A T L A B (R) > >>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>> November 23, 2020 >>>>> >>>>> >>>>> To get started, type doc. >>>>> For product information, visit www.mathworks.com. >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>> wrote: >>>>> >>>>>> You are missing one more step: >>>>>> >>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> >>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>> >>>>>> Does this work for you? As the message indicates this command is >>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>> >>>>>> Satish >>>>>> >>>>>> >>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>> >>>>>> > Hi Sathish, >>>>>> > >>>>>> > I tried the following procedure >>>>>> > >>>>>> > *$make * >>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > Building with 'gcc'. >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > In function ?PetscBinaryWrite?: >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > warning: ?err? may be used uninitialized in this function >>>>>> > [-Wmaybe-uninitialized] >>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > | ^ >>>>>> > >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > MEX completed successfully. >>>>>> > Building with 'gcc'. >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > In function ?PetscBinaryWrite?: >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > warning: ?err? may be used uninitialized in this function >>>>>> > [-Wmaybe-uninitialized] >>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> > | ^ >>>>>> > >>>>>> > MEX completed successfully. >>>>>> > ========================================= >>>>>> > Now to check if the libraries are working do: >>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>> > >>>>>> > *$make test query=requires queryval=matlab >>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>> queryval=matlab >>>>>> > query=requires >>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Error in external library >>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>> > # [0]PETSC ERROR: >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: >>>>>> > >>>>>> ------------------------------------------------------------------------ >>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>> Violation, >>>>>> > probably memory access out of range >>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>> -on_error_attach_debugger >>>>>> > # [0]PETSC ERROR: or see >>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>> Apple Mac OS >>>>>> > X to find memory corruption errors >>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>>>>> link, >>>>>> > and run >>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Signal received >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Mon Sep >>>>>> > 4 10:02:32 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>> file >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> > # with errorcode 50162059. >>>>>> > # >>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > # You may or may not see output from other processes, depending on >>>>>> > # exactly when Open MPI kills them. >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> > CC >>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > CLINKER >>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > TEST >>>>>> > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> code: 124 >>>>>> > # Running problem 5 >>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > # [0]PETSC ERROR: Error in external library >>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > # [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>> MB108SMEC028 by >>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>> > # [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire >>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > # with errorcode 126076. >>>>>> > # >>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > # You may or may not see output from other processes, depending on >>>>>> > # exactly when Open MPI kills them. >>>>>> > # >>>>>> -------------------------------------------------------------------------- >>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>> failed >>>>>> > so no diff >>>>>> > >>>>>> > # ------------- >>>>>> > # Summary >>>>>> > # ------------- >>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > # success 0/2 tests (0.0%) >>>>>> > # failed 2/2 tests (100.0%) >>>>>> > # todo 0/2 tests (0.0%) >>>>>> > # skip 0/2 tests (0.0%) >>>>>> > # >>>>>> > # Wall clock time for tests: 4 sec >>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>> > # >>>>>> > # To rerun failed tests: >>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> > # >>>>>> > # Timing summary (actual test time / total CPU time): >>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>> 0.01 sec >>>>>> > >>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>> > *$make matlab_ls_test* >>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>> -Wwrite-strings >>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> -Wno-strict-aliasing >>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>> -lmx >>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>> -lmpi_mpifh >>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>> -lquadmath >>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>> > >>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>> processors = 1 >>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>> > MB108SMEC028.(none) >>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>> > Running problem 5 >>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>> > 94202473157392 max tags = 2147483647 >>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>> > -------------------------------------------------------------- >>>>>> > [0]PETSC ERROR: Error in external library >>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > [0]PETSC ERROR: See >>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > for trouble shooting. >>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 >>>>>> by vit >>>>>> > Mon Sep 4 10:09:56 2023 >>>>>> > [0]PETSC ERROR: Configure options >>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > [0]PETSC ERROR: -info >>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire >>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > >>>>>> -------------------------------------------------------------------------- >>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>> > with errorcode 126076. >>>>>> > >>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> > You may or may not see output from other processes, depending on >>>>>> > exactly when Open MPI kills them. >>>>>> > >>>>>> > Please find the attachment for configure.log and make.log files >>>>>> > >>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>> wrote: >>>>>> > >>>>>> > > To use datafiles in the test suite: >>>>>> > > >>>>>> > > cd $HOME >>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>> > > >>>>> - or set >>>>>> > > manually with make> >>>>>> > > >>>>>> > > make test query=requires queryval=matlab >>>>>> DATAFILESPATH=$HOME/datafiles >>>>>> > > >>>>>> > > Satish >>>>>> > > >>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>> > > >>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>> > > > >>>>>> > > > > Hi Matthew, >>>>>> > > > > >>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do >>>>>> not have >>>>>> > > any >>>>>> > > > > separate test files to test PETSc alone. Can you please help >>>>>> me how to >>>>>> > > > > define this DATAFILESPATH? >>>>>> > > > > >>>>>> > > > >>>>>> > > > That test you tried uses a certain matrix. On our machine, we >>>>>> point to >>>>>> > > this >>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>>>>> have those >>>>>> > > > matrices, since they are just for testing here. That >>>>>> > > > is why I suggested just using a different matrix, or running a >>>>>> problem >>>>>> > > you >>>>>> > > > care about in IBAMR. >>>>>> > > > >>>>>> > > > Thanks, >>>>>> > > > >>>>>> > > > Matt >>>>>> > > > >>>>>> > > > >>>>>> > > > > Thanks and regards >>>>>> > > > > Srinivas. >>>>>> > > > > >>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>> knepley at gmail.com> >>>>>> > > wrote: >>>>>> > > > > >>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>> > > petsc-users < >>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>> > > > >> >>>>>> > > > >>> Hi Sathish, >>>>>> > > > >>> >>>>>> > > > >>> Thank you so much for your efforts and the support you are >>>>>> giving me >>>>>> > > to >>>>>> > > > >>> sort this out. >>>>>> > > > >>> >>>>>> > > > >>> I tried to follow the same procedure which you followed to >>>>>> build >>>>>> > > Petsc >>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>> > > > >>> >>>>>> > > > >>> *$./configure >>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> PETSC_ARCH=linux-opt >>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>> > > > >>> Using python3 for Python >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> It appears you do >>>>>> not have >>>>>> > > valgrind >>>>>> > > > >>> installed on your system. >>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>> > > > >>> Or install >>>>>> > > valgrind-devel or >>>>>> > > > >>> equivalent using your package manager. >>>>>> > > > >>> Then rerun ./configure >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> =============================================================================== >>>>>> > > > >>> Compilers: >>>>>> > > > >>> >>>>>> > > > >>> C Compiler: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -fPIC >>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>> C++ Compiler: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>> > > > >>> Fortran Compiler: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>> -Wno-unused-dummy-argument -O3 >>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>> 9.4.0 >>>>>> > > > >>> Linkers: >>>>>> > > > >>> Shared linker: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -shared >>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > > -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Dynamic linker: >>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > -shared >>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> > > -Wno-unknown-pragmas >>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> > > > >>> make: >>>>>> > > > >>> Version: 4.2 >>>>>> > > > >>> /usr/bin/make >>>>>> > > > >>> BlasLapack: >>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>> -omp_num_threads >>>>>> > >

to >>>>>> > > > >>> control the number of threads >>>>>> > > > >>> uses 8 byte integers >>>>>> > > > >>> MPI: >>>>>> > > > >>> Version: 3 >>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>> > > --oversubscribe >>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>> > > > >>> pthread: >>>>>> > > > >>> cmake: >>>>>> > > > >>> Version: 3.16.3 >>>>>> > > > >>> /usr/bin/cmake >>>>>> > > > >>> regex: >>>>>> > > > >>> Matlab: >>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>> > > > >>> MatlabEngine: >>>>>> > > > >>> Library: >>>>>> > > > >>> >>>>>> > > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>>>> -lmx -lmat >>>>>> > > -lut >>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>> > > > >>> Language used to compile PETSc: C >>>>>> > > > >>> PETSc: >>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>> > > > >>> Scalar type: real >>>>>> > > > >>> Precision: double >>>>>> > > > >>> Support for __float128 >>>>>> > > > >>> Integer size: 4 bytes >>>>>> > > > >>> shared libraries: enabled >>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>> PETSC_ARCH=linux-opt all >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>> >>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>>>>> -licuuc as >>>>>> > > > >>> you suggested earlier. >>>>>> > > > >>> >>>>>> > > > >>> *$make* >>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> socket\n"); >>>>>> > > > >>> | ^ >>>>>> > > > >>> >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> Building with 'gcc'. >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> socket\n"); >>>>>> > > > >>> | ^ >>>>>> > > > >>> >>>>>> > > > >>> MEX completed successfully. >>>>>> > > > >>> ========================================= >>>>>> > > > >>> Now to check if the libraries are working do: >>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>> PETSC_ARCH=linux-opt check >>>>>> > > > >>> =============================================== >>>>>> > > > >>> >>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > > > >>> TEST >>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>> >>>>>> -------------------------------------------------------------- >>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>> > > > >>> >>>>>> > > > >> >>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>> defined, so it >>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>> yours. >>>>>> > > > >> >>>>>> > > > >> Thanks, >>>>>> > > > >> >>>>>> > > > >> Matt >>>>>> > > > >> >>>>>> > > > >> >>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>> trouble >>>>>> > > > >>> shooting. >>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 >>>>>> by vit >>>>>> > > Sun >>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> COPTFLAGS=-O3 >>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>> line 1444 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>> -------send >>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>> MPI_COMM_SELF >>>>>> > > > >>> # with errorcode 113065. >>>>>> > > > >>> # >>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > > > >>> # You may or may not see output from other processes, >>>>>> depending on >>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>>> diff >>>>>> > > > >>> CC >>>>>> > > > >>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > > > >>> CLINKER >>>>>> > > > >>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>> TEST >>>>>> > > > >>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> Error >>>>>> > > code: 124 >>>>>> > > > >>> # Running problem 5 >>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>> >>>>>> -------------------------------------------------------------- >>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>> trouble >>>>>> > > > >>> shooting. >>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>> > > MB108SMEC028 by >>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> COPTFLAGS=-O3 >>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> --with-debugging=0 >>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>> > > > >>> >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>> -------send >>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>> MPI_COMM_SELF >>>>>> > > > >>> # with errorcode 126076. >>>>>> > > > >>> # >>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>> processes. >>>>>> > > > >>> # You may or may not see output from other processes, >>>>>> depending on >>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>> > > > >>> # >>>>>> > > > >>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>> Command >>>>>> > > > >>> failed so no diff >>>>>> > > > >>> >>>>>> > > > >>> # ------------- >>>>>> > > > >>> # Summary >>>>>> > > > >>> # ------------- >>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>> > > > >>> # >>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>> > > > >>> # >>>>>> > > > >>> # To rerun failed tests: >>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> > > > >>> # >>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 >>>>>> sec / >>>>>> > > 0.02 sec >>>>>> > > > >>> >>>>>> > > > >>> *How to sort out this error?* >>>>>> > > > >>> >>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>> > > > >>> *$make matlab_ls_test* >>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>> > > -Wwrite-strings >>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> > > -Wno-strict-aliasing >>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>>> -O3 >>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>> matlab_ls_test.c >>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> > > > >>> >>>>>> > > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>> -lmex >>>>>> > > -lmx >>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>> > > -lmpi_mpifh >>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>> -lpthread >>>>>> > > -lquadmath >>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>> > > > >>> >>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>>>> find the >>>>>> > > > >>> attachment and do the needful. >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> Thanks and regards >>>>>> > > > >>> Srinivas >>>>>> > > > >>> >>>>>> > > > >>> >>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>> balay at mcs.anl.gov> >>>>>> > > wrote: >>>>>> > > > >>> >>>>>> > > > >>>> Perhaps you can try the following to get additional info - >>>>>> and debug >>>>>> > > > >>>> >>>>>> > > > >>>> Satish >>>>>> > > > >>>> ---------- >>>>>> > > > >>>> >>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> make matlab_ls_test >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>> > > -Wno-strict-aliasing >>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>>> -O3 >>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>> > > > >>>> >>>>>> > > >>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>> > > > >>>> matlab_ls_test.c >>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread >>>>>> -lm -leng >>>>>> > > -lmex >>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>>>>> -lmpifort >>>>>> > > -lmpi >>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>>>>> -ldl -o >>>>>> > > > >>>> matlab_ls_test >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>> ./matlab_ls_test >>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number >>>>>> of >>>>>> > > processors >>>>>> > > > >>>> = 1 >>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>> > > > >>>> compute-386-07.(none) >>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>> > > > >>>> Running problem 5 >>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>> 1140850689 >>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>> command >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>> > > > >>>> TestingInitialize >>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>> string: >>>>>> > > > >>>> TestingInitialize >>>>>> > > > >>>> 5 >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works >>>>>> for you >>>>>> > > - on >>>>>> > > > >>>> this machine..>>>>> >>>>>> > > > >>>> >>>>>> > > > >>>> balay at compute-386-07 >>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> < M A T L A B (R) > >>>>>> > > > >>>> >>>>>> > > > >>>> Copyright 1984-2021 The >>>>>> MathWorks, Inc. >>>>>> > > > >>>> >>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>> (glnxa64) >>>>>> > > > >>>> >>>>>> > > > >>>> February 17, 2021 >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> To get started, type doc. >>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>> > > > >>>> >>>>>> > > > >>>> >> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>> > > > >>>> >>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>> [reverting >>>>>> > > thread >>>>>> > > > >>>> to petsc-users only] >>>>>> > > > >>>> > >>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>> > > corresponding >>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>> > > > >>>> > >>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>> Ubuntu-20.04, >>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>> > > > >>>> > >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>> > > > >>>> > main >>>>>> > > > >>>> > release >>>>>> > > > >>>> > * release-3.13 >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>> > > matlab/R2021a >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>> > > > >>>> >>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> PETSC_ARCH=linux-opt >>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>> > > > >>>> >>>>>> > > >>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> >>>>>> > > >>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> > > > >>>> > >>>>>> > > > >>>> > Compilers: >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> > C Compiler: >>>>>> > > > >>>> >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > C++ Compiler: >>>>>> > > > >>>> >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>> > > -fstack-protector >>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> > > > >>>> > Fortran Compiler: >>>>>> > > > >>>> >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>> > > -Wall >>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>> 9.4.0 >>>>>> > > > >>>> > Linkers: >>>>>> > > > >>>> > Shared linker: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> > > -shared -fPIC >>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> > Dynamic linker: >>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>> > > -shared -fPIC >>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>> -Wno-unknown-pragmas >>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> > > > >>>> > make: >>>>>> > > > >>>> > Version: 4.2 >>>>>> > > > >>>> > /usr/bin/make >>>>>> > > > >>>> > BlasLapack: >>>>>> > > > >>>> > Library: >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>> > > > >>>> -liomp5 -lpthread >>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>> -omp_num_threads >>>>>> > >

>>>>>> > > > >>>> to control the number of threads >>>>>> > > > >>>> > uses 8 byte integers >>>>>> > > > >>>> > MPI: >>>>>> > > > >>>> > Version: 4 >>>>>> > > > >>>> > Includes: >>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>> > > > >>>> > Mpiexec: >>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>> > > > >>>> > pthread: >>>>>> > > > >>>> > Library: -lpthread >>>>>> > > > >>>> > cmake: >>>>>> > > > >>>> > Version: 3.16.3 >>>>>> > > > >>>> > /usr/bin/cmake >>>>>> > > > >>>> > regex: >>>>>> > > > >>>> > Matlab: >>>>>> > > > >>>> > Includes: >>>>>> > > > >>>> >>>>>> > > >>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>> > > > >>>> > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>> > > > >>>> > MatlabEngine: >>>>>> > > > >>>> > Library: >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>> > > > >>>> > sowing: >>>>>> > > > >>>> > Version: 1.1.25 >>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>> > > > >>>> > valgrind: >>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>> > > > >>>> > PETSc: >>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>> > > > >>>> > Scalar type: real >>>>>> > > > >>>> > Precision: double >>>>>> > > > >>>> > Support for __float128 >>>>>> > > > >>>> > Integer size: 4 bytes >>>>>> > > > >>>> > shared libraries: enabled >>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>> with: >>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>> PETSC_ARCH=linux-opt all >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> xxx=========================================================================xxx >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> > > socket\n"); >>>>>> > > > >>>> > | ^ >>>>>> > > > >>>> > >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > Building with 'gcc'. >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>> > > > >>>> > >>>>>> > > > >>>> >>>>>> > > >>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>> > > socket\n"); >>>>>> > > > >>>> > | ^ >>>>>> > > > >>>> > >>>>>> > > > >>>> > MEX completed successfully. >>>>>> > > > >>>> > ========================================= >>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt >>>>>> check >>>>>> > > > >>>> > ========================================= >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>> > > query=requires >>>>>> > > > >>>> queryval=matlab >>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> > > > >>>> > TEST >>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>> > > > >>>> > # ../ex72: >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>> no diff >>>>>> > > > >>>> > CC >>>>>> > > > >>>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>> > > > >>>> > CLINKER >>>>>> > > > >>>> >>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>>> > TEST >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> # Error >>>>>> > > code: >>>>>> > > > >>>> 1 >>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> SKIP >>>>>> > > Command >>>>>> > > > >>>> failed so no diff >>>>>> > > > >>>> > >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>> > > query=requires >>>>>> > > > >>>> queryval=matlab >>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>> > > > >>>> > TEST >>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>> > > > >>>> > TEST >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> > >>>>>> > > > >>>> > # ------------- >>>>>> > > > >>>> > # Summary >>>>>> > > > >>>> > # ------------- >>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>> > > > >>>> > # >>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>> 15.190000000000001 >>>>>> > > sec >>>>>> > > > >>>> > # >>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>> 6.47 sec / >>>>>> > > 7.54 >>>>>> > > > >>>> sec >>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > >>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>> > > > >>>> > >>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>> tried to >>>>>> > > > >>>> configure petsc >>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. >>>>>> After >>>>>> > > > >>>> running make >>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>> message. >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > not ok >>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>> > > > >>>> code: 124 >>>>>> > > > >>>> > > # Running problem 5 >>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>> > > > >>>> > > >>>>>> -------------------------------------------------------------- >>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> > > for trouble shooting. >>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>> 01, 2020 >>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>> named >>>>>> > > > >>>> MB108SMEC028 by >>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> COPTFLAGS=-O3 >>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>> > > > >>>> --with-debugging=0 >>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>>> in >>>>>> > > > >>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>> > > -------send >>>>>> > > > >>>> entire >>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > # >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>> MPI_COMM_SELF >>>>>> > > > >>>> > > # with errorcode 126076. >>>>>> > > > >>>> > > # >>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>> MPI >>>>>> > > > >>>> processes. >>>>>> > > > >>>> > > # You may or may not see output from other processes, >>>>>> depending >>>>>> > > on >>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>> > > > >>>> > > # >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > Thanks >>>>>> > > > >>>> > > Srinivas >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>> > > > >>>> > > >>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > i.e.: >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>> 20PHD0548 via >>>>>> > > > >>>> petsc-users < >>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>> > > > >>>> > > > >>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>> balay at mcs.anl.gov> >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >> >>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>>>> will work >>>>>> > > > >>>> here]. >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> i.e: >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> ./configure >>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> > > PETSC_ARCH=linux-opt >>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> Satish >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>> > > petsc-users >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>> > > balay at mcs.anl.gov> >>>>>> > > > >>>> wrote: >>>>>> > > > >>>> > > >>> > >>>>>> > > > >>>> > > >>> > > Also: >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in >>>>>> this mode. >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>> dependency/conflicts >>>>>> > > across >>>>>> > > > >>>> packages] >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > Satish >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>> petsc-users wrote: >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > >>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] >>>>>> conflict >>>>>> > > with >>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>> blas/lapack with >>>>>> > > > >>>> matlab - to >>>>>> > > > >>>> > > >>> have a >>>>>> > > > >>>> > > >>> > > compatible build >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > Satish >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>> 20PHD0548 via >>>>>> > > > >>>> petsc-users >>>>>> > > > >>>> > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>> MATLAB is not >>>>>> > > > >>>> working. It is >>>>>> > > > >>>> > > >>> > > showing >>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>> cluster with >>>>>> > > > >>>> libmesh and >>>>>> > > > >>>> > > >>> this is >>>>>> > > > >>>> > > >>> > > for >>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I >>>>>> tried without >>>>>> > > > >>>> linking >>>>>> > > > >>>> > > >>> Matlab >>>>>> > > > >>>> > > >>> > > with >>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>>>> configuring >>>>>> > > > >>>> libmesh 1.6.2 >>>>>> > > > >>>> > > >>> that >>>>>> > > > >>>> > > >>> > > PETSc >>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required >>>>>> is >>>>>> > > specified. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>>>> libmesh with >>>>>> > > > >>>> PETSc and >>>>>> > > > >>>> > > >>> Matlab >>>>>> > > > >>>> > > >>> > > is in >>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for >>>>>> complicated >>>>>> > > geometries >>>>>> > > > >>>> it is >>>>>> > > > >>>> > > >>> > > mentioned to >>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>>>> various >>>>>> > > things >>>>>> > > > >>>> and ended >>>>>> > > > >>>> > > >>> up with >>>>>> > > > >>>> > > >>> > > > > errors. >>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further >>>>>> to do my >>>>>> > > > >>>> research work. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>>>>> possible. >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>> > > > >>>> mail2amneet at gmail.com> >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>>> libMesh for >>>>>> > > the >>>>>> > > > >>>> WEC >>>>>> > > > >>>> > > >>> application. >>>>>> > > > >>>> > > >>> > > You >>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>>>> builds with >>>>>> > > > >>>> Matlab. >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for >>>>>> wanting to build >>>>>> > > > >>>> libMesh? >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU >>>>>> SRINIVAS >>>>>> > > > >>>> 20PHD0548 via >>>>>> > > > >>>> > > >>> > > petsc-users >>>>>> > > > >>>> > > >>> > > > > > wrote: >>>>>> > > > >>>> > > >>> > > > > > >>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>>>>> removing all >>>>>> > > > >>>> occurrences >>>>>> > > > >>>> > > >>> of >>>>>> > > > >>>> > > >>> > > "-lut >>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I >>>>>> ran "make >>>>>> > > test" >>>>>> > > > >>>> got the >>>>>> > > > >>>> > > >>> > > following >>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> > > > >>>> > > >>> Error >>>>>> > > > >>>> > > >>> > > code: 124 >>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>>>>> Error >>>>>> > > Message >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> >>>>>> -------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>> library >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>> MATLAB engine >>>>>> > > on >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> for >>>>>> > > > >>>> > > >>> trouble >>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>>>>> 3.13.4, >>>>>> > > Aug >>>>>> > > > >>>> 01, 2020 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>> > > linux-debug >>>>>> > > > >>>> named >>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>>> --download-fblaslapack=1 >>>>>> > > > >>>> --with-x=0 >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>> PetscMatlabEngineCreate() >>>>>> > > line >>>>>> > > > >>>> 67 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>> entries: >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End >>>>>> of Error >>>>>> > > > >>>> Message >>>>>> > > > >>>> > > >>> -------send >>>>>> > > > >>>> > > >>> > > entire >>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>> communicator >>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>>>> MPI to >>>>>> > > kill >>>>>> > > > >>>> all MPI >>>>>> > > > >>>> > > >>> > > processes. >>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>> other >>>>>> > > processes, >>>>>> > > > >>>> > > >>> depending on >>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> # SKIP >>>>>> > > > >>>> > > >>> Command >>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>> > > > >>>> > > >>> Error >>>>>> > > > >>>> > > >>> > > code: 124 >>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- >>>>>> Error >>>>>> > > Message >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> >>>>>> -------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>> library >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>> MATLAB engine >>>>>> > > on >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>> > > > >>>> for >>>>>> > > > >>>> > > >>> trouble >>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version >>>>>> 3.13.4, >>>>>> > > Aug >>>>>> > > > >>>> 01, 2020 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>> > > linux-opt >>>>>> > > > >>>> named >>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>> > > > >>>> --download-fblaslapack=1 >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>> PetscMatlabEngineCreate() >>>>>> > > line >>>>>> > > > >>>> 67 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> >>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>> entries: >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End >>>>>> of Error >>>>>> > > > >>>> Message >>>>>> > > > >>>> > > >>> -------send >>>>>> > > > >>>> > > >>> > > entire >>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>> communicator >>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>>>> MPI to >>>>>> > > kill >>>>>> > > > >>>> all MPI >>>>>> > > > >>>> > > >>> > > processes. >>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>> other >>>>>> > > processes, >>>>>> > > > >>>> > > >>> depending on >>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>> > > > >>>> > > >>> > > > > >> # >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -------------------------------------------------------------------------- >>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>> > > > >>>> # SKIP >>>>>> > > > >>>> > > >>> Command >>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc >>>>>> 3.17.5 >>>>>> > > version. I >>>>>> > > > >>>> am >>>>>> > > > >>>> > > >>> sharing the >>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc >>>>>> 3.13.4 and >>>>>> > > > >>>> petsc >>>>>> > > > >>>> > > >>> 3.17.5. >>>>>> > > > >>>> > > >>> > > Please find >>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish >>>>>> Balay < >>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>>>> petsc's >>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>> > > > >>>> > > >>> > > for >>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> > > -leng >>>>>> > > > >>>> -lmex >>>>>> > > > >>>> > > >>> -lmx >>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - >>>>>> we are >>>>>> > > seeing: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" >>>>>> are not >>>>>> > > > >>>> preset here. >>>>>> > > > >>>> > > >>> This >>>>>> > > > >>>> > > >>> > > might >>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>> > > > >>>> > > >>> > > and >>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>>> -licudata >>>>>> > > -licui18n >>>>>> > > > >>>> -licuuc" >>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>> 20PHD0548 >>>>>> > > via >>>>>> > > > >>>> > > >>> petsc-users >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>>>> building >>>>>> > > > >>>> petsc3.13.4 with >>>>>> > > > >>>> > > >>> > > matlab and >>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh >>>>>> with >>>>>> > > > >>>> petsc3.17.5 and >>>>>> > > > >>>> > > >>> matlab. >>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>> > > successfully. >>>>>> > > > >>>> But >>>>>> > > > >>>> > > >>> libmesh is >>>>>> > > > >>>> > > >>> > > not >>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>>> Satish Balay < >>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from >>>>>> both >>>>>> > > > >>>> petsc-3.13 and >>>>>> > > > >>>> > > >>> 3.17 [or >>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>>> > > friendly to >>>>>> > > > >>>> mailing >>>>>> > > > >>>> > > >>> list - >>>>>> > > > >>>> > > >>> > > or >>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with >>>>>> 3.17? [or >>>>>> > > 3.19?] >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU >>>>>> SRINIVAS >>>>>> > > 20PHD0548 >>>>>> > > > >>>> via >>>>>> > > > >>>> > > >>> petsc-users >>>>>> > > > >>>> > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file >>>>>> while >>>>>> > > building >>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>> > > > >>>> > > >>> > > with >>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and >>>>>> do the >>>>>> > > needful. >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM >>>>>> INTURU >>>>>> > > > >>>> SRINIVAS >>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. >>>>>> During >>>>>> > > building >>>>>> > > > >>>> of >>>>>> > > > >>>> > > >>> libmesh, the >>>>>> > > > >>>> > > >>> > > error >>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at >>>>>> 9:43?PM Satish >>>>>> > > > >>>> Balay < >>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux >>>>>> says >>>>>> > > > >>>> petsc-3.17 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>>> petsc-3.17.5? >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU >>>>>> SRINIVAS >>>>>> > > > >>>> 20PHD0548 via >>>>>> > > > >>>> > > >>> > > petsc-users >>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with >>>>>> MATLAB for >>>>>> > > > >>>> working on >>>>>> > > > >>>> > > >>> the >>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>>> building the >>>>>> > > PETSc, >>>>>> > > > >>>> using the >>>>>> > > > >>>> > > >>> > > following >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export >>>>>> PETSC_ARCH=linux-debug >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> > > >>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld >>>>>> returned 1 exit >>>>>> > > > >>>> status >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>>> [gmakefile.test:185: >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> >>>>>> > > > >>>> >>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>>> unfinished >>>>>> > > jobs.... >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve >>>>>> this issue >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>> > > > >>>> > > >>> > > > > >>> >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> >>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from >>>>>> Vellore >>>>>> > > > >>>> Institute of >>>>>> > > > >>>> > > >>> > > Technology. >>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain >>>>>> legally >>>>>> > > > >>>> protected >>>>>> > > > >>>> > > >>> > > confidential or >>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>>> Institute of >>>>>> > > > >>>> Technology?. >>>>>> > > > >>>> > > >>> If >>>>>> > > > >>>> > > >>> > > you are >>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should >>>>>> not >>>>>> > > > >>>> disseminate, >>>>>> > > > >>>> > > >>> distribute >>>>>> > > > >>>> > > >>> > > or copy >>>>>> > > > >>>> > > >>> > > > > >> this e-mail. 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URL: From inturu.srinivas2020 at vitstudent.ac.in Tue Sep 5 13:12:38 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Tue, 5 Sep 2023 23:42:38 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: Thank you professor. I will try to run this on Matlab. On Tue, Sep 5, 2023, 23:39 Amneet Bhalla wrote: > BTW, what Barry is suggesting is the following: > > Compile a sample code with a command line this: > > > g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ > -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine > > > This command is provided here: > > https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html > > > A sample MATLAB code is here: > > https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html > > > (You can just pick a few lines of code from here to create a barebone example) > > > On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: > >> Srinivas --- Do you have a different version of MATLAB that you can >> install? If your organization has a MATLAB license, you can install recent >> versions of MATLAB from mathworks.com >> >> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >> >>> >>> Ok, I have no suggestions. It seems to be more an issue with the >>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>> (in the Matlab documentation) and try it to see if it works. >>> >>> Barry >>> >>> >>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> >>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>> I got the same errors for petsc 3.17.5 >>> >>> >>> *make all* >>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> Building with 'gcc'. >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> ========================================= >>> ========================================= >>> Now to check if the libraries are working do: >>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>> >>> *make test query=requires queryval=matlab >>> DATAFILESPATH=/home/vit/datafiles/* >>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>> query=requires >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>> # [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> # [0]PETSC ERROR: Error in external library >>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>> shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>> Sep 5 21:39:22 2023 >>> # [0]PETSC ERROR: Configure options >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>> # [0]PETSC ERROR: #7 PCSetUp() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>> # [0]PETSC ERROR: #8 KSPSetUp() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>> # [0]PETSC ERROR: #9 main() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>> # [0]PETSC ERROR: -error_output_stdout >>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>> # [0]PETSC ERROR: -malloc_dump >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> # [0]PETSC ERROR: -pc_type lu >>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> # >>> -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> # with errorcode 85. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # >>> -------------------------------------------------------------------------- >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> >>> >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> # >>> # To rerun failed tests: >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>> >>>> >>>> The error is occuring during >>>> >>>> e->ep = engOpen(buffer); >>>> >>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 >>>> -nodisplay -nosplash from your terminal shell worked we have to assume the >>>> problem is occuring when engOpen() is attempting to connect the stdout and >>>> stdin from the Matlab session that is launched to the executable. >>>> >>>> You can try the following. In 3.17.5 edit the >>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>> >>>> e->ep = engOpen(buffer); >>>> >>>> replace it with >>>> >>>> e->ep = engOpen(""); >>>> >>>> Now in the PETSc directory do make all (it should recompile one file) >>>> and then run the >>>> >>>> make test query=requires queryval=matlab >>>> DATAFILESPATH=/home/vit/datafiles/ >>>> >>>> again >>>> >>>> >>>> >>>> >>>> >>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < >>>> petsc-users at mcs.anl.gov> wrote: >>>> >>>> Hi Amneeth, >>>> >>>> I think the errors are different with petsc 3.17.5 >>>> >>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>> >>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> The version of PETSc you are using is out-of-date, we recommend >>>> updating to the new release >>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>> https://petsc.org/release/download/ >>>> >>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> ============================================================================================= >>>> Configuring PETSc to compile on your system >>>> >>>> >>>> ============================================================================================= >>>> Compilers: >>>> >>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>> -fvisibility=hidden -O3 >>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> Linkers: >>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>> -fvisibility=hidden -O3 >>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>> -fstack-protector -fvisibility=hidden -O3 >>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>> BlasLapack: >>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>>> to control the number of threads >>>> uses 8 byte integers >>>> MPI: >>>> Version: 3 >>>> mpiexec: /usr/bin/mpiexec >>>> Implementation: openmpi >>>> OMPI_VERSION: 4.0.3 >>>> pthread: >>>> cmake: >>>> Version: 3.16.3 >>>> /usr/bin/cmake >>>> regex: >>>> Matlab: >>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>> /usr/local/MATLAB/R2020b >>>> MatlabEngine: >>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>> Language used to compile PETSc: C >>>> PETSc: >>>> PETSC_ARCH: linux-opt >>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>> Prefix: >>>> Scalar type: real >>>> Precision: double >>>> Support for __float128 >>>> Integer size: 4 bytes >>>> Single library: yes >>>> Shared libraries: yes >>>> Memory alignment from malloc(): 16 bytes >>>> Using GNU make: /usr/bin/make >>>> >>>> xxx=========================================================================xxx >>>> Configure stage complete. Now build PETSc libraries with: >>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>> all >>>> >>>> xxx=========================================================================xxx >>>> >>>> *$make* >>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>> Building with 'gcc'. >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> In function ?PetscBinaryWrite?: >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> | ^ >>>> >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> In function ?PetscBinaryWrite?: >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> | ^ >>>> >>>> MEX completed successfully. >>>> ========================================= >>>> ========================================= >>>> Now to check if the libraries are working do: >>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>> check >>>> >>>> *$make test query=requires queryval=matlab >>>> DATAFILESPATH=/home/vit/datafiles/* >>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>> --testdir=./linux-opt/tests >>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>> query=requires >>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>> # [0]PETSC ERROR: --------------------- Error Message >>>> -------------------------------------------------------------- >>>> # [0]PETSC ERROR: Error in external library >>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>> shooting. >>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>>> Sep 5 10:15:57 2023 >>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>> # [0]PETSC ERROR: #9 main() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>> # [0]PETSC ERROR: -error_output_stdout >>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>> # [0]PETSC ERROR: -malloc_dump >>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>> # [0]PETSC ERROR: -pc_type lu >>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> # >>>> -------------------------------------------------------------------------- >>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>> # with errorcode 85. >>>> # >>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> # You may or may not see output from other processes, depending on >>>> # exactly when Open MPI kills them. >>>> # >>>> -------------------------------------------------------------------------- >>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> >>>> >>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>> # >>>> # To rerun failed tests: >>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>> >>>> To get the info of the error there is no specific probe id reported. >>>> >>>> How to check error info and proceed further? >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>> wrote: >>>> >>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>> options that Satish mentioned? >>>>> >>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>> petsc-users wrote: >>>>> >>>>>> Sorry for missing that. >>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>>> >>>>>> < M A T L A B (R) > >>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>> November 23, 2020 >>>>>> >>>>>> >>>>>> To get started, type doc. >>>>>> For product information, visit www.mathworks.com. >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>> wrote: >>>>>> >>>>>>> You are missing one more step: >>>>>>> >>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> >>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>> >>>>>>> Does this work for you? As the message indicates this command is >>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>> >>>>>>> Satish >>>>>>> >>>>>>> >>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>> >>>>>>> > Hi Sathish, >>>>>>> > >>>>>>> > I tried the following procedure >>>>>>> > >>>>>>> > *$make * >>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> > Building with 'gcc'. >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > In function ?PetscBinaryWrite?: >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>> > [-Wmaybe-uninitialized] >>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > | ^ >>>>>>> > >>>>>>> > MEX completed successfully. >>>>>>> > Building with 'gcc'. >>>>>>> > MEX completed successfully. >>>>>>> > Building with 'gcc'. >>>>>>> > MEX completed successfully. >>>>>>> > Building with 'gcc'. >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > In function ?PetscBinaryWrite?: >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>> > [-Wmaybe-uninitialized] >>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > | ^ >>>>>>> > >>>>>>> > MEX completed successfully. >>>>>>> > ========================================= >>>>>>> > Now to check if the libraries are working do: >>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>> check >>>>>>> > >>>>>>> > *$make test query=requires queryval=matlab >>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>> queryval=matlab >>>>>>> > query=requires >>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> > TEST >>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Mon Sep >>>>>>> > 4 10:02:32 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>> > # [0]PETSC ERROR: >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Mon Sep >>>>>>> > 4 10:02:32 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > # [0]PETSC ERROR: >>>>>>> > >>>>>>> ------------------------------------------------------------------------ >>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>> Violation, >>>>>>> > probably memory access out of range >>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>> -on_error_attach_debugger >>>>>>> > # [0]PETSC ERROR: or see >>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>> Apple Mac OS >>>>>>> > X to find memory corruption errors >>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>>>>>> link, >>>>>>> > and run >>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Mon Sep >>>>>>> > 4 10:02:32 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>>> file >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>> > # with errorcode 50162059. >>>>>>> > # >>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > # You may or may not see output from other processes, depending on >>>>>>> > # exactly when Open MPI kills them. >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>> > CC >>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>> > CLINKER >>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > TEST >>>>>>> > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>> code: 124 >>>>>>> > # Running problem 5 >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>> MB108SMEC028 by >>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire >>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>> > # with errorcode 126076. >>>>>>> > # >>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > # You may or may not see output from other processes, depending on >>>>>>> > # exactly when Open MPI kills them. >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>> Command failed >>>>>>> > so no diff >>>>>>> > >>>>>>> > # ------------- >>>>>>> > # Summary >>>>>>> > # ------------- >>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > # success 0/2 tests (0.0%) >>>>>>> > # failed 2/2 tests (100.0%) >>>>>>> > # todo 0/2 tests (0.0%) >>>>>>> > # skip 0/2 tests (0.0%) >>>>>>> > # >>>>>>> > # Wall clock time for tests: 4 sec >>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>> > # >>>>>>> > # To rerun failed tests: >>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> > # >>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>>> 0.01 sec >>>>>>> > >>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>> > *$make matlab_ls_test* >>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>> -Wwrite-strings >>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>> -Wno-strict-aliasing >>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>> -lmx >>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>> -lmpi_mpifh >>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>> -lquadmath >>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>> > >>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>> ./matlab_ls_test >>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>> processors = 1 >>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>> > MB108SMEC028.(none) >>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>> > Running problem 5 >>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>> 140155238476992 >>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 >>>>>>> by vit >>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>> > [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > [0]PETSC ERROR: -info >>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire >>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>> > with errorcode 126076. >>>>>>> > >>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>> > You may or may not see output from other processes, depending on >>>>>>> > exactly when Open MPI kills them. >>>>>>> > >>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>> > >>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>> wrote: >>>>>>> > >>>>>>> > > To use datafiles in the test suite: >>>>>>> > > >>>>>>> > > cd $HOME >>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>> > > >>>>>> DATAFILESPATH - or set >>>>>>> > > manually with make> >>>>>>> > > >>>>>>> > > make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>> > > >>>>>>> > > Satish >>>>>>> > > >>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>> > > >>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>> > > > >>>>>>> > > > > Hi Matthew, >>>>>>> > > > > >>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do >>>>>>> not have >>>>>>> > > any >>>>>>> > > > > separate test files to test PETSc alone. Can you please help >>>>>>> me how to >>>>>>> > > > > define this DATAFILESPATH? >>>>>>> > > > > >>>>>>> > > > >>>>>>> > > > That test you tried uses a certain matrix. On our machine, we >>>>>>> point to >>>>>>> > > this >>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>>>>>> have those >>>>>>> > > > matrices, since they are just for testing here. That >>>>>>> > > > is why I suggested just using a different matrix, or running a >>>>>>> problem >>>>>>> > > you >>>>>>> > > > care about in IBAMR. >>>>>>> > > > >>>>>>> > > > Thanks, >>>>>>> > > > >>>>>>> > > > Matt >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > > Thanks and regards >>>>>>> > > > > Srinivas. >>>>>>> > > > > >>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>> knepley at gmail.com> >>>>>>> > > wrote: >>>>>>> > > > > >>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>>> > > petsc-users < >>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>> > > > >> >>>>>>> > > > >>> Hi Sathish, >>>>>>> > > > >>> >>>>>>> > > > >>> Thank you so much for your efforts and the support you are >>>>>>> giving me >>>>>>> > > to >>>>>>> > > > >>> sort this out. >>>>>>> > > > >>> >>>>>>> > > > >>> I tried to follow the same procedure which you followed to >>>>>>> build >>>>>>> > > Petsc >>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>> > > > >>> >>>>>>> > > > >>> *$./configure >>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> PETSC_ARCH=linux-opt >>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>> > > > >>> Using python3 for Python >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> It appears you do >>>>>>> not have >>>>>>> > > valgrind >>>>>>> > > > >>> installed on your system. >>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>>> > > > >>> Or install >>>>>>> > > valgrind-devel or >>>>>>> > > > >>> equivalent using your package manager. >>>>>>> > > > >>> Then rerun ./configure >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> Compilers: >>>>>>> > > > >>> >>>>>>> > > > >>> C Compiler: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > -fPIC >>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>> C++ Compiler: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>> > > > >>> Fortran Compiler: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>> 9.4.0 >>>>>>> > > > >>> Linkers: >>>>>>> > > > >>> Shared linker: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > -shared >>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> > > -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>> Dynamic linker: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > -shared >>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> > > -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>> > > > >>> make: >>>>>>> > > > >>> Version: 4.2 >>>>>>> > > > >>> /usr/bin/make >>>>>>> > > > >>> BlasLapack: >>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>> -omp_num_threads >>>>>>> > >

to >>>>>>> > > > >>> control the number of threads >>>>>>> > > > >>> uses 8 byte integers >>>>>>> > > > >>> MPI: >>>>>>> > > > >>> Version: 3 >>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>> > > --oversubscribe >>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>> > > > >>> pthread: >>>>>>> > > > >>> cmake: >>>>>>> > > > >>> Version: 3.16.3 >>>>>>> > > > >>> /usr/bin/cmake >>>>>>> > > > >>> regex: >>>>>>> > > > >>> Matlab: >>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>> > > > >>> MatlabEngine: >>>>>>> > > > >>> Library: >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>>>>> -lmx -lmat >>>>>>> > > -lut >>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>> > > > >>> PETSc: >>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>> > > > >>> Scalar type: real >>>>>>> > > > >>> Precision: double >>>>>>> > > > >>> Support for __float128 >>>>>>> > > > >>> Integer size: 4 bytes >>>>>>> > > > >>> shared libraries: enabled >>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>> PETSC_ARCH=linux-opt all >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>> >>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>>>>>> -licuuc as >>>>>>> > > > >>> you suggested earlier. >>>>>>> > > > >>> >>>>>>> > > > >>> *$make* >>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > > > >>> | ^ >>>>>>> > > > >>> >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > > > >>> | ^ >>>>>>> > > > >>> >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> ========================================= >>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>> PETSC_ARCH=linux-opt check >>>>>>> > > > >>> =============================================== >>>>>>> > > > >>> >>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> > > > >>> TEST >>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > > > >>> >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>> > > > >>> >>>>>>> > > > >> >>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>> defined, so it >>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>> yours. >>>>>>> > > > >> >>>>>>> > > > >> Thanks, >>>>>>> > > > >> >>>>>>> > > > >> Matt >>>>>>> > > > >> >>>>>>> > > > >> >>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>>> trouble >>>>>>> > > > >>> shooting. >>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>> 2020 >>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>> MB108SMEC028 by vit >>>>>>> > > Sun >>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> COPTFLAGS=-O3 >>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>> line 1444 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>> -------send >>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>> MPI_COMM_SELF >>>>>>> > > > >>> # with errorcode 113065. >>>>>>> > > > >>> # >>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>> depending on >>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>>>> diff >>>>>>> > > > >>> CC >>>>>>> > > > >>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>> > > > >>> CLINKER >>>>>>> > > > >>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > > > >>> TEST >>>>>>> > > > >>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> Error >>>>>>> > > code: 124 >>>>>>> > > > >>> # Running problem 5 >>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > > > >>> >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>>> trouble >>>>>>> > > > >>> shooting. >>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>> 2020 >>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>> > > MB108SMEC028 by >>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> COPTFLAGS=-O3 >>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>> -------send >>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>> MPI_COMM_SELF >>>>>>> > > > >>> # with errorcode 126076. >>>>>>> > > > >>> # >>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>> depending on >>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> SKIP Command >>>>>>> > > > >>> failed so no diff >>>>>>> > > > >>> >>>>>>> > > > >>> # ------------- >>>>>>> > > > >>> # Summary >>>>>>> > > > >>> # ------------- >>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>> > > > >>> # >>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>> > > > >>> # >>>>>>> > > > >>> # To rerun failed tests: >>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> > > > >>> # >>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 >>>>>>> sec / >>>>>>> > > 0.02 sec >>>>>>> > > > >>> >>>>>>> > > > >>> *How to sort out this error?* >>>>>>> > > > >>> >>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>> > > -Wwrite-strings >>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>> > > -Wno-strict-aliasing >>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>>>> -O3 >>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>> matlab_ls_test.c >>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>> -leng -lmex >>>>>>> > > -lmx >>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>> > > -lmpi_mpifh >>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>> -lpthread >>>>>>> > > -lquadmath >>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>> > > > >>> >>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>>>>> find the >>>>>>> > > > >>> attachment and do the needful. >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> Thanks and regards >>>>>>> > > > >>> Srinivas >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>> balay at mcs.anl.gov> >>>>>>> > > wrote: >>>>>>> > > > >>> >>>>>>> > > > >>>> Perhaps you can try the following to get additional info >>>>>>> - and debug >>>>>>> > > > >>>> >>>>>>> > > > >>>> Satish >>>>>>> > > > >>>> ---------- >>>>>>> > > > >>>> >>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>> > > > >>>> balay at compute-386-07 >>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>> > > > >>>> make matlab_ls_test >>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>> -fPIC >>>>>>> > > -Wall >>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> > > -fstack-protector >>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>> > > -Wno-strict-aliasing >>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>> -fvisibility=hidden -O3 >>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>> > > > >>>> matlab_ls_test.c >>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> >>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread >>>>>>> -lm -leng >>>>>>> > > -lmex >>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>>>>>> -lmpifort >>>>>>> > > -lmpi >>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>>>>>> -ldl -o >>>>>>> > > > >>>> matlab_ls_test >>>>>>> > > > >>>> balay at compute-386-07 >>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>> ./matlab_ls_test >>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number >>>>>>> of >>>>>>> > > processors >>>>>>> > > > >>>> = 1 >>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is >>>>>>> NIS >>>>>>> > > > >>>> compute-386-07.(none) >>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>> > > > >>>> Running problem 5 >>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>> 1140850689 >>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>> with command >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>>> > > > >>>> TestingInitialize >>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>>> string: >>>>>>> > > > >>>> TestingInitialize >>>>>>> > > > >>>> 5 >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>> works for you >>>>>>> > > - on >>>>>>> > > > >>>> this machine..>>>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> balay at compute-386-07 >>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>> > > > >>>> >>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>> MathWorks, Inc. >>>>>>> > > > >>>> >>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>>> (glnxa64) >>>>>>> > > > >>>> >>>>>>> > > > >>>> February 17, 2021 >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> To get started, type doc. >>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>> > > > >>>> >>>>>>> > > > >>>> >> >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>> > > > >>>> >>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>> [reverting >>>>>>> > > thread >>>>>>> > > > >>>> to petsc-users only] >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>> > > corresponding >>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>> Ubuntu-20.04, >>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>> > > > >>>> > main >>>>>>> > > > >>>> > release >>>>>>> > > > >>>> > * release-3.13 >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>> > > matlab/R2021a >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>> > > > >>>> >>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> PETSC_ARCH=linux-opt >>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > Compilers: >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> > C Compiler: >>>>>>> > > > >>>> >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>> > > -Wall >>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> > > -fstack-protector >>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>>> > C++ Compiler: >>>>>>> > > > >>>> >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> > > -fstack-protector >>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>>> > Fortran Compiler: >>>>>>> > > > >>>> >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>> > > -Wall >>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>>> > Linkers: >>>>>>> > > > >>>> > Shared linker: >>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>> > > -shared -fPIC >>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>>> > Dynamic linker: >>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>> > > -shared -fPIC >>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>> > > > >>>> > make: >>>>>>> > > > >>>> > Version: 4.2 >>>>>>> > > > >>>> > /usr/bin/make >>>>>>> > > > >>>> > BlasLapack: >>>>>>> > > > >>>> > Library: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>> -omp_num_threads >>>>>>> > >

>>>>>>> > > > >>>> to control the number of threads >>>>>>> > > > >>>> > uses 8 byte integers >>>>>>> > > > >>>> > MPI: >>>>>>> > > > >>>> > Version: 4 >>>>>>> > > > >>>> > Includes: >>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>> > > > >>>> > Mpiexec: >>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>> > > > >>>> > pthread: >>>>>>> > > > >>>> > Library: -lpthread >>>>>>> > > > >>>> > cmake: >>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>> > > > >>>> > regex: >>>>>>> > > > >>>> > Matlab: >>>>>>> > > > >>>> > Includes: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>> > > > >>>> > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>> > > > >>>> > MatlabEngine: >>>>>>> > > > >>>> > Library: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>> > > > >>>> > sowing: >>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>> > > > >>>> > valgrind: >>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>> > > > >>>> > PETSc: >>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>> > > > >>>> > Scalar type: real >>>>>>> > > > >>>> > Precision: double >>>>>>> > > > >>>> > Support for __float128 >>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>> > > > >>>> > shared libraries: enabled >>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>> with: >>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>> PETSC_ARCH=linux-opt all >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> > > socket\n"); >>>>>>> > > > >>>> > | ^ >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> > > socket\n"); >>>>>>> > > > >>>> > | ^ >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > ========================================= >>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>> PETSC_ARCH=linux-opt check >>>>>>> > > > >>>> > ========================================= >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>> > > query=requires >>>>>>> > > > >>>> queryval=matlab >>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> > > > >>>> > TEST >>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>> > > > >>>> > # ../ex72: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>> no diff >>>>>>> > > > >>>> > CC >>>>>>> > > > >>>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>> > > > >>>> > CLINKER >>>>>>> > > > >>>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > > > >>>> > TEST >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> # Error >>>>>>> > > code: >>>>>>> > > > >>>> 1 >>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> SKIP >>>>>>> > > Command >>>>>>> > > > >>>> failed so no diff >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>> test >>>>>>> > > query=requires >>>>>>> > > > >>>> queryval=matlab >>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>> > > > >>>> > TEST >>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>> > > > >>>> > TEST >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>>> > ok >>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > # ------------- >>>>>>> > > > >>>> > # Summary >>>>>>> > > > >>>> > # ------------- >>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>> > > > >>>> > # >>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>> 15.190000000000001 >>>>>>> > > sec >>>>>>> > > > >>>> > # >>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>> 6.47 sec / >>>>>>> > > 7.54 >>>>>>> > > > >>>> sec >>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>> tried to >>>>>>> > > > >>>> configure petsc >>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>> successful. After >>>>>>> > > > >>>> running make >>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>> message. >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > not ok >>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>> > > > >>>> code: 124 >>>>>>> > > > >>>> > > # Running problem 5 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > > > >>>> > > >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > > > >>>> > > for trouble shooting. >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>> 01, 2020 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>> named >>>>>>> > > > >>>> MB108SMEC028 by >>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> COPTFLAGS=-O3 >>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> > > > >>>> --with-debugging=0 >>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>>>>> 67 in >>>>>>> > > > >>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>> > > -------send >>>>>>> > > > >>>> entire >>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>>> > > # >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>> MPI_COMM_SELF >>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>> > > > >>>> > > # >>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>>>>> all MPI >>>>>>> > > > >>>> processes. >>>>>>> > > > >>>> > > # You may or may not see output from other processes, >>>>>>> depending >>>>>>> > > on >>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>> > > > >>>> > > # >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > Thanks >>>>>>> > > > >>>> > > Srinivas >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > i.e.: >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>>> 20PHD0548 via >>>>>>> > > > >>>> petsc-users < >>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>>> balay at mcs.anl.gov> >>>>>>> > > > >>>> wrote: >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>>>>> will work >>>>>>> > > > >>>> here]. >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> i.e: >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> ./configure >>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> > > PETSC_ARCH=linux-opt >>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> --known-64-bit-blas-indic >>>>>> >>>>>> -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From carljohanthore at gmail.com Wed Sep 6 01:13:53 2023 From: carljohanthore at gmail.com (Carl-Johan Thore) Date: Wed, 6 Sep 2023 08:13:53 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: <98308F14-CC1C-4B6B-8082-559D6867E32E@lip6.fr> References: <68909B9F-A693-46FD-97B0-23AA5531E814@lip6.fr> <009EB5B4-E65F-4486-8045-6CA5E20DBD94@lip6.fr> <98308F14-CC1C-4B6B-8082-559D6867E32E@lip6.fr> Message-ID: Thanks for this! I now get convergence with sbaij and fieldsplit. However, as can be seen in the attached file, it requires around three times as many outer iterations as with aij to reach the same point (to within rtol). Switching from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct" choice?) helps quite a bit, but still sbaij takes many more iterations. So it seems that your sbaij-implementation works but that I'm doing something wrong when setting up the fieldsplit pc, or that some of the subsolvers doesn't work properly with sbaij. I've tried bjacobi as you had in your logs, but not hypre yet. But anyway, one doesn't expect the matrix format to have this much impact on convergence? Any other suggestions? /Carl-Johan On Mon, Sep 4, 2023 at 9:31?PM Pierre Jolivet wrote: > The branch should now be good to go ( > https://gitlab.com/petsc/petsc/-/merge_requests/6841). > Sorry, I made a mistake before, hence the error on PetscObjectQuery(). > I?m not sure the code will be covered by the pipeline, but I have tested > this on a Raviart?Thomas discretization with PCFIELDSPLIT. > You?ll see in the attached logs that: > 1) the numerics match > 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} > block from the global (symmetric) A and we get the A_{10} block cheaply by > just using MatCreateHermitianTranspose(), instead of calling another time > MatCreateSubMatrix() > Please let me know if you have some time to test the branch and whether it > fails or succeeds on your test cases. > > Also, I do not agree with what Hong said. > Sometimes, the assembly of a coefficient can be more expensive than the > communication of the said coefficient. > So they are instances where SBAIJ would be more efficient than AIJ even if > it would require more communication, it is not a black and white picture. > > Thanks, > Pierre > > > On 28 Aug 2023, at 12:12 PM, Pierre Jolivet > wrote: > > > On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore > wrote: > > I've tried the new files, and with them, PCFIELDSPLIT now gets set up > without crashes (but the setup is significantly slower than for MATAIJ) > > > I?ll be back from Japan at the end of this week, my schedule is too packed > to get anything done in the meantime. > But I?ll let you know when things are working properly (last I checked, I > think it was working, but I may have forgotten about a corner case or two). > But yes, though one would except things to be faster and less memory > intensive with SBAIJ, it?s unfortunately not always the case. > > Thanks, > Pierre > > Unfortunately I still get errors later in the process: > > [0]PETSC ERROR: Null argument, when expecting valid pointer > [0]PETSC ERROR: Null Pointer: Parameter # 1 > [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d > GIT Date: 2023-08-22 20:32:33 -0400 > [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 --with-cuda > --with-cusp --download-scalapack --download-hdf5 --download-zlib > --download-mumps --download-parmetis --download-metis --download-ptscotch > --download-hypre --download-spai > [0]PETSC ERROR: #1 PetscObjectQuery() at > /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 > [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at > /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 > [0]PETSC ERROR: #3 MatCreateSubMatrix() at > /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 > [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at > /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 > [0]PETSC ERROR: #5 PCSetUp() at > /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 > [0]PETSC ERROR: #6 KSPSetUp() at > /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 > > The code I'm running here works without any problems for MATAIJ. To run it > with MATSBAIJ I've simply used the command-line option > -dm_mat_type sbaij > > > Kind regards, > Carl-Johan > > > On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users < > petsc-users at mcs.anl.gov> wrote: > >> >> >> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore >> wrote: >> >> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up >> with the same issue.? >> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices from >> these blocks, or is there >> somewhere else in the code that things will go wrong? >> >> >> Ah, no, you are right, in that case it should work. >> >> For the MATNEST I was thinking to get some savings from the >> block-symmetry at least >> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for them >> would just be a >> (pretty big) bonus. >> >> ?I?ll rebase on top of main and try to get it integrated if it could be >> useful to you (but I?m traveling >> right now so everything gets done more slowly, sorry).? >> Sound great, Thanks again! >> >> >> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >> I need to add a new code path in MatCreateRedundantMatrix() to make sure >> the resulting Mat is indeed SBAIJ, but that is orthogonal to the >> PCFIELDSPLIT issue. >> The branch should be usable in its current state. >> >> Thanks, >> Pierre >> >> >> *From:* Pierre Jolivet >> *Sent:* Saturday, August 26, 2023 4:36 PM >> *To:* Carl-Johan Thore >> *Cc:* Carl-Johan Thore ; >> petsc-users at mcs.anl.gov >> *Subject:* Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >> >> >> >> >> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore >> wrote: >> >> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used >> to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get >> the A01 and A10 blocks in PCFIELDSPLIT. >> I have a branch that fixes this, but I haven?t rebased in a while (and >> I?m AFK right now), would you want me to rebase and give it a go, or must >> you stick to a release tarball?" >> >> Ok, would be great if you could look at this! I don't need to stick to >> any particular branch. >> >> Do you think MATNEST could be an alternative here? >> >> >> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with >> the same issue. >> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was >> crashing but I think it was thoroughly fixed in >> https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >> It is ugly code on top of ugly code, so I didn?t try to get it integrated >> and just used the branch locally, and then moved to some other stuff. >> I?ll rebase on top of main and try to get it integrated if it could be >> useful to you (but I?m traveling right now so everything gets done more >> slowly, sorry). >> >> Thanks, >> Pierre >> >> >> My matrix is >> [A00 A01; >> A01^t A11] >> so perhaps with MATNEST I can make use of the block-symmetry at least, >> and then use MATSBAIJ for >> A00 and A11 if it's possible to combine matrix types which the manual >> seems to imply. >> >> Kind regards >> Carl-Johan >> >> >> >> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore >> wrote: >> ? >> Hi, >> >> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >> According to the manual "[t]he fieldsplit preconditioner cannot >> currently be used with the MATBAIJ or MATSBAIJ data formats if the >> blocksize is larger than 1". Since my blocksize is exactly 1 it would >> seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For >> symmetric format, iscol must equal isrow" >> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >> fieldsplit.c at >> >> /* extract the A01 and A10 matrices */ ilink = jac->head; >> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >> MAT_INITIAL_MATRIX, &jac->B)); } >> >> This, since my A01 and A10 are not square, seems to explain why iscol is >> not equal to isrow. >> From this I gather that it is in general NOT possible to use >> PCFIELDSPLIT with MATSBAIJ even with block size 1? >> >> Kind regards, >> Carl-Johan >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- %%% With AIJ: ... 307 KSP Residual norm 1.854926995470e-09 308 KSP Residual norm 1.751893310256e-09 309 KSP Residual norm 1.646593329093e-09 310 KSP Residual norm 1.543009494478e-09 311 KSP Residual norm 1.452641639917e-09 312 KSP Residual norm 1.369620969855e-09 313 KSP Residual norm 1.302155745365e-09 314 KSP Residual norm 1.252174189783e-09 315 KSP Residual norm 1.192872051154e-09 316 KSP Residual norm 1.138612609555e-09 Linear solve converged due to CONVERGED_RTOL iterations 316 %%% With SBAIJ (More detailed output at the end of this file, also output from factorization FULL) ... 965 KSP Residual norm 1.346789114008e-09 966 KSP Residual norm 1.306538742039e-09 967 KSP Residual norm 1.247901915750e-09 968 KSP Residual norm 1.186932599681e-09 969 KSP Residual norm 1.141186989549e-09 Linear solve converged due to CONVERGED_RTOL iterations 969 %%% KSPVIEW with SBAIJ : KSP Object: 4 MPI processes type: fgmres restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement happy breakdown tolerance 1e-30 maximum iterations=1000, nonzero initial guess minimum iterations=3 tolerances: relative=1e-10, absolute=1e-50, divergence=1e+09 right preconditioning using UNPRECONDITIONED norm type for convergence test PC Object: 4 MPI processes type: fieldsplit FieldSplit with Schur preconditioner, factorization LOWER Preconditioner for the Schur complement formed from Sp, an assembled approximation to S, which uses A00's diagonal's inverse Split info: Split number 0 Defined by IS Split number 1 Defined by IS KSP solver for A00 block KSP Object: (fieldsplit_0_) 4 MPI processes type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_0_) 4 MPI processes type: asm total subdomain blocks = 4, amount of overlap = 1 restriction/interpolation type - RESTRICT Local solver information for first block is in the following KSP and PC objects on rank 0: Use -fieldsplit_0_ksp_view ::ascii_info_detail to display information for all blocks KSP Object: (fieldsplit_0_sub_) 1 MPI process type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_0_sub_) 1 MPI process type: icc out-of-place factorization 0 levels of fill tolerance for zero pivot 2.22045e-14 using Manteuffel shift [POSITIVE_DEFINITE] matrix ordering: natural factor fill ratio given 1., needed 1. Factored matrix follows: Mat Object: (fieldsplit_0_sub_) 1 MPI process type: seqsbaij rows=97788, cols=97788 package used to perform factorization: petsc total: nonzeros=1153455, allocated nonzeros=1153455 block size is 1 linear system matrix = precond matrix: Mat Object: (fieldsplit_0_sub_) 1 MPI process type: seqsbaij rows=97788, cols=97788 total: nonzeros=1153455, allocated nonzeros=1153455 total number of mallocs used during MatSetValues calls=0 block size is 1 linear system matrix = precond matrix: Mat Object: (fieldsplit_0_) 4 MPI processes type: mpisbaij rows=392931, cols=392931 total: nonzeros=5739651, allocated nonzeros=5739651 total number of mallocs used during MatSetValues calls=0 block size is 1 KSP solver for S = A11 - A10 inv(A00) A01 KSP Object: (fieldsplit_1_) 4 MPI processes type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_1_) 4 MPI processes type: asm total subdomain blocks = 4, amount of overlap = 1 restriction/interpolation type - RESTRICT Local solver information for first block is in the following KSP and PC objects on rank 0: Use -fieldsplit_1_ksp_view ::ascii_info_detail to display information for all blocks KSP Object: (fieldsplit_1_sub_) 1 MPI process type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_1_sub_) 1 MPI process type: ilu out-of-place factorization 0 levels of fill tolerance for zero pivot 2.22045e-14 matrix ordering: natural factor fill ratio given 1., needed 1. Factored matrix follows: Mat Object: (fieldsplit_1_sub_) 1 MPI process type: seqaij rows=31038, cols=31038 package used to perform factorization: petsc total: nonzeros=223972, allocated nonzeros=223972 not using I-node routines linear system matrix = precond matrix: Mat Object: (fieldsplit_1_sub_) 1 MPI process type: seqaij rows=31038, cols=31038 total: nonzeros=223972, allocated nonzeros=223972 total number of mallocs used during MatSetValues calls=0 not using I-node routines linear system matrix followed by preconditioner matrix: Mat Object: (fieldsplit_1_) 4 MPI processes type: schurcomplement rows=121600, cols=121600 Schur complement A11 - A10 inv(A00) A01 A11 Mat Object: (fieldsplit_1_) 4 MPI processes type: mpisbaij rows=121600, cols=121600 total: nonzeros=242540, allocated nonzeros=242540 total number of mallocs used during MatSetValues calls=0 block size is 1 A10 Mat Object: 4 MPI processes type: hermitiantranspose rows=121600, cols=392931 KSP solver for A00 block viewable with the additional option -fieldsplit_0_ksp_view A01 Mat Object: 4 MPI processes type: mpiaij rows=392931, cols=121600 total: nonzeros=1018872, allocated nonzeros=1018872 total number of mallocs used during MatSetValues calls=0 using I-node (on process 0) routines: found 23081 nodes, limit used is 5 Mat Object: 4 MPI processes type: mpiaij rows=121600, cols=121600 total: nonzeros=1120336, allocated nonzeros=1120336 total number of mallocs used during MatSetValues calls=0 not using I-node (on process 0) routines linear system matrix = precond matrix: Mat Object: 4 MPI processes type: mpisbaij rows=514531, cols=514531 total: nonzeros=7001063, allocated nonzeros=26569279 total number of mallocs used during MatSetValues calls=0 block size is 1 %% SBAIJ AGAIN WITH MORE DETAILED OUTPUT: .... 848 KSP Residual norm 7.104369530073e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997543072e-01 1 KSP Residual norm 3.002328976968e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.004801268598e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.106461054312e-01 1 KSP Residual norm 9.032329726351e-03 1 KSP Residual norm 6.971835623451e-04 849 KSP Residual norm 6.950875510226e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997408161e-01 1 KSP Residual norm 2.988085947538e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.193961257338e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.387629868742e-01 1 KSP Residual norm 8.835757046845e-03 1 KSP Residual norm 7.160201171420e-04 850 KSP Residual norm 6.792871940409e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997211093e-01 1 KSP Residual norm 2.806859529571e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.463113208838e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.463497493063e-01 1 KSP Residual norm 8.969428389311e-03 1 KSP Residual norm 7.429684096268e-04 851 KSP Residual norm 6.633256020443e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997044515e-01 1 KSP Residual norm 2.645025742398e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.681680406391e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.591871186086e-01 1 KSP Residual norm 9.326676402818e-03 1 KSP Residual norm 7.649711247555e-04 852 KSP Residual norm 6.488673644160e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997190302e-01 1 KSP Residual norm 2.614714200275e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.489198714589e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.588925897545e-01 1 KSP Residual norm 9.242833701551e-03 1 KSP Residual norm 7.455683026848e-04 853 KSP Residual norm 6.373470520032e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997676684e-01 1 KSP Residual norm 2.700531175710e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.811087731693e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.402443837288e-01 1 KSP Residual norm 9.505505737547e-03 1 KSP Residual norm 6.774446464568e-04 854 KSP Residual norm 6.276004379688e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997984917e-01 1 KSP Residual norm 2.974092924210e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.339611385305e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.252539481806e-01 1 KSP Residual norm 9.734258685392e-03 1 KSP Residual norm 6.302508777492e-04 855 KSP Residual norm 6.179752138080e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997971420e-01 1 KSP Residual norm 2.993089069965e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.362463802669e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.329578047938e-01 1 KSP Residual norm 9.380111691525e-03 1 KSP Residual norm 6.324339399561e-04 856 KSP Residual norm 6.075772917666e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997755989e-01 1 KSP Residual norm 2.969200049264e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.693003909781e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.418766186278e-01 1 KSP Residual norm 9.399399487587e-03 1 KSP Residual norm 6.656554238335e-04 857 KSP Residual norm 5.964043172989e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997513769e-01 1 KSP Residual norm 2.957682018798e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.044315948253e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.312769868691e-01 1 KSP Residual norm 9.609354497625e-03 1 KSP Residual norm 7.011054335511e-04 858 KSP Residual norm 5.836067800148e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997035756e-01 1 KSP Residual norm 2.872816376259e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.694755749377e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.541154918731e-01 1 KSP Residual norm 9.433228788725e-03 1 KSP Residual norm 7.662132564765e-04 859 KSP Residual norm 5.706276444297e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999996843365e-01 1 KSP Residual norm 2.880361159842e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.938909858461e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.830052055871e-01 1 KSP Residual norm 9.499862082307e-03 1 KSP Residual norm 7.906577788230e-04 860 KSP Residual norm 5.617583613817e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997765805e-01 1 KSP Residual norm 2.777252773447e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.678302112735e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.424164602895e-01 1 KSP Residual norm 8.849911913621e-03 1 KSP Residual norm 6.642132850462e-04 861 KSP Residual norm 5.561524925175e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999998577848e-01 1 KSP Residual norm 2.988351670810e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 5.323587005378e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.912319135071e-01 1 KSP Residual norm 8.263259855887e-03 1 KSP Residual norm 5.281070035682e-04 862 KSP Residual norm 5.506766166665e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999998617170e-01 1 KSP Residual norm 2.845994126117e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 5.250474194834e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.260796113127e-01 1 KSP Residual norm 9.811742550036e-03 1 KSP Residual norm 5.203946455451e-04 863 KSP Residual norm 5.439915701058e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999998293776e-01 1 KSP Residual norm 2.727333121556e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 5.832172367101e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 6.441137952198e-01 1 KSP Residual norm 1.095694768745e-02 1 KSP Residual norm 5.783308321627e-04 864 KSP Residual norm 5.403748531336e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999076505e-01 1 KSP Residual norm 2.946574403519e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 4.284720832619e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.468942171326e-01 1 KSP Residual norm 1.008737195428e-02 1 KSP Residual norm 4.226715398658e-04 865 KSP Residual norm 5.390145255217e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999680097e-01 1 KSP Residual norm 2.682345341857e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.513585515632e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.917467950759e-01 1 KSP Residual norm 8.647135665273e-03 1 KSP Residual norm 2.417216343103e-04 866 KSP Residual norm 5.380625495115e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999810804e-01 1 KSP Residual norm 2.716840513330e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.924843435164e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.107512032702e-01 1 KSP Residual norm 9.149302558168e-03 1 KSP Residual norm 1.792387424209e-04 867 KSP Residual norm 5.372335239833e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999876245e-01 1 KSP Residual norm 2.568578816344e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.558982763978e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.905650299337e-01 1 KSP Residual norm 8.903714362140e-03 1 KSP Residual norm 1.400939970262e-04 868 KSP Residual norm 5.360438558152e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999864784e-01 1 KSP Residual norm 2.699420168709e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.614606040709e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.810945846549e-01 1 KSP Residual norm 9.180051719635e-03 1 KSP Residual norm 1.443011750042e-04 869 KSP Residual norm 5.348297140501e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999894059e-01 1 KSP Residual norm 2.650620998028e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.427955851890e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.386304184444e-01 1 KSP Residual norm 9.455476649684e-03 1 KSP Residual norm 1.243623777490e-04 870 KSP Residual norm 5.332375540684e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999907753587e-01 1 KSP Residual norm 1.397049625888e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 4.294988477916e-03 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.943871296139e-01 1 KSP Residual norm 1.398563480253e-02 1 KSP Residual norm 4.293847237178e-03 871 KSP Residual norm 5.321236219875e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999651286e-01 1 KSP Residual norm 3.081023329909e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.645953802241e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 3.642004434000e-01 1 KSP Residual norm 7.705417280598e-03 1 KSP Residual norm 2.566454735225e-04 872 KSP Residual norm 5.311640476046e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999744831e-01 1 KSP Residual norm 2.490733310825e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.235044817215e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.548255612027e-01 1 KSP Residual norm 8.856512457730e-03 1 KSP Residual norm 2.122746642681e-04 873 KSP Residual norm 5.304028133887e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999828602e-01 1 KSP Residual norm 2.549044979155e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.828871960928e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.622312578666e-01 1 KSP Residual norm 9.072031411109e-03 1 KSP Residual norm 1.683717190982e-04 874 KSP Residual norm 5.297958730745e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999897053e-01 1 KSP Residual norm 2.530617076025e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.405564820886e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.907914926001e-01 1 KSP Residual norm 8.583515677868e-03 1 KSP Residual norm 1.227759379058e-04 875 KSP Residual norm 5.289797950943e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999910240e-01 1 KSP Residual norm 2.589040425820e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.313546481415e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.516770543897e-01 1 KSP Residual norm 8.446815143534e-03 1 KSP Residual norm 1.131801128714e-04 876 KSP Residual norm 5.265823936593e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999816999e-01 1 KSP Residual norm 2.626792233723e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.886975236830e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.923140627679e-01 1 KSP Residual norm 8.298469925643e-03 1 KSP Residual norm 1.758810885662e-04 877 KSP Residual norm 5.206582915262e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999613590e-01 1 KSP Residual norm 2.645003250652e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.762824921229e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.371189304468e-01 1 KSP Residual norm 9.648412215549e-03 1 KSP Residual norm 2.670491947781e-04 878 KSP Residual norm 5.098934275848e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999323304e-01 1 KSP Residual norm 2.764456965888e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.668724930676e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.648246014540e-01 1 KSP Residual norm 1.033089944388e-02 1 KSP Residual norm 3.596241951589e-04 879 KSP Residual norm 4.962827438525e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999142388e-01 1 KSP Residual norm 2.744339887142e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 4.130484934034e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.653261835339e-01 1 KSP Residual norm 1.047142410600e-02 1 KSP Residual norm 4.066851512318e-04 880 KSP Residual norm 4.826880938808e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999143318e-01 1 KSP Residual norm 2.727921880673e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 4.124153963081e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.438052544487e-01 1 KSP Residual norm 9.594505730934e-03 1 KSP Residual norm 4.063984102255e-04 881 KSP Residual norm 4.702015308248e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999240689e-01 1 KSP Residual norm 2.503756452900e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.883465220153e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.474951146516e-01 1 KSP Residual norm 8.828569486257e-03 1 KSP Residual norm 3.815594530755e-04 882 KSP Residual norm 4.589486600871e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999343353e-01 1 KSP Residual norm 2.594473594854e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.607979673769e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.225293861142e-01 1 KSP Residual norm 1.005442966904e-02 1 KSP Residual norm 3.538440193504e-04 883 KSP Residual norm 4.470395006935e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999316322e-01 1 KSP Residual norm 2.787682281979e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.681898764376e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.600575563823e-01 1 KSP Residual norm 9.176573483881e-03 1 KSP Residual norm 3.609997684272e-04 884 KSP Residual norm 4.362037158339e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999361837e-01 1 KSP Residual norm 2.590346560085e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.556683123661e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.439810481135e-01 1 KSP Residual norm 8.344777001285e-03 1 KSP Residual norm 3.486444125855e-04 885 KSP Residual norm 4.264818647925e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999425552e-01 1 KSP Residual norm 2.624793333346e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.378604015147e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.375951095518e-01 1 KSP Residual norm 8.743941451579e-03 1 KSP Residual norm 3.304139236914e-04 886 KSP Residual norm 4.162077613245e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999407085e-01 1 KSP Residual norm 2.421854578387e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 3.427145476426e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 6.105235783101e-01 1 KSP Residual norm 9.394677258658e-03 1 KSP Residual norm 3.347473805044e-04 887 KSP Residual norm 4.104041459006e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999706516e-01 1 KSP Residual norm 2.552848945740e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.408542694160e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.961473288921e-01 1 KSP Residual norm 8.475489690816e-03 1 KSP Residual norm 2.310730104914e-04 888 KSP Residual norm 4.051594385824e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999797607e-01 1 KSP Residual norm 2.640672731384e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.987378501134e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.282294805377e-01 1 KSP Residual norm 8.446521503361e-03 1 KSP Residual norm 1.867003266355e-04 889 KSP Residual norm 3.994747088446e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999824683e-01 1 KSP Residual norm 2.578572337607e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.847695200729e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.319020713275e-01 1 KSP Residual norm 8.655303071130e-03 1 KSP Residual norm 1.716565401001e-04 890 KSP Residual norm 3.927017960813e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999849653e-01 1 KSP Residual norm 2.893843148694e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.714913923829e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 4.627146296301e-01 1 KSP Residual norm 8.613991808792e-03 1 KSP Residual norm 1.593386879312e-04 891 KSP Residual norm 3.781726178385e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999742928e-01 1 KSP Residual norm 2.543822657309e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.242105260143e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.670862528763e-01 1 KSP Residual norm 9.237998555973e-03 1 KSP Residual norm 2.131571070562e-04 892 KSP Residual norm 3.597384146255e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999734849e-01 1 KSP Residual norm 2.654311462169e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.293579633553e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.712717598573e-01 1 KSP Residual norm 9.357065900445e-03 1 KSP Residual norm 2.182717164772e-04 893 KSP Residual norm 3.407287854869e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999762235e-01 1 KSP Residual norm 2.510163216278e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.155987237242e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.690915456306e-01 1 KSP Residual norm 9.282701730130e-03 1 KSP Residual norm 2.042695827417e-04 894 KSP Residual norm 3.243283927127e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999829098e-01 1 KSP Residual norm 2.698253063950e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.820080242004e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.223887505680e-01 1 KSP Residual norm 8.483960541761e-03 1 KSP Residual norm 1.688953333530e-04 895 KSP Residual norm 3.066143682941e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999851791e-01 1 KSP Residual norm 2.470643280024e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.696519487503e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.328976774892e-01 1 KSP Residual norm 8.719873280040e-03 1 KSP Residual norm 1.550364098784e-04 896 KSP Residual norm 2.858172087964e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999855601e-01 1 KSP Residual norm 2.568660438411e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.674644418657e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.161607679354e-01 1 KSP Residual norm 8.669875299815e-03 1 KSP Residual norm 1.528608785186e-04 897 KSP Residual norm 2.588954412031e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999825789e-01 1 KSP Residual norm 2.753012309020e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.843315447895e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.212180337037e-01 1 KSP Residual norm 8.684708427077e-03 1 KSP Residual norm 1.710031196471e-04 898 KSP Residual norm 2.256718151201e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999760160e-01 1 KSP Residual norm 2.682264127232e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.170701569099e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.702072364353e-01 1 KSP Residual norm 9.698055434273e-03 1 KSP Residual norm 2.049959694642e-04 899 KSP Residual norm 1.976711538311e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999999748076e-01 1 KSP Residual norm 2.831721853798e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 2.222663050362e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.750514624447e-01 1 KSP Residual norm 9.404384631283e-03 1 KSP Residual norm 2.105552239259e-04 900 KSP Residual norm 1.786462293904e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999983468747e-01 1 KSP Residual norm 1.364269546626e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 1.817756705757e-03 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.493098953106e-01 1 KSP Residual norm 1.198945933762e-02 1 KSP Residual norm 1.815174387380e-03 901 KSP Residual norm 1.690320893601e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999998115411e-01 1 KSP Residual norm 3.269248862736e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.138700673278e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 3.758899308390e-01 1 KSP Residual norm 7.951667253883e-03 1 KSP Residual norm 6.108132284271e-04 902 KSP Residual norm 1.574339227111e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999997338107e-01 1 KSP Residual norm 2.708769142179e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.288071587055e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.135596800446e-01 1 KSP Residual norm 9.135297858300e-03 1 KSP Residual norm 7.256674055521e-04 903 KSP Residual norm 1.430140155907e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999995817412e-01 1 KSP Residual norm 2.780472261188e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 9.143042178830e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.763929125962e-01 1 KSP Residual norm 1.002153942926e-02 1 KSP Residual norm 9.114575342396e-04 904 KSP Residual norm 1.300000530638e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999995028410e-01 1 KSP Residual norm 2.785877931845e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 9.968269364968e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.811489563167e-01 1 KSP Residual norm 1.062384504647e-02 1 KSP Residual norm 9.942193439674e-04 905 KSP Residual norm 1.211080970732e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.999995693878e-01 1 KSP Residual norm 2.983280892357e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 9.275726050786e-04 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.275115786546e-01 1 KSP Residual norm 9.761851016203e-03 1 KSP Residual norm 9.249820914173e-04 906 KSP Residual norm 1.139759024126e-09 %%%% SBAIJ again with -pc_fieldsplit_schur_fact_type FULL. This helps quite a bit 503 KSP Residual norm 1.335198148782e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.972328162111e-01 1 KSP Residual norm 4.518715383704e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 7.434142477591e-02 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.659720275605e+01 1 KSP Residual norm 6.189926845964e-01 1 KSP Residual norm 7.403062361616e-02 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.673081251569e+01 1 KSP Residual norm 6.239752505178e-01 504 KSP Residual norm 1.279949951034e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.976716150443e-01 1 KSP Residual norm 4.866857915634e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 6.820038403874e-02 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.135988214250e+01 1 KSP Residual norm 5.144348811046e-01 1 KSP Residual norm 6.781410979594e-02 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 5.144970605895e+01 1 KSP Residual norm 5.148763638488e-01 505 KSP Residual norm 1.186275242447e-09 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 9.953591307188e-01 1 KSP Residual norm 4.518765750227e-02 Residual norms for fieldsplit_1_ solve. 0 KSP Residual norm 9.622980462164e-02 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 6.474321429841e+01 1 KSP Residual norm 6.421404156501e-01 1 KSP Residual norm 9.592264156459e-02 Residual norms for fieldsplit_0_ solve. 0 KSP Residual norm 6.482110598687e+01 1 KSP Residual norm 6.359439449320e-01 506 KSP Residual norm 1.128137176971e-09 Linear solve converged due to CONVERGED_RTOL iterations 506 KSP Object: 4 MPI processes type: fgmres restart=30, using Classical (unmodified) Gram-Schmidt Orthogonalization with no iterative refinement happy breakdown tolerance 1e-30 maximum iterations=1000, nonzero initial guess minimum iterations=3 tolerances: relative=1e-10, absolute=1e-50, divergence=1e+09 right preconditioning using UNPRECONDITIONED norm type for convergence test PC Object: 4 MPI processes type: fieldsplit FieldSplit with Schur preconditioner, factorization FULL Preconditioner for the Schur complement formed from Sp, an assembled approximation to S, which uses A00's diagonal's inverse Split info: Split number 0 Defined by IS Split number 1 Defined by IS KSP solver for A00 block KSP Object: (fieldsplit_0_) 4 MPI processes type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_0_) 4 MPI processes type: asm total subdomain blocks = 4, amount of overlap = 1 restriction/interpolation type - RESTRICT Local solver information for first block is in the following KSP and PC objects on rank 0: Use -fieldsplit_0_ksp_view ::ascii_info_detail to display information for all blocks KSP Object: (fieldsplit_0_sub_) 1 MPI process type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_0_sub_) 1 MPI process type: icc out-of-place factorization 0 levels of fill tolerance for zero pivot 2.22045e-14 using Manteuffel shift [POSITIVE_DEFINITE] matrix ordering: natural factor fill ratio given 1., needed 1. Factored matrix follows: Mat Object: (fieldsplit_0_sub_) 1 MPI process type: seqsbaij rows=97788, cols=97788 package used to perform factorization: petsc total: nonzeros=1153455, allocated nonzeros=1153455 block size is 1 linear system matrix = precond matrix: Mat Object: (fieldsplit_0_sub_) 1 MPI process type: seqsbaij rows=97788, cols=97788 total: nonzeros=1153455, allocated nonzeros=1153455 total number of mallocs used during MatSetValues calls=0 block size is 1 linear system matrix = precond matrix: Mat Object: (fieldsplit_0_) 4 MPI processes type: mpisbaij rows=392931, cols=392931 total: nonzeros=5739651, allocated nonzeros=5739651 total number of mallocs used during MatSetValues calls=0 block size is 1 KSP solver for S = A11 - A10 inv(A00) A01 KSP Object: (fieldsplit_1_) 4 MPI processes type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_1_) 4 MPI processes type: asm total subdomain blocks = 4, amount of overlap = 1 restriction/interpolation type - RESTRICT Local solver information for first block is in the following KSP and PC objects on rank 0: Use -fieldsplit_1_ksp_view ::ascii_info_detail to display information for all blocks KSP Object: (fieldsplit_1_sub_) 1 MPI process type: preonly maximum iterations=10000, initial guess is zero tolerances: relative=1e-05, absolute=1e-50, divergence=10000. left preconditioning using NONE norm type for convergence test PC Object: (fieldsplit_1_sub_) 1 MPI process type: ilu out-of-place factorization 0 levels of fill tolerance for zero pivot 2.22045e-14 matrix ordering: natural factor fill ratio given 1., needed 1. Factored matrix follows: Mat Object: (fieldsplit_1_sub_) 1 MPI process type: seqaij rows=31038, cols=31038 package used to perform factorization: petsc total: nonzeros=223972, allocated nonzeros=223972 not using I-node routines linear system matrix = precond matrix: Mat Object: (fieldsplit_1_sub_) 1 MPI process type: seqaij rows=31038, cols=31038 total: nonzeros=223972, allocated nonzeros=223972 total number of mallocs used during MatSetValues calls=0 not using I-node routines linear system matrix followed by preconditioner matrix: Mat Object: (fieldsplit_1_) 4 MPI processes type: schurcomplement rows=121600, cols=121600 Schur complement A11 - A10 inv(A00) A01 A11 Mat Object: (fieldsplit_1_) 4 MPI processes type: mpisbaij rows=121600, cols=121600 total: nonzeros=242540, allocated nonzeros=242540 total number of mallocs used during MatSetValues calls=0 block size is 1 A10 Mat Object: 4 MPI processes type: hermitiantranspose rows=121600, cols=392931 KSP solver for A00 block viewable with the additional option -fieldsplit_0_ksp_view A01 Mat Object: 4 MPI processes type: mpiaij rows=392931, cols=121600 total: nonzeros=1018872, allocated nonzeros=1018872 total number of mallocs used during MatSetValues calls=0 using I-node (on process 0) routines: found 23081 nodes, limit used is 5 Mat Object: 4 MPI processes type: mpiaij rows=121600, cols=121600 total: nonzeros=1120336, allocated nonzeros=1120336 total number of mallocs used during MatSetValues calls=0 not using I-node (on process 0) routines linear system matrix = precond matrix: Mat Object: 4 MPI processes type: mpisbaij rows=514531, cols=514531 total: nonzeros=7001063, allocated nonzeros=26569279 total number of mallocs used during MatSetValues calls=0 block size is 1 From pierre.jolivet at lip6.fr Wed Sep 6 01:21:34 2023 From: pierre.jolivet at lip6.fr (Pierre Jolivet) Date: Wed, 6 Sep 2023 08:21:34 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: References: Message-ID: <8B433012-D804-4865-9C77-C074BEB68DE9@lip6.fr> Na?ve question, but is your problem really symmetric? For example, if you do FEM, how do you impose Dirichlet boundary conditions? If you can reproduce this on a smaller example and are at liberty to share the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov, I can have a look. Thanks, Pierre > On 6 Sep 2023, at 8:14 AM, Carl-Johan Thore wrote: > > ? > Thanks for this! > I now get convergence with sbaij and fieldsplit. However, as can be seen in the attached file, it requires around three times as many outer iterations as with aij to reach the same point (to within rtol). Switching from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct" choice?) helps quite a bit, but still sbaij takes many more iterations. So it seems that your sbaij-implementation works but that I'm doing something wrong when setting up the fieldsplit pc, or that some of the subsolvers doesn't work properly with sbaij. I've tried bjacobi as you had in your logs, but not hypre yet. But anyway, one doesn't expect the matrix format to have this much impact on convergence? Any other suggestions? > /Carl-Johan > >> On Mon, Sep 4, 2023 at 9:31?PM Pierre Jolivet wrote: >> The branch should now be good to go (https://gitlab.com/petsc/petsc/-/merge_requests/6841). >> Sorry, I made a mistake before, hence the error on PetscObjectQuery(). >> I?m not sure the code will be covered by the pipeline, but I have tested this on a Raviart?Thomas discretization with PCFIELDSPLIT. >> You?ll see in the attached logs that: >> 1) the numerics match >> 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} block from the global (symmetric) A and we get the A_{10} block cheaply by just using MatCreateHermitianTranspose(), instead of calling another time MatCreateSubMatrix() >> Please let me know if you have some time to test the branch and whether it fails or succeeds on your test cases. >> >> Also, I do not agree with what Hong said. >> Sometimes, the assembly of a coefficient can be more expensive than the communication of the said coefficient. >> So they are instances where SBAIJ would be more efficient than AIJ even if it would require more communication, it is not a black and white picture. >> >> Thanks, >> Pierre >> >> >>>> On 28 Aug 2023, at 12:12 PM, Pierre Jolivet wrote: >>>> >>>> >>>> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore wrote: >>>> >>>> I've tried the new files, and with them, PCFIELDSPLIT now gets set up without crashes (but the setup is significantly slower than for MATAIJ) >>> >>> I?ll be back from Japan at the end of this week, my schedule is too packed to get anything done in the meantime. >>> But I?ll let you know when things are working properly (last I checked, I think it was working, but I may have forgotten about a corner case or two). >>> But yes, though one would except things to be faster and less memory intensive with SBAIJ, it?s unfortunately not always the case. >>> >>> Thanks, >>> Pierre >>> >>>> Unfortunately I still get errors later in the process: >>>> >>>> [0]PETSC ERROR: Null argument, when expecting valid pointer >>>> [0]PETSC ERROR: Null Pointer: Parameter # 1 >>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d GIT Date: 2023-08-22 20:32:33 -0400 >>>> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 --with-cuda --with-cusp --download-scalapack --download-hdf5 --download-zlib --download-mumps --download-parmetis --download-metis --download-ptscotch --download-hypre --download-spai >>>> [0]PETSC ERROR: #1 PetscObjectQuery() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 >>>> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 >>>> [0]PETSC ERROR: #3 MatCreateSubMatrix() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 >>>> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 >>>> [0]PETSC ERROR: #5 PCSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 >>>> [0]PETSC ERROR: #6 KSPSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 >>>> >>>> The code I'm running here works without any problems for MATAIJ. To run it with MATSBAIJ I've simply used the command-line option >>>> -dm_mat_type sbaij >>>> >>>> >>>> Kind regards, >>>> Carl-Johan >>>> >>>> >>>>> On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users wrote: >>>>> >>>>> >>>>>>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore wrote: >>>>>>> >>>>>>> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue.? >>>>>>> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices from these blocks, or is there >>>>>>> somewhere else in the code that things will go wrong? >>>>>> >>>>>> Ah, no, you are right, in that case it should work. >>>>>> >>>>>> For the MATNEST I was thinking to get some savings from the block-symmetry at least >>>>>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for them would just be a >>>>>> (pretty big) bonus. >>>>>> >>>>>> ?I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling >>>>>> right now so everything gets done more slowly, sorry).? >>>>>> Sound great, Thanks again! >>>>> >>>>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >>>>> I need to add a new code path in MatCreateRedundantMatrix() to make sure the resulting Mat is indeed SBAIJ, but that is orthogonal to the PCFIELDSPLIT issue. >>>>> The branch should be usable in its current state. >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>>> >>>>>> From: Pierre Jolivet >>>>>> Sent: Saturday, August 26, 2023 4:36 PM >>>>>> To: Carl-Johan Thore >>>>>> Cc: Carl-Johan Thore ; petsc-users at mcs.anl.gov >>>>>> Subject: Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore wrote: >>>>>> >>>>>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get the A01 and A10 blocks in PCFIELDSPLIT. >>>>>> I have a branch that fixes this, but I haven?t rebased in a while (and I?m AFK right now), would you want me to rebase and give it a go, or must you stick to a release tarball?" >>>>>> >>>>>> Ok, would be great if you could look at this! I don't need to stick to any particular branch. >>>>>> >>>>>> Do you think MATNEST could be an alternative here? >>>>>> >>>>>> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue. >>>>>> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was crashing but I think it was thoroughly fixed in https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >>>>>> It is ugly code on top of ugly code, so I didn?t try to get it integrated and just used the branch locally, and then moved to some other stuff. >>>>>> I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling right now so everything gets done more slowly, sorry). >>>>>> >>>>>> Thanks, >>>>>> Pierre >>>>>> >>>>>> >>>>>> My matrix is >>>>>> [A00 A01; >>>>>> A01^t A11] >>>>>> so perhaps with MATNEST I can make use of the block-symmetry at least, and then use MATSBAIJ for >>>>>> A00 and A11 if it's possible to combine matrix types which the manual seems to imply. >>>>>> >>>>>> Kind regards >>>>>> Carl-Johan >>>>>> >>>>>> >>>>>> >>>>>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore wrote: >>>>>> ? >>>>>> Hi, >>>>>> >>>>>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >>>>>> According to the manual "[t]he fieldsplit preconditioner cannot >>>>>> currently be used with the MATBAIJ or MATSBAIJ data formats if the >>>>>> blocksize is larger than 1". Since my blocksize is exactly 1 it would seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For symmetric format, iscol must equal isrow" >>>>>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >>>>>> fieldsplit.c at >>>>>> >>>>>> /* extract the A01 and A10 matrices */ ilink = jac->head; >>>>>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >>>>>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >>>>>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >>>>>> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >>>>>> MAT_INITIAL_MATRIX, &jac->B)); } >>>>>> >>>>>> This, since my A01 and A10 are not square, seems to explain why iscol is not equal to isrow. >>>>>> From this I gather that it is in general NOT possible to use >>>>>> PCFIELDSPLIT with MATSBAIJ even with block size 1? >>>>>> >>>>>> Kind regards, >>>>>> Carl-Johan >>>>> >>> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Wed Sep 6 01:47:29 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Wed, 6 Sep 2023 12:17:29 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: Hi Amneet, I tried the following example to run a matlab engine. #include "MatlabDataArray.hpp" #include "MatlabEngine.hpp" #include void callSQRT() { using namespace matlab::engine; // Start MATLAB engine synchronously std::unique_ptr matlabPtr = startMATLAB(); //Create MATLAB data array factory matlab::data::ArrayFactory factory; // Define a four-element typed array matlab::data::TypedArray const argArray = factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); // Call MATLAB sqrt function on the data array matlab::data::Array const results = matlabPtr->feval(u"sqrt", argArray); // Display results for (int i = 0; i < results.getNumberOfElements(); i++) { double a = argArray[i]; std::complex v = results[i]; double realPart = v.real(); double imgPart = v.imag(); std::cout << "Square root of " << a << " is " << realPart << " + " << imgPart << "i" << std::endl; } } int main() { callSQRT(); return 0; } *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine* *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* *$export LD_LIBRARY_PATH* *$./a.out* Starting Error: The import statement 'import matlab.internal.engine.input' cannot be found or cannot be imported. Imported names must end with '.*' or be fully qualified. terminate called after throwing an instance of 'matlab::engine::EngineException' what(): MATLAB process cannot be created. Aborted (core dumped) I got the above error for Matlab R2020b. Please help me to sort out this. Thanks and regards Srinivas On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla wrote: > BTW, what Barry is suggesting is the following: > > Compile a sample code with a command line this: > > > g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ > -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine > > > This command is provided here: > > https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html > > > A sample MATLAB code is here: > > https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html > > > (You can just pick a few lines of code from here to create a barebone example) > > > On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: > >> Srinivas --- Do you have a different version of MATLAB that you can >> install? If your organization has a MATLAB license, you can install recent >> versions of MATLAB from mathworks.com >> >> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >> >>> >>> Ok, I have no suggestions. It seems to be more an issue with the >>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>> (in the Matlab documentation) and try it to see if it works. >>> >>> Barry >>> >>> >>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> >>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>> I got the same errors for petsc 3.17.5 >>> >>> >>> *make all* >>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>> BEGINNING TO COMPILE MATLAB INTERFACE >>> Building with 'gcc'. >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> MEX completed successfully. >>> Building with 'gcc'. >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>> In function ?PetscBinaryWrite?: >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>> warning: ?err? may be used uninitialized in this function >>> [-Wmaybe-uninitialized] >>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>> | ^ >>> >>> MEX completed successfully. >>> ========================================= >>> ========================================= >>> Now to check if the libraries are working do: >>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>> >>> *make test query=requires queryval=matlab >>> DATAFILESPATH=/home/vit/datafiles/* >>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>> query=requires >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>> # [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> # [0]PETSC ERROR: Error in external library >>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>> shooting. >>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>> Sep 5 21:39:22 2023 >>> # [0]PETSC ERROR: Configure options >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>> --known-64-bit-blas-indices=1 >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>> # [0]PETSC ERROR: #7 PCSetUp() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>> # [0]PETSC ERROR: #8 KSPSetUp() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>> # [0]PETSC ERROR: #9 main() at >>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>> # [0]PETSC ERROR: PETSc Option Table entries: >>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>> # [0]PETSC ERROR: -error_output_stdout >>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>> # [0]PETSC ERROR: -malloc_dump >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>> # [0]PETSC ERROR: -pc_type lu >>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>> entire error message to petsc-maint at mcs.anl.gov---------- >>> # >>> -------------------------------------------------------------------------- >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> # with errorcode 85. >>> # >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> # You may or may not see output from other processes, depending on >>> # exactly when Open MPI kills them. >>> # >>> -------------------------------------------------------------------------- >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>> >>> >>> # FAILED ksp_ksp_tutorials-ex72_12 >>> # >>> # To rerun failed tests: >>> # /usr/bin/make -f gmakefile test test-fail=1 >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>> >>>> >>>> The error is occuring during >>>> >>>> e->ep = engOpen(buffer); >>>> >>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 >>>> -nodisplay -nosplash from your terminal shell worked we have to assume the >>>> problem is occuring when engOpen() is attempting to connect the stdout and >>>> stdin from the Matlab session that is launched to the executable. >>>> >>>> You can try the following. In 3.17.5 edit the >>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>> >>>> e->ep = engOpen(buffer); >>>> >>>> replace it with >>>> >>>> e->ep = engOpen(""); >>>> >>>> Now in the PETSc directory do make all (it should recompile one file) >>>> and then run the >>>> >>>> make test query=requires queryval=matlab >>>> DATAFILESPATH=/home/vit/datafiles/ >>>> >>>> again >>>> >>>> >>>> >>>> >>>> >>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < >>>> petsc-users at mcs.anl.gov> wrote: >>>> >>>> Hi Amneeth, >>>> >>>> I think the errors are different with petsc 3.17.5 >>>> >>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>> >>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> The version of PETSc you are using is out-of-date, we recommend >>>> updating to the new release >>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>> https://petsc.org/release/download/ >>>> >>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> ============================================================================================= >>>> Configuring PETSc to compile on your system >>>> >>>> >>>> ============================================================================================= >>>> Compilers: >>>> >>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>> -fvisibility=hidden -O3 >>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>> Linkers: >>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings >>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>> -fvisibility=hidden -O3 >>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>> -fstack-protector -fvisibility=hidden -O3 >>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>> BlasLapack: >>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>>> to control the number of threads >>>> uses 8 byte integers >>>> MPI: >>>> Version: 3 >>>> mpiexec: /usr/bin/mpiexec >>>> Implementation: openmpi >>>> OMPI_VERSION: 4.0.3 >>>> pthread: >>>> cmake: >>>> Version: 3.16.3 >>>> /usr/bin/cmake >>>> regex: >>>> Matlab: >>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>> /usr/local/MATLAB/R2020b >>>> MatlabEngine: >>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>> Language used to compile PETSc: C >>>> PETSc: >>>> PETSC_ARCH: linux-opt >>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>> Prefix: >>>> Scalar type: real >>>> Precision: double >>>> Support for __float128 >>>> Integer size: 4 bytes >>>> Single library: yes >>>> Shared libraries: yes >>>> Memory alignment from malloc(): 16 bytes >>>> Using GNU make: /usr/bin/make >>>> >>>> xxx=========================================================================xxx >>>> Configure stage complete. Now build PETSc libraries with: >>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>> all >>>> >>>> xxx=========================================================================xxx >>>> >>>> *$make* >>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>> Building with 'gcc'. >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> In function ?PetscBinaryWrite?: >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> | ^ >>>> >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> In function ?PetscBinaryWrite?: >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> | ^ >>>> >>>> MEX completed successfully. >>>> ========================================= >>>> ========================================= >>>> Now to check if the libraries are working do: >>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>> check >>>> >>>> *$make test query=requires queryval=matlab >>>> DATAFILESPATH=/home/vit/datafiles/* >>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>> --testdir=./linux-opt/tests >>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>> query=requires >>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>> # [0]PETSC ERROR: --------------------- Error Message >>>> -------------------------------------------------------------- >>>> # [0]PETSC ERROR: Error in external library >>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>> shooting. >>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>>> Sep 5 10:15:57 2023 >>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>> # [0]PETSC ERROR: #9 main() at >>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>> # [0]PETSC ERROR: -error_output_stdout >>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>> # [0]PETSC ERROR: -malloc_dump >>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>> # [0]PETSC ERROR: -pc_type lu >>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> # >>>> -------------------------------------------------------------------------- >>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>> # with errorcode 85. >>>> # >>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> # You may or may not see output from other processes, depending on >>>> # exactly when Open MPI kills them. >>>> # >>>> -------------------------------------------------------------------------- >>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> >>>> >>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>> # >>>> # To rerun failed tests: >>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>> >>>> To get the info of the error there is no specific probe id reported. >>>> >>>> How to check error info and proceed further? >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>> wrote: >>>> >>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>> options that Satish mentioned? >>>>> >>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>> petsc-users wrote: >>>>> >>>>>> Sorry for missing that. >>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>>> >>>>>> < M A T L A B (R) > >>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>> November 23, 2020 >>>>>> >>>>>> >>>>>> To get started, type doc. >>>>>> For product information, visit www.mathworks.com. >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>> wrote: >>>>>> >>>>>>> You are missing one more step: >>>>>>> >>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> >>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>> >>>>>>> Does this work for you? As the message indicates this command is >>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>> >>>>>>> Satish >>>>>>> >>>>>>> >>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>> >>>>>>> > Hi Sathish, >>>>>>> > >>>>>>> > I tried the following procedure >>>>>>> > >>>>>>> > *$make * >>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> > Building with 'gcc'. >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > In function ?PetscBinaryWrite?: >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>> > [-Wmaybe-uninitialized] >>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > | ^ >>>>>>> > >>>>>>> > MEX completed successfully. >>>>>>> > Building with 'gcc'. >>>>>>> > MEX completed successfully. >>>>>>> > Building with 'gcc'. >>>>>>> > MEX completed successfully. >>>>>>> > Building with 'gcc'. >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > In function ?PetscBinaryWrite?: >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>> > [-Wmaybe-uninitialized] >>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > | ^ >>>>>>> > >>>>>>> > MEX completed successfully. >>>>>>> > ========================================= >>>>>>> > Now to check if the libraries are working do: >>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>> check >>>>>>> > >>>>>>> > *$make test query=requires queryval=matlab >>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>> queryval=matlab >>>>>>> > query=requires >>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> > TEST >>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Mon Sep >>>>>>> > 4 10:02:32 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>> > # [0]PETSC ERROR: >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Mon Sep >>>>>>> > 4 10:02:32 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > # [0]PETSC ERROR: >>>>>>> > >>>>>>> ------------------------------------------------------------------------ >>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>> Violation, >>>>>>> > probably memory access out of range >>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>> -on_error_attach_debugger >>>>>>> > # [0]PETSC ERROR: or see >>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>> Apple Mac OS >>>>>>> > X to find memory corruption errors >>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, >>>>>>> link, >>>>>>> > and run >>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Mon Sep >>>>>>> > 4 10:02:32 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>>> file >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>> > # with errorcode 50162059. >>>>>>> > # >>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > # You may or may not see output from other processes, depending on >>>>>>> > # exactly when Open MPI kills them. >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>> > CC >>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>> > CLINKER >>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > TEST >>>>>>> > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>> code: 124 >>>>>>> > # Running problem 5 >>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > # [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>> MB108SMEC028 by >>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire >>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>> > # with errorcode 126076. >>>>>>> > # >>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > # You may or may not see output from other processes, depending on >>>>>>> > # exactly when Open MPI kills them. >>>>>>> > # >>>>>>> -------------------------------------------------------------------------- >>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>> Command failed >>>>>>> > so no diff >>>>>>> > >>>>>>> > # ------------- >>>>>>> > # Summary >>>>>>> > # ------------- >>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > # success 0/2 tests (0.0%) >>>>>>> > # failed 2/2 tests (100.0%) >>>>>>> > # todo 0/2 tests (0.0%) >>>>>>> > # skip 0/2 tests (0.0%) >>>>>>> > # >>>>>>> > # Wall clock time for tests: 4 sec >>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>> > # >>>>>>> > # To rerun failed tests: >>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> > # >>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>>> 0.01 sec >>>>>>> > >>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>> > *$make matlab_ls_test* >>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>> -Wwrite-strings >>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>> -Wno-strict-aliasing >>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>> -lmx >>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>> -lmpi_mpifh >>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>> -lquadmath >>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>> > >>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>> ./matlab_ls_test >>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>> processors = 1 >>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>> > MB108SMEC028.(none) >>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>> > Running problem 5 >>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>> 140155238476992 >>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>> > -------------------------------------------------------------- >>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > [0]PETSC ERROR: See >>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > for trouble shooting. >>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 >>>>>>> by vit >>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>> > [0]PETSC ERROR: Configure options >>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > [0]PETSC ERROR: -info >>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire >>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>> > with errorcode 126076. >>>>>>> > >>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>> > You may or may not see output from other processes, depending on >>>>>>> > exactly when Open MPI kills them. >>>>>>> > >>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>> > >>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>> wrote: >>>>>>> > >>>>>>> > > To use datafiles in the test suite: >>>>>>> > > >>>>>>> > > cd $HOME >>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>> > > >>>>>> DATAFILESPATH - or set >>>>>>> > > manually with make> >>>>>>> > > >>>>>>> > > make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>> > > >>>>>>> > > Satish >>>>>>> > > >>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>> > > >>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>> > > > >>>>>>> > > > > Hi Matthew, >>>>>>> > > > > >>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do >>>>>>> not have >>>>>>> > > any >>>>>>> > > > > separate test files to test PETSc alone. Can you please help >>>>>>> me how to >>>>>>> > > > > define this DATAFILESPATH? >>>>>>> > > > > >>>>>>> > > > >>>>>>> > > > That test you tried uses a certain matrix. On our machine, we >>>>>>> point to >>>>>>> > > this >>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't >>>>>>> have those >>>>>>> > > > matrices, since they are just for testing here. That >>>>>>> > > > is why I suggested just using a different matrix, or running a >>>>>>> problem >>>>>>> > > you >>>>>>> > > > care about in IBAMR. >>>>>>> > > > >>>>>>> > > > Thanks, >>>>>>> > > > >>>>>>> > > > Matt >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > > Thanks and regards >>>>>>> > > > > Srinivas. >>>>>>> > > > > >>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>> knepley at gmail.com> >>>>>>> > > wrote: >>>>>>> > > > > >>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>>> > > petsc-users < >>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>> > > > >> >>>>>>> > > > >>> Hi Sathish, >>>>>>> > > > >>> >>>>>>> > > > >>> Thank you so much for your efforts and the support you are >>>>>>> giving me >>>>>>> > > to >>>>>>> > > > >>> sort this out. >>>>>>> > > > >>> >>>>>>> > > > >>> I tried to follow the same procedure which you followed to >>>>>>> build >>>>>>> > > Petsc >>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>> > > > >>> >>>>>>> > > > >>> *$./configure >>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> PETSC_ARCH=linux-opt >>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>> > > > >>> Using python3 for Python >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> It appears you do >>>>>>> not have >>>>>>> > > valgrind >>>>>>> > > > >>> installed on your system. >>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>>> > > > >>> Or install >>>>>>> > > valgrind-devel or >>>>>>> > > > >>> equivalent using your package manager. >>>>>>> > > > >>> Then rerun ./configure >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> =============================================================================== >>>>>>> > > > >>> Compilers: >>>>>>> > > > >>> >>>>>>> > > > >>> C Compiler: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > -fPIC >>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>> C++ Compiler: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>> > > > >>> Fortran Compiler: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>> 9.4.0 >>>>>>> > > > >>> Linkers: >>>>>>> > > > >>> Shared linker: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > -shared >>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> > > -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>> Dynamic linker: >>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > -shared >>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> > > -Wno-unknown-pragmas >>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>> > > > >>> make: >>>>>>> > > > >>> Version: 4.2 >>>>>>> > > > >>> /usr/bin/make >>>>>>> > > > >>> BlasLapack: >>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>> -omp_num_threads >>>>>>> > >

to >>>>>>> > > > >>> control the number of threads >>>>>>> > > > >>> uses 8 byte integers >>>>>>> > > > >>> MPI: >>>>>>> > > > >>> Version: 3 >>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>> > > --oversubscribe >>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>> > > > >>> pthread: >>>>>>> > > > >>> cmake: >>>>>>> > > > >>> Version: 3.16.3 >>>>>>> > > > >>> /usr/bin/cmake >>>>>>> > > > >>> regex: >>>>>>> > > > >>> Matlab: >>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>> > > > >>> MatlabEngine: >>>>>>> > > > >>> Library: >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>>>>> -lmx -lmat >>>>>>> > > -lut >>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>> > > > >>> PETSc: >>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>> > > > >>> Scalar type: real >>>>>>> > > > >>> Precision: double >>>>>>> > > > >>> Support for __float128 >>>>>>> > > > >>> Integer size: 4 bytes >>>>>>> > > > >>> shared libraries: enabled >>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>> PETSC_ARCH=linux-opt all >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>> >>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n >>>>>>> -licuuc as >>>>>>> > > > >>> you suggested earlier. >>>>>>> > > > >>> >>>>>>> > > > >>> *$make* >>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > > > >>> | ^ >>>>>>> > > > >>> >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> Building with 'gcc'. >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> socket\n"); >>>>>>> > > > >>> | ^ >>>>>>> > > > >>> >>>>>>> > > > >>> MEX completed successfully. >>>>>>> > > > >>> ========================================= >>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>> PETSC_ARCH=linux-opt check >>>>>>> > > > >>> =============================================== >>>>>>> > > > >>> >>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> > > > >>> TEST >>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > > > >>> >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>> > > > >>> >>>>>>> > > > >> >>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>> defined, so it >>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>> yours. >>>>>>> > > > >> >>>>>>> > > > >> Thanks, >>>>>>> > > > >> >>>>>>> > > > >> Matt >>>>>>> > > > >> >>>>>>> > > > >> >>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>>> trouble >>>>>>> > > > >>> shooting. >>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>> 2020 >>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>> MB108SMEC028 by vit >>>>>>> > > Sun >>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> COPTFLAGS=-O3 >>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>> line 1444 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>> -------send >>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>> MPI_COMM_SELF >>>>>>> > > > >>> # with errorcode 113065. >>>>>>> > > > >>> # >>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>> depending on >>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>>>> diff >>>>>>> > > > >>> CC >>>>>>> > > > >>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>> > > > >>> CLINKER >>>>>>> > > > >>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > > > >>> TEST >>>>>>> > > > >>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> Error >>>>>>> > > code: 124 >>>>>>> > > > >>> # Running problem 5 >>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > > > >>> >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>>> trouble >>>>>>> > > > >>> shooting. >>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>> 2020 >>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>> > > MB108SMEC028 by >>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> COPTFLAGS=-O3 >>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> --with-debugging=0 >>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>> > > > >>> >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > > > >>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>> -------send >>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>> MPI_COMM_SELF >>>>>>> > > > >>> # with errorcode 126076. >>>>>>> > > > >>> # >>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>> processes. >>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>> depending on >>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>> > > > >>> # >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> SKIP Command >>>>>>> > > > >>> failed so no diff >>>>>>> > > > >>> >>>>>>> > > > >>> # ------------- >>>>>>> > > > >>> # Summary >>>>>>> > > > >>> # ------------- >>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>> > > > >>> # >>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>> > > > >>> # >>>>>>> > > > >>> # To rerun failed tests: >>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> > > > >>> # >>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 >>>>>>> sec / >>>>>>> > > 0.02 sec >>>>>>> > > > >>> >>>>>>> > > > >>> *How to sort out this error?* >>>>>>> > > > >>> >>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>> > > -Wwrite-strings >>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>> > > -Wno-strict-aliasing >>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden >>>>>>> -O3 >>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>> matlab_ls_test.c >>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> > > > >>> >>>>>>> > > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>> -leng -lmex >>>>>>> > > -lmx >>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>> > > -lmpi_mpifh >>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>> -lpthread >>>>>>> > > -lquadmath >>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>> > > > >>> >>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>>>>> find the >>>>>>> > > > >>> attachment and do the needful. >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> Thanks and regards >>>>>>> > > > >>> Srinivas >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>> balay at mcs.anl.gov> >>>>>>> > > wrote: >>>>>>> > > > >>> >>>>>>> > > > >>>> Perhaps you can try the following to get additional info >>>>>>> - and debug >>>>>>> > > > >>>> >>>>>>> > > > >>>> Satish >>>>>>> > > > >>>> ---------- >>>>>>> > > > >>>> >>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>> > > > >>>> balay at compute-386-07 >>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>> > > > >>>> make matlab_ls_test >>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>> -fPIC >>>>>>> > > -Wall >>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> > > -fstack-protector >>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>> > > -Wno-strict-aliasing >>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>> -fvisibility=hidden -O3 >>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>> > > > >>>> matlab_ls_test.c >>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> >>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread >>>>>>> -lm -leng >>>>>>> > > -lmex >>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl >>>>>>> -lmpifort >>>>>>> > > -lmpi >>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ >>>>>>> -ldl -o >>>>>>> > > > >>>> matlab_ls_test >>>>>>> > > > >>>> balay at compute-386-07 >>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>> ./matlab_ls_test >>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number >>>>>>> of >>>>>>> > > processors >>>>>>> > > > >>>> = 1 >>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is >>>>>>> NIS >>>>>>> > > > >>>> compute-386-07.(none) >>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>> > > > >>>> Running problem 5 >>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>> 1140850689 >>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>> with command >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>>> > > > >>>> TestingInitialize >>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>>> string: >>>>>>> > > > >>>> TestingInitialize >>>>>>> > > > >>>> 5 >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>> works for you >>>>>>> > > - on >>>>>>> > > > >>>> this machine..>>>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> balay at compute-386-07 >>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>> > > > >>>> >>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>> MathWorks, Inc. >>>>>>> > > > >>>> >>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>>> (glnxa64) >>>>>>> > > > >>>> >>>>>>> > > > >>>> February 17, 2021 >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> To get started, type doc. >>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>> > > > >>>> >>>>>>> > > > >>>> >> >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>> > > > >>>> >>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>> [reverting >>>>>>> > > thread >>>>>>> > > > >>>> to petsc-users only] >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>> > > corresponding >>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>> Ubuntu-20.04, >>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>> > > > >>>> > main >>>>>>> > > > >>>> > release >>>>>>> > > > >>>> > * release-3.13 >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>> > > matlab/R2021a >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>> > > > >>>> >>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> PETSC_ARCH=linux-opt >>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > Compilers: >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> > C Compiler: >>>>>>> > > > >>>> >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>> > > -Wall >>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> > > -fstack-protector >>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>>> > C++ Compiler: >>>>>>> > > > >>>> >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>> > > -fstack-protector >>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>>> > Fortran Compiler: >>>>>>> > > > >>>> >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>> > > -Wall >>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> > > > >>>> > Linkers: >>>>>>> > > > >>>> > Shared linker: >>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>> > > -shared -fPIC >>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>>> > Dynamic linker: >>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>> > > -shared -fPIC >>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>> -Wno-unknown-pragmas >>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>> > > > >>>> > make: >>>>>>> > > > >>>> > Version: 4.2 >>>>>>> > > > >>>> > /usr/bin/make >>>>>>> > > > >>>> > BlasLapack: >>>>>>> > > > >>>> > Library: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>> -omp_num_threads >>>>>>> > >

>>>>>>> > > > >>>> to control the number of threads >>>>>>> > > > >>>> > uses 8 byte integers >>>>>>> > > > >>>> > MPI: >>>>>>> > > > >>>> > Version: 4 >>>>>>> > > > >>>> > Includes: >>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>> > > > >>>> > Mpiexec: >>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>> > > > >>>> > pthread: >>>>>>> > > > >>>> > Library: -lpthread >>>>>>> > > > >>>> > cmake: >>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>> > > > >>>> > regex: >>>>>>> > > > >>>> > Matlab: >>>>>>> > > > >>>> > Includes: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>> > > > >>>> > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>> > > > >>>> > MatlabEngine: >>>>>>> > > > >>>> > Library: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>> > > > >>>> > sowing: >>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>> > > > >>>> > valgrind: >>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>> > > > >>>> > PETSc: >>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>> > > > >>>> > Scalar type: real >>>>>>> > > > >>>> > Precision: double >>>>>>> > > > >>>> > Support for __float128 >>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>> > > > >>>> > shared libraries: enabled >>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>> with: >>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>> PETSC_ARCH=linux-opt all >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> xxx=========================================================================xxx >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> > > socket\n"); >>>>>>> > > > >>>> > | ^ >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>> > > socket\n"); >>>>>>> > > > >>>> > | ^ >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > MEX completed successfully. >>>>>>> > > > >>>> > ========================================= >>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>> PETSC_ARCH=linux-opt check >>>>>>> > > > >>>> > ========================================= >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>> > > query=requires >>>>>>> > > > >>>> queryval=matlab >>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> > > > >>>> > TEST >>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>> > > > >>>> > # ../ex72: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>> no diff >>>>>>> > > > >>>> > CC >>>>>>> > > > >>>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>> > > > >>>> > CLINKER >>>>>>> > > > >>>> >>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > > > >>>> > TEST >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> # Error >>>>>>> > > code: >>>>>>> > > > >>>> 1 >>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> SKIP >>>>>>> > > Command >>>>>>> > > > >>>> failed so no diff >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>> test >>>>>>> > > query=requires >>>>>>> > > > >>>> queryval=matlab >>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>> > > > >>>> > TEST >>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>> > > > >>>> > TEST >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>>> > ok >>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > # ------------- >>>>>>> > > > >>>> > # Summary >>>>>>> > > > >>>> > # ------------- >>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>> > > > >>>> > # >>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>> 15.190000000000001 >>>>>>> > > sec >>>>>>> > > > >>>> > # >>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>> 6.47 sec / >>>>>>> > > 7.54 >>>>>>> > > > >>>> sec >>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>> > > > >>>> > >>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>> tried to >>>>>>> > > > >>>> configure petsc >>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>> successful. After >>>>>>> > > > >>>> running make >>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>> message. >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > not ok >>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>> > > > >>>> code: 124 >>>>>>> > > > >>>> > > # Running problem 5 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>> > > > >>>> > > >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > > > >>>> > > for trouble shooting. >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>> 01, 2020 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>> named >>>>>>> > > > >>>> MB108SMEC028 by >>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> COPTFLAGS=-O3 >>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>> > > > >>>> --with-debugging=0 >>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>>>>> 67 in >>>>>>> > > > >>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>> > > -------send >>>>>>> > > > >>>> entire >>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>>> > > # >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>> MPI_COMM_SELF >>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>> > > > >>>> > > # >>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>>>>> all MPI >>>>>>> > > > >>>> processes. >>>>>>> > > > >>>> > > # You may or may not see output from other processes, >>>>>>> depending >>>>>>> > > on >>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>> > > > >>>> > > # >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > Thanks >>>>>>> > > > >>>> > > Srinivas >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > i.e.: >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>>> 20PHD0548 via >>>>>>> > > > >>>> petsc-users < >>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>>> balay at mcs.anl.gov> >>>>>>> > > > >>>> wrote: >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>>>>> will work >>>>>>> > > > >>>> here]. >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> i.e: >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> ./configure >>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> > > PETSC_ARCH=linux-opt >>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> Satish >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>> > > petsc-users >>>>>>> > > > >>>> wrote: >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>> > > > >>>> > > >>> > >>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>> > > > >>>> > > >>> > >>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>> > > > >>>> > > >>> > >>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>> > > balay at mcs.anl.gov> >>>>>>> > > > >>>> wrote: >>>>>>> > > > >>>> > > >>> > >>>>>>> > > > >>>> > > >>> > > Also: >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in >>>>>>> this mode. >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>>> dependency/conflicts >>>>>>> > > across >>>>>>> > > > >>>> packages] >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > > Satish >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>>> petsc-users wrote: >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > >>>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > >>>>>>> config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] >>>>>>> conflict >>>>>>> > > with >>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>>> blas/lapack with >>>>>>> > > > >>>> matlab - to >>>>>>> > > > >>>> > > >>> have a >>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>>> 20PHD0548 via >>>>>>> > > > >>>> petsc-users >>>>>>> > > > >>>> > > >>> wrote: >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>>> MATLAB is not >>>>>>> > > > >>>> working. It is >>>>>>> > > > >>>> > > >>> > > showing >>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>>> cluster with >>>>>>> > > > >>>> libmesh and >>>>>>> > > > >>>> > > >>> this is >>>>>>> > > > >>>> > > >>> > > for >>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I >>>>>>> tried without >>>>>>> > > > >>>> linking >>>>>>> > > > >>>> > > >>> Matlab >>>>>>> > > > >>>> > > >>> > > with >>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>>>>> configuring >>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>> > > > >>>> > > >>> that >>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required >>>>>>> is >>>>>>> > > specified. >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>>>>> libmesh with >>>>>>> > > > >>>> PETSc and >>>>>>> > > > >>>> > > >>> Matlab >>>>>>> > > > >>>> > > >>> > > is in >>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for >>>>>>> complicated >>>>>>> > > geometries >>>>>>> > > > >>>> it is >>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>>>>> various >>>>>>> > > things >>>>>>> > > > >>>> and ended >>>>>>> > > > >>>> > > >>> up with >>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further >>>>>>> to do my >>>>>>> > > > >>>> research work. >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>>>>>> possible. >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>>> > > > >>>> mail2amneet at gmail.com> >>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>> > > > >>>> > > >>> > > > > > >>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>>>> libMesh for >>>>>>> > > the >>>>>>> > > > >>>> WEC >>>>>>> > > > >>>> > > >>> application. >>>>>>> > > > >>>> > > >>> > > You >>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>>>>> builds with >>>>>>> > > > >>>> Matlab. >>>>>>> > > > >>>> > > >>> > > > > > >>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for >>>>>>> wanting to build >>>>>>> > > > >>>> libMesh? >>>>>>> > > > >>>> > > >>> > > > > > >>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>> > > > >>>> > > >>> > > > > > >>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU >>>>>>> SRINIVAS >>>>>>> > > > >>>> 20PHD0548 via >>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>> > > > >>>> > > >>> > > > > > wrote: >>>>>>> > > > >>>> > > >>> > > > > > >>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>>>>>> removing all >>>>>>> > > > >>>> occurrences >>>>>>> > > > >>>> > > >>> of >>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I >>>>>>> ran "make >>>>>>> > > test" >>>>>>> > > > >>>> got the >>>>>>> > > > >>>> > > >>> > > following >>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> > > > >>>> > > >>> Error >>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>> --------------------- Error >>>>>>> > > Message >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>> library >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>> MATLAB engine >>>>>>> > > on >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > > > >>>> for >>>>>>> > > > >>>> > > >>> trouble >>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>> Version 3.13.4, >>>>>>> > > Aug >>>>>>> > > > >>>> 01, 2020 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on >>>>>>> a >>>>>>> > > linux-debug >>>>>>> > > > >>>> named >>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>>>> --download-fblaslapack=1 >>>>>>> > > > >>>> --with-x=0 >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>> PetscMatlabEngineCreate() >>>>>>> > > line >>>>>>> > > > >>>> 67 in >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> >>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>>> entries: >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End >>>>>>> of Error >>>>>>> > > > >>>> Message >>>>>>> > > > >>>> > > >>> -------send >>>>>>> > > > >>>> > > >>> > > entire >>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>>> communicator >>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>>>>> MPI to >>>>>>> > > kill >>>>>>> > > > >>>> all MPI >>>>>>> > > > >>>> > > >>> > > processes. >>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>>> other >>>>>>> > > processes, >>>>>>> > > > >>>> > > >>> depending on >>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>>> # SKIP >>>>>>> > > > >>>> > > >>> Command >>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>> > > > >>>> > > >>> Error >>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>> --------------------- Error >>>>>>> > > Message >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> >>>>>>> -------------------------------------------------------------- >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>> library >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>> MATLAB engine >>>>>>> > > on >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>> > > > >>>> for >>>>>>> > > > >>>> > > >>> trouble >>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>> Version 3.13.4, >>>>>>> > > Aug >>>>>>> > > > >>>> 01, 2020 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on >>>>>>> a >>>>>>> > > linux-opt >>>>>>> > > > >>>> named >>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>> PetscMatlabEngineCreate() >>>>>>> > > line >>>>>>> > > > >>>> 67 in >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> >>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>>> entries: >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End >>>>>>> of Error >>>>>>> > > > >>>> Message >>>>>>> > > > >>>> > > >>> -------send >>>>>>> > > > >>>> > > >>> > > entire >>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>>> communicator >>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open >>>>>>> MPI to >>>>>>> > > kill >>>>>>> > > > >>>> all MPI >>>>>>> > > > >>>> > > >>> > > processes. >>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>>> other >>>>>>> > > processes, >>>>>>> > > > >>>> > > >>> depending on >>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -------------------------------------------------------------------------- >>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>> > > > >>>> # SKIP >>>>>>> > > > >>>> > > >>> Command >>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc >>>>>>> 3.17.5 >>>>>>> > > version. I >>>>>>> > > > >>>> am >>>>>>> > > > >>>> > > >>> sharing the >>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc >>>>>>> 3.13.4 and >>>>>>> > > > >>>> petsc >>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>> > > > >>>> > > >>> > > Please find >>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM >>>>>>> Satish Balay < >>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>>>>> petsc's >>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>> > > > >>>> > > >>> > > for >>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> > > -leng >>>>>>> > > > >>>> -lmex >>>>>>> > > > >>>> > > >>> -lmx >>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - >>>>>>> we are >>>>>>> > > seeing: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> >>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n >>>>>>> -licuuc" are not >>>>>>> > > > >>>> preset here. >>>>>>> > > > >>>> > > >>> This >>>>>>> > > > >>>> > > >>> > > might >>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>> > > > >>>> > > >>> > > and >>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>>>> -licudata >>>>>>> > > -licui18n >>>>>>> > > > >>>> -licuuc" >>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>>> 20PHD0548 >>>>>>> > > via >>>>>>> > > > >>>> > > >>> petsc-users >>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>>>>> building >>>>>>> > > > >>>> petsc3.13.4 with >>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh >>>>>>> with >>>>>>> > > > >>>> petsc3.17.5 and >>>>>>> > > > >>>> > > >>> matlab. >>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>> > > successfully. >>>>>>> > > > >>>> But >>>>>>> > > > >>>> > > >>> libmesh is >>>>>>> > > > >>>> > > >>> > > not >>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>>>> Satish Balay < >>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from >>>>>>> both >>>>>>> > > > >>>> petsc-3.13 and >>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the >>>>>>> logs >>>>>>> > > friendly to >>>>>>> > > > >>>> mailing >>>>>>> > > > >>>> > > >>> list - >>>>>>> > > > >>>> > > >>> > > or >>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with >>>>>>> 3.17? [or >>>>>>> > > 3.19?] >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU >>>>>>> SRINIVAS >>>>>>> > > 20PHD0548 >>>>>>> > > > >>>> via >>>>>>> > > > >>>> > > >>> petsc-users >>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file >>>>>>> while >>>>>>> > > building >>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>> > > > >>>> > > >>> > > with >>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and >>>>>>> do the >>>>>>> > > needful. >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at >>>>>>> 10:19?AM INTURU >>>>>>> > > > >>>> SRINIVAS >>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>>>> > > wrote: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. >>>>>>> During >>>>>>> > > building >>>>>>> > > > >>>> of >>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>> > > > >>>> > > >>> > > error >>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at >>>>>>> 9:43?PM Satish >>>>>>> > > > >>>> Balay < >>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> https://ibamr.github.io/linux says >>>>>>> > > > >>>> petsc-3.17 >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>>>> petsc-3.17.5? >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU >>>>>>> SRINIVAS >>>>>>> > > > >>>> 20PHD0548 via >>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with >>>>>>> MATLAB for >>>>>>> > > > >>>> working on >>>>>>> > > > >>>> > > >>> the >>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>>>> building the >>>>>>> > > PETSc, >>>>>>> > > > >>>> using the >>>>>>> > > > >>>> > > >>> > > following >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export >>>>>>> PETSC_ARCH=linux-debug >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 >>>>>>> \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>> `EvaluateResidual': >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>> `EvaluateJacobian': >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> > > >>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld >>>>>>> returned 1 exit >>>>>>> > > > >>>> status >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>>>> [gmakefile.test:185: >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> >>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>>>> unfinished >>>>>>> > > jobs.... >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve >>>>>>> this issue >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from >>>>>>> Vellore >>>>>>> > > > >>>> Institute of >>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain >>>>>>> legally >>>>>>> > > > >>>> protected >>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>>>> Institute of >>>>>>> > > > >>>> Technology?. >>>>>>> > > > >>>> > > >>> If >>>>>>> > > > >>>> > > >>> > > you are >>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should >>>>>>> not >>>>>>> > > > >>>> disseminate, >>>>>>> > > > >>>> > > >>> distribute >>>>>>> > > > >>>> > > >>> > > or copy >>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender >>>>>>> immediately >>>>>>> > > > >>>> and destroy >>>>>>> > > > >>>> > > >>> all >>>>>>> > > > >>>> > > >>> > > copies of >>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If >>>>>>> you have >>>>>>> > > > >>>> received this >>>>>>> > > > >>>> > > >>> email >>>>>>> > > > >>>> > > >>> > > in error, >>>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by >>>>>>> reply email >>>>>>> > > and >>>>>>> > > > >>>> delete >>>>>>> > > > >>>> > > >>> the >>>>>>> > > > >>>> > > >>> > > original >>>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without >>>>>>> reading >>>>>>> > > them.* >>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>> > > > >>>> > > >>> > > > > > >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > > >>>>>>> > > > >>>> > > >>> > > > >>>>>>> > > > >>>> > > >>> > > >>>>>>> > > > >>>> > > >>> > >>>>>>> > > > >>>> > > >>> > >>>>>>> > > > >>>> > > >>> >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore >>>>>>> Institute of >>>>>>> > > > >>>> Technology. >>>>>>> > > > >>>> > > >> The contents of this email may contain legally >>>>>>> protected >>>>>>> > > > >>>> confidential or >>>>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>>>> > > Technology?. If >>>>>>> > > > >>>> you are >>>>>>> > > > >>>> > > >> not the intended recipient, you should not >>>>>>> disseminate, >>>>>>> > > > >>>> distribute or copy >>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately >>>>>>> and destroy >>>>>>> > > > >>>> all copies of >>>>>>> > > > >>>> > > >> this message and any attachments. If you have >>>>>>> received this >>>>>>> > > > >>>> email in error, >>>>>>> > > > >>>> > > >> please promptly notify the sender by reply email >>>>>>> and delete >>>>>>> > > the >>>>>>> > > > >>>> original >>>>>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>>>>> > > > >>>> > > >> >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > -- >>>>>>> > > > >>>> > > > --Amneet >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > > >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> > > >>>>>>> > > > >>>> >>>>>>> > > > >>> >>>>>>> > > > >>> >>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>> > > Technology. >>>>>>> > > > >>> The contents of this email may contain legally protected >>>>>>> > > confidential or >>>>>>> > > > >>> privileged information of ?Vellore Institute of >>>>>>> Technology?. If you >>>>>>> > > are >>>>>>> > > > >>> not the intended recipient, you should not disseminate, >>>>>>> distribute >>>>>>> > > or copy >>>>>>> > > > >>> this e-mail. Please notify the sender immediately and >>>>>>> destroy all >>>>>>> > > copies of >>>>>>> > > > >>> this message and any attachments. If you have received >>>>>>> this email in >>>>>>> > > error, >>>>>>> > > > >>> please promptly notify the sender by reply email and >>>>>>> delete the >>>>>>> > > original >>>>>>> > > > >>> email and any backup copies without reading them.* >>>>>>> > > > >>> >>>>>>> > > > >> >>>>>>> > > > >> >>>>>>> > > > >> -- >>>>>>> > > > >> What most experimenters take for granted before they begin >>>>>>> their >>>>>>> > > > >> experiments is infinitely more interesting than any results >>>>>>> to which >>>>>>> > > their >>>>>>> > > > >> experiments lead. >>>>>>> > > > >> -- Norbert Wiener >>>>>>> > > > >> >>>>>>> > > > >> https://www.cse.buffalo.edu/~knepley/ >>>>>>> > > > >> >>>>>>> > > > >> >>>>>>> > > > > >>>>>>> > > > > >>>>>>> > > > > *Disclaimer:This message was sent from Vellore Institute of >>>>>>> Technology. >>>>>>> > > > > The contents of this email may contain legally protected >>>>>>> confidential >>>>>>> > > or >>>>>>> > > > > privileged information of ?Vellore Institute of >>>>>>> Technology?. If you >>>>>>> > > are >>>>>>> > > > > not the intended recipient, you should not disseminate, >>>>>>> distribute or >>>>>>> > > copy >>>>>>> > > > > this e-mail. Please notify the sender immediately and >>>>>>> destroy all >>>>>>> > > copies of >>>>>>> > > > > this message and any attachments. If you have received this >>>>>>> email in >>>>>>> > > error, >>>>>>> > > > > please promptly notify the sender by reply email and delete >>>>>>> the >>>>>>> > > original >>>>>>> > > > > email and any backup copies without reading them.* >>>>>>> > > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> > > >>>>>>> > >>>>>>> > >>>>>> >>>>>> >>>>>> >>>>>> *Disclaimer:This message was sent from Vellore Institute of >>>>>> Technology. The contents of this email may contain legally protected >>>>>> confidential or privileged information of ?Vellore Institute of >>>>>> Technology?. If you are not the intended recipient, you should not >>>>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>>>> immediately and destroy all copies of this message and any attachments. If >>>>>> you have received this email in error, please promptly notify the sender by >>>>>> reply email and delete the original email and any backup copies without >>>>>> reading them.* >>>>>> >>>>> >>>>> >>>>> -- >>>>> --Amneet >>>>> >>>>> >>>>> >>>>> >>>> >>>> *Disclaimer:This message was sent from Vellore Institute of >>>> Technology. The contents of this email may contain legally protected >>>> confidential or privileged information of ?Vellore Institute of >>>> Technology?. If you are not the intended recipient, you should not >>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>> immediately and destroy all copies of this message and any attachments. If >>>> you have received this email in error, please promptly notify the sender by >>>> reply email and delete the original email and any backup copies without >>>> reading them.* >>>> >>>> >>>> >>> >>> *Disclaimer:This message was sent from Vellore Institute of Technology. >>> The contents of this email may contain legally protected confidential or >>> privileged information of ?Vellore Institute of Technology?. If you are >>> not the intended recipient, you should not disseminate, distribute or copy >>> this e-mail. Please notify the sender immediately and destroy all copies of >>> this message and any attachments. If you have received this email in error, >>> please promptly notify the sender by reply email and delete the original >>> email and any backup copies without reading them.* >>> >>> >>> >> >> -- >> --Amneet >> >> >> >> > > -- > --Amneet > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? 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URL: From inturu.srinivas2020 at vitstudent.ac.in Wed Sep 6 02:58:03 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Wed, 6 Sep 2023 13:28:03 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: Hi Amneet, I repeated the same procedure again and this time it is working. *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp -lMatlabDataArray -lMatlabEngine* *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* *$export LD_LIBRARY_PATH* *$./a.out* Square root of -2 is 0 + 1.41421i Square root of 2 is 1.41421 + 0i Square root of 6 is 2.44949 + 0i Square root of 8 is 2.82843 + 0i I don't know how it is working this time? Thanks and regards Srinivas On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < inturu.srinivas2020 at vitstudent.ac.in> wrote: > Hi Amneet, > I tried the following example to run a matlab engine. > > #include "MatlabDataArray.hpp" > #include "MatlabEngine.hpp" > #include > void callSQRT() { > > using namespace matlab::engine; > > // Start MATLAB engine synchronously > std::unique_ptr matlabPtr = startMATLAB(); > > //Create MATLAB data array factory > matlab::data::ArrayFactory factory; > > // Define a four-element typed array > matlab::data::TypedArray const argArray = > factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); > > // Call MATLAB sqrt function on the data array > matlab::data::Array const results = matlabPtr->feval(u"sqrt", > argArray); > > // Display results > for (int i = 0; i < results.getNumberOfElements(); i++) { > double a = argArray[i]; > std::complex v = results[i]; > double realPart = v.real(); > double imgPart = v.imag(); > std::cout << "Square root of " << a << " is " << > realPart << " + " << imgPart << "i" << std::endl; > } > } > > int main() { > callSQRT(); > return 0; > } > > *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp > -lMatlabDataArray -lMatlabEngine* > > *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* > *$export LD_LIBRARY_PATH* > *$./a.out* > Starting > Error: The import statement 'import matlab.internal.engine.input' cannot > be found or cannot be imported. Imported names must end with '.*' or be > fully qualified. > > terminate called after throwing an instance of > 'matlab::engine::EngineException' > what(): MATLAB process cannot be created. > Aborted (core dumped) > > I got the above error for Matlab R2020b. Please help me to sort out this. > > Thanks and regards > Srinivas > > On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: > >> BTW, what Barry is suggesting is the following: >> >> Compile a sample code with a command line this: >> >> >> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >> >> >> This command is provided here: >> >> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >> >> >> A sample MATLAB code is here: >> >> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >> >> >> (You can just pick a few lines of code from here to create a barebone example) >> >> >> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >> wrote: >> >>> Srinivas --- Do you have a different version of MATLAB that you can >>> install? If your organization has a MATLAB license, you can install recent >>> versions of MATLAB from mathworks.com >>> >>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>> >>>> >>>> Ok, I have no suggestions. It seems to be more an issue with the >>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>> (in the Matlab documentation) and try it to see if it works. >>>> >>>> Barry >>>> >>>> >>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>> >>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>> I got the same errors for petsc 3.17.5 >>>> >>>> >>>> *make all* >>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>> Building with 'gcc'. >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> In function ?PetscBinaryWrite?: >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> | ^ >>>> >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> MEX completed successfully. >>>> Building with 'gcc'. >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>> In function ?PetscBinaryWrite?: >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>> warning: ?err? may be used uninitialized in this function >>>> [-Wmaybe-uninitialized] >>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>> | ^ >>>> >>>> MEX completed successfully. >>>> ========================================= >>>> ========================================= >>>> Now to check if the libraries are working do: >>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>> >>>> *make test query=requires queryval=matlab >>>> DATAFILESPATH=/home/vit/datafiles/* >>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>> query=requires >>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>> # [0]PETSC ERROR: --------------------- Error Message >>>> -------------------------------------------------------------- >>>> # [0]PETSC ERROR: Error in external library >>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>> shooting. >>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>>> Sep 5 21:39:22 2023 >>>> # [0]PETSC ERROR: Configure options >>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>> --known-64-bit-blas-indices=1 >>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>> # [0]PETSC ERROR: #9 main() at >>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>> # [0]PETSC ERROR: -error_output_stdout >>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>> # [0]PETSC ERROR: -malloc_dump >>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>> # [0]PETSC ERROR: -pc_type lu >>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>> # >>>> -------------------------------------------------------------------------- >>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>> # with errorcode 85. >>>> # >>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> # You may or may not see output from other processes, depending on >>>> # exactly when Open MPI kills them. >>>> # >>>> -------------------------------------------------------------------------- >>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>> >>>> >>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>> # >>>> # To rerun failed tests: >>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>> >>>>> >>>>> The error is occuring during >>>>> >>>>> e->ep = engOpen(buffer); >>>>> >>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>> stdout and stdin from the Matlab session that is launched to the >>>>> executable. >>>>> >>>>> You can try the following. In 3.17.5 edit the >>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>> >>>>> e->ep = engOpen(buffer); >>>>> >>>>> replace it with >>>>> >>>>> e->ep = engOpen(""); >>>>> >>>>> Now in the PETSc directory do make all (it should recompile one file) >>>>> and then run the >>>>> >>>>> make test query=requires queryval=matlab >>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>> >>>>> again >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users < >>>>> petsc-users at mcs.anl.gov> wrote: >>>>> >>>>> Hi Amneeth, >>>>> >>>>> I think the errors are different with petsc 3.17.5 >>>>> >>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>> >>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>> The version of PETSc you are using is out-of-date, we recommend >>>>> updating to the new release >>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>> https://petsc.org/release/download/ >>>>> >>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>> >>>>> ============================================================================================= >>>>> Configuring PETSc to compile on your system >>>>> >>>>> >>>>> ============================================================================================= >>>>> Compilers: >>>>> >>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>> -fvisibility=hidden -O3 >>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>> Linkers: >>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>> -fstack-protector -fvisibility=hidden -O3 >>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>> -fstack-protector -fvisibility=hidden -O3 >>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>> BlasLapack: >>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>>>> to control the number of threads >>>>> uses 8 byte integers >>>>> MPI: >>>>> Version: 3 >>>>> mpiexec: /usr/bin/mpiexec >>>>> Implementation: openmpi >>>>> OMPI_VERSION: 4.0.3 >>>>> pthread: >>>>> cmake: >>>>> Version: 3.16.3 >>>>> /usr/bin/cmake >>>>> regex: >>>>> Matlab: >>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>> /usr/local/MATLAB/R2020b >>>>> MatlabEngine: >>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>> Language used to compile PETSc: C >>>>> PETSc: >>>>> PETSC_ARCH: linux-opt >>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>> Prefix: >>>>> Scalar type: real >>>>> Precision: double >>>>> Support for __float128 >>>>> Integer size: 4 bytes >>>>> Single library: yes >>>>> Shared libraries: yes >>>>> Memory alignment from malloc(): 16 bytes >>>>> Using GNU make: /usr/bin/make >>>>> >>>>> xxx=========================================================================xxx >>>>> Configure stage complete. Now build PETSc libraries with: >>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>> all >>>>> >>>>> xxx=========================================================================xxx >>>>> >>>>> *$make* >>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>> Building with 'gcc'. >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> In function ?PetscBinaryWrite?: >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>> warning: ?err? may be used uninitialized in this function >>>>> [-Wmaybe-uninitialized] >>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> | ^ >>>>> >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> In function ?PetscBinaryWrite?: >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>> warning: ?err? may be used uninitialized in this function >>>>> [-Wmaybe-uninitialized] >>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> | ^ >>>>> >>>>> MEX completed successfully. >>>>> ========================================= >>>>> ========================================= >>>>> Now to check if the libraries are working do: >>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>> check >>>>> >>>>> *$make test query=requires queryval=matlab >>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>> /usr/bin/python3 >>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>> --testdir=./linux-opt/tests >>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>> query=requires >>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> # [0]PETSC ERROR: Error in external library >>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>> shooting. >>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>>>> Sep 5 10:15:57 2023 >>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>> # [0]PETSC ERROR: #9 main() at >>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>> # [0]PETSC ERROR: -error_output_stdout >>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>> # [0]PETSC ERROR: -malloc_dump >>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>> # [0]PETSC ERROR: -pc_type lu >>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>> # >>>>> -------------------------------------------------------------------------- >>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>> # with errorcode 85. >>>>> # >>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> # You may or may not see output from other processes, depending on >>>>> # exactly when Open MPI kills them. >>>>> # >>>>> -------------------------------------------------------------------------- >>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>> >>>>> >>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>> # >>>>> # To rerun failed tests: >>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>> >>>>> To get the info of the error there is no specific probe id reported. >>>>> >>>>> How to check error info and proceed further? >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>> wrote: >>>>> >>>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>>> options that Satish mentioned? >>>>>> >>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>> petsc-users wrote: >>>>>> >>>>>>> Sorry for missing that. >>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>>>> >>>>>>> < M A T L A B (R) > >>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>> November 23, 2020 >>>>>>> >>>>>>> >>>>>>> To get started, type doc. >>>>>>> For product information, visit www.mathworks.com. >>>>>>> >>>>>>> Thanks and regards >>>>>>> Srinivas >>>>>>> >>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>> wrote: >>>>>>> >>>>>>>> You are missing one more step: >>>>>>>> >>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> >>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>> >>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>> >>>>>>>> Satish >>>>>>>> >>>>>>>> >>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>>> >>>>>>>> > Hi Sathish, >>>>>>>> > >>>>>>>> > I tried the following procedure >>>>>>>> > >>>>>>>> > *$make * >>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> > Building with 'gcc'. >>>>>>>> > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>> > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>> socket\n"); >>>>>>>> > | ^ >>>>>>>> > >>>>>>>> > MEX completed successfully. >>>>>>>> > Building with 'gcc'. >>>>>>>> > MEX completed successfully. >>>>>>>> > Building with 'gcc'. >>>>>>>> > MEX completed successfully. >>>>>>>> > Building with 'gcc'. >>>>>>>> > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>> > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>> socket\n"); >>>>>>>> > | ^ >>>>>>>> > >>>>>>>> > MEX completed successfully. >>>>>>>> > ========================================= >>>>>>>> > Now to check if the libraries are working do: >>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>> check >>>>>>>> > >>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> queryval=matlab >>>>>>>> > query=requires >>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> > TEST >>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > -------------------------------------------------------------- >>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>> > # [0]PETSC ERROR: See >>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > for trouble shooting. >>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>> vit Mon Sep >>>>>>>> > 4 10:02:32 2023 >>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > -------------------------------------------------------------- >>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>> > # [0]PETSC ERROR: >>>>>>>> > # [0]PETSC ERROR: See >>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > for trouble shooting. >>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>> vit Mon Sep >>>>>>>> > 4 10:02:32 2023 >>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > # [0]PETSC ERROR: >>>>>>>> > >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>> Violation, >>>>>>>> > probably memory access out of range >>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>> -on_error_attach_debugger >>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>> Apple Mac OS >>>>>>>> > X to find memory corruption errors >>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>> recompile, link, >>>>>>>> > and run >>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > -------------------------------------------------------------- >>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>> > # [0]PETSC ERROR: See >>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > for trouble shooting. >>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>> vit Mon Sep >>>>>>>> > 4 10:02:32 2023 >>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>>>> file >>>>>>>> > # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>> > # with errorcode 50162059. >>>>>>>> > # >>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>> processes. >>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>> > # exactly when Open MPI kills them. >>>>>>>> > # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>> > CC >>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>> > CLINKER >>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>> > TEST >>>>>>>> > >>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>> code: 124 >>>>>>>> > # Running problem 5 >>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > -------------------------------------------------------------- >>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>> > # [0]PETSC ERROR: See >>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > for trouble shooting. >>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>> MB108SMEC028 by >>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>> > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>> -------send entire >>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> > # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>> > # with errorcode 126076. >>>>>>>> > # >>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>> processes. >>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>> > # exactly when Open MPI kills them. >>>>>>>> > # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>> Command failed >>>>>>>> > so no diff >>>>>>>> > >>>>>>>> > # ------------- >>>>>>>> > # Summary >>>>>>>> > # ------------- >>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>> > # >>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>> > # >>>>>>>> > # To rerun failed tests: >>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> > # >>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>>>> 0.01 sec >>>>>>>> > >>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>> > *$make matlab_ls_test* >>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>> -Wwrite-strings >>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>> -Wno-strict-aliasing >>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> > >>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>>> -lmx >>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>> -lmpi_mpifh >>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>> -lquadmath >>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>> > >>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>> ./matlab_ls_test >>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>> processors = 1 >>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>> > MB108SMEC028.(none) >>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>> > Running problem 5 >>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>> 140155238476992 >>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > -------------------------------------------------------------- >>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>> > [0]PETSC ERROR: See >>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > for trouble shooting. >>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>> MB108SMEC028 by vit >>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> > [0]PETSC ERROR: -info >>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>> entire >>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>> > with errorcode 126076. >>>>>>>> > >>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>> processes. >>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>> > exactly when Open MPI kills them. >>>>>>>> > >>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>> > >>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>> wrote: >>>>>>>> > >>>>>>>> > > To use datafiles in the test suite: >>>>>>>> > > >>>>>>>> > > cd $HOME >>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>> > > >>>>>>> DATAFILESPATH - or set >>>>>>>> > > manually with make> >>>>>>>> > > >>>>>>>> > > make test query=requires queryval=matlab >>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>> > > >>>>>>>> > > Satish >>>>>>>> > > >>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>> > > >>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>> > > > >>>>>>>> > > > > Hi Matthew, >>>>>>>> > > > > >>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do >>>>>>>> not have >>>>>>>> > > any >>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>> help me how to >>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>> > > > > >>>>>>>> > > > >>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we >>>>>>>> point to >>>>>>>> > > this >>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>> don't have those >>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>> > > > is why I suggested just using a different matrix, or running >>>>>>>> a problem >>>>>>>> > > you >>>>>>>> > > > care about in IBAMR. >>>>>>>> > > > >>>>>>>> > > > Thanks, >>>>>>>> > > > >>>>>>>> > > > Matt >>>>>>>> > > > >>>>>>>> > > > >>>>>>>> > > > > Thanks and regards >>>>>>>> > > > > Srinivas. >>>>>>>> > > > > >>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>> knepley at gmail.com> >>>>>>>> > > wrote: >>>>>>>> > > > > >>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 >>>>>>>> via >>>>>>>> > > petsc-users < >>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>> > > > >> >>>>>>>> > > > >>> Hi Sathish, >>>>>>>> > > > >>> >>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>> are giving me >>>>>>>> > > to >>>>>>>> > > > >>> sort this out. >>>>>>>> > > > >>> >>>>>>>> > > > >>> I tried to follow the same procedure which you followed >>>>>>>> to build >>>>>>>> > > Petsc >>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>> > > > >>> >>>>>>>> > > > >>> *$./configure >>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>> PETSC_ARCH=linux-opt >>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>> > > > >>> Using python3 for Python >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> =============================================================================== >>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> =============================================================================== >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> =============================================================================== >>>>>>>> > > > >>> It appears you do >>>>>>>> not have >>>>>>>> > > valgrind >>>>>>>> > > > >>> installed on your system. >>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>> www.valgrind.org >>>>>>>> > > > >>> Or install >>>>>>>> > > valgrind-devel or >>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>> > > > >>> Then rerun ./configure >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> =============================================================================== >>>>>>>> > > > >>> Compilers: >>>>>>>> > > > >>> >>>>>>>> > > > >>> C Compiler: >>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>> > > -fPIC >>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>> -Wno-unknown-pragmas >>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> > > > >>> C++ Compiler: >>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>> -Wno-unknown-pragmas >>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>> > > > >>> Fortran Compiler: >>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>> 9.4.0 >>>>>>>> > > > >>> Linkers: >>>>>>>> > > > >>> Shared linker: >>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>> > > -shared >>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>> > > -Wno-unknown-pragmas >>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> > > > >>> Dynamic linker: >>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>> > > -shared >>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>> > > -Wno-unknown-pragmas >>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>> > > > >>> make: >>>>>>>> > > > >>> Version: 4.2 >>>>>>>> > > > >>> /usr/bin/make >>>>>>>> > > > >>> BlasLapack: >>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>> -lpthread >>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>> -omp_num_threads >>>>>>>> > >

to >>>>>>>> > > > >>> control the number of threads >>>>>>>> > > > >>> uses 8 byte integers >>>>>>>> > > > >>> MPI: >>>>>>>> > > > >>> Version: 3 >>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>> > > --oversubscribe >>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>> > > > >>> pthread: >>>>>>>> > > > >>> cmake: >>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>> > > > >>> regex: >>>>>>>> > > > >>> Matlab: >>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>> > > > >>> MatlabEngine: >>>>>>>> > > > >>> Library: >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex >>>>>>>> -lmx -lmat >>>>>>>> > > -lut >>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>> > > > >>> PETSc: >>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>> > > > >>> Scalar type: real >>>>>>>> > > > >>> Precision: double >>>>>>>> > > > >>> Support for __float128 >>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>> > > > >>> shared libraries: enabled >>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> xxx=========================================================================xxx >>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> xxx=========================================================================xxx >>>>>>>> > > > >>> >>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>> -licui18n -licuuc as >>>>>>>> > > > >>> you suggested earlier. >>>>>>>> > > > >>> >>>>>>>> > > > >>> *$make* >>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>> socket\n"); >>>>>>>> > > > >>> | ^ >>>>>>>> > > > >>> >>>>>>>> > > > >>> MEX completed successfully. >>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>> > > > >>> MEX completed successfully. >>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>> > > > >>> MEX completed successfully. >>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>> socket\n"); >>>>>>>> > > > >>> | ^ >>>>>>>> > > > >>> >>>>>>>> > > > >>> MEX completed successfully. >>>>>>>> > > > >>> ========================================= >>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>> > > > >>> =============================================== >>>>>>>> > > > >>> >>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> > > > >>> TEST >>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > > > >>> >>>>>>>> -------------------------------------------------------------- >>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>> > > > >>> >>>>>>>> > > > >> >>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>> defined, so it >>>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>>> yours. >>>>>>>> > > > >> >>>>>>>> > > > >> Thanks, >>>>>>>> > > > >> >>>>>>>> > > > >> Matt >>>>>>>> > > > >> >>>>>>>> > > > >> >>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>>>> trouble >>>>>>>> > > > >>> shooting. >>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>> 2020 >>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>> MB108SMEC028 by vit >>>>>>>> > > Sun >>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>> COPTFLAGS=-O3 >>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>>> line 1444 in >>>>>>>> > > > >>> >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 >>>>>>>> in >>>>>>>> > > > >>> >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>> > > > >>> >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>> -------send >>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> > > > >>> # >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>> MPI_COMM_SELF >>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>> > > > >>> # >>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>> MPI processes. >>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>> depending on >>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>> > > > >>> # >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no >>>>>>>> diff >>>>>>>> > > > >>> CC >>>>>>>> > > > >>> >>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>> > > > >>> CLINKER >>>>>>>> > > > >>> >>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>> > > > >>> TEST >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>> Error >>>>>>>> > > code: 124 >>>>>>>> > > > >>> # Running problem 5 >>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > > > >>> >>>>>>>> -------------------------------------------------------------- >>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for >>>>>>>> trouble >>>>>>>> > > > >>> shooting. >>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>> 2020 >>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>> > > MB108SMEC028 by >>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>> COPTFLAGS=-O3 >>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> --with-debugging=0 >>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>> > > > >>> >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>> -------send >>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> > > > >>> # >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>> MPI_COMM_SELF >>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>> > > > >>> # >>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>> MPI processes. >>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>> depending on >>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>> > > > >>> # >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>> SKIP Command >>>>>>>> > > > >>> failed so no diff >>>>>>>> > > > >>> >>>>>>>> > > > >>> # ------------- >>>>>>>> > > > >>> # Summary >>>>>>>> > > > >>> # ------------- >>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>> > > > >>> # >>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>> > > > >>> # >>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> > > > >>> # >>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>> 0.02 sec / >>>>>>>> > > 0.02 sec >>>>>>>> > > > >>> >>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>> > > > >>> >>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>> > > -Wwrite-strings >>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>> -fstack-protector >>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>> > > -Wno-strict-aliasing >>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>> -fvisibility=hidden -O3 >>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>> matlab_ls_test.c >>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> > > > >>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>> -leng -lmex >>>>>>>> > > -lmx >>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>> > > -lmpi_mpifh >>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>> -lpthread >>>>>>>> > > -lquadmath >>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>> > > > >>> >>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please >>>>>>>> find the >>>>>>>> > > > >>> attachment and do the needful. >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > > >>> Thanks and regards >>>>>>>> > > > >>> Srinivas >>>>>>>> > > > >>> >>>>>>>> > > > >>> >>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>> balay at mcs.anl.gov> >>>>>>>> > > wrote: >>>>>>>> > > > >>> >>>>>>>> > > > >>>> Perhaps you can try the following to get additional info >>>>>>>> - and debug >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> Satish >>>>>>>> > > > >>>> ---------- >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>> > > > >>>> >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>> > > -Wall >>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>> > > -fstack-protector >>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>> > > -Wno-strict-aliasing >>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>> -fvisibility=hidden -O3 >>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>> > > > >>>> >>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>> -lpthread -lm -leng >>>>>>>> > > -lmex >>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>> -ldl -lmpifort >>>>>>>> > > -lmpi >>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>> -lstdc++ -ldl -o >>>>>>>> > > > >>>> matlab_ls_test >>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>> ./matlab_ls_test >>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>> number of >>>>>>>> > > processors >>>>>>>> > > > >>>> = 1 >>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is >>>>>>>> NIS >>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>>> > > > >>>> Running problem 5 >>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>> 1140850689 >>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>> with command >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>> string: >>>>>>>> > > > >>>> TestingInitialize >>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>>>> string: >>>>>>>> > > > >>>> TestingInitialize >>>>>>>> > > > >>>> 5 >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>> works for you >>>>>>>> > > - on >>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>> MathWorks, Inc. >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>>>> (glnxa64) >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> February 17, 2021 >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> To get started, type doc. >>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>> [reverting >>>>>>>> > > thread >>>>>>>> > > > >>>> to petsc-users only] >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>> > > corresponding >>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>>> Ubuntu-20.04, >>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>> > > > >>>> > main >>>>>>>> > > > >>>> > release >>>>>>>> > > > >>>> > * release-3.13 >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>>> > > matlab/R2021a >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>> matlab >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>>> > > > >>>> >>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>> PETSC_ARCH=linux-opt >>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > Compilers: >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> > C Compiler: >>>>>>>> > > > >>>> >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>> > > -Wall >>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>> > > -fstack-protector >>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>> > > > >>>> >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>> > > -fstack-protector >>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>> > > > >>>> >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>> > > -Wall >>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> > > > >>>> > Linkers: >>>>>>>> > > > >>>> > Shared linker: >>>>>>>> > > > >>>> >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>> > > -shared -fPIC >>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>> -Wno-unknown-pragmas >>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>> > > > >>>> >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>> > > -shared -fPIC >>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>> -Wno-unknown-pragmas >>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>> > > > >>>> > make: >>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>> > > > >>>> > BlasLapack: >>>>>>>> > > > >>>> > Library: >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>> -omp_num_threads >>>>>>>> > >

>>>>>>>> > > > >>>> to control the number of threads >>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>> > > > >>>> > MPI: >>>>>>>> > > > >>>> > Version: 4 >>>>>>>> > > > >>>> > Includes: >>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>> > > > >>>> > Mpiexec: >>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>> > > > >>>> > pthread: >>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>> > > > >>>> > cmake: >>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>> > > > >>>> > regex: >>>>>>>> > > > >>>> > Matlab: >>>>>>>> > > > >>>> > Includes: >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>> > > > >>>> > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>> > > > >>>> > Library: >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>> > > > >>>> > sowing: >>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>> > > > >>>> > valgrind: >>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>> > > > >>>> > PETSc: >>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>> > > > >>>> > Scalar type: real >>>>>>>> > > > >>>> > Precision: double >>>>>>>> > > > >>>> > Support for __float128 >>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> xxx=========================================================================xxx >>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>>> with: >>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> xxx=========================================================================xxx >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>> to >>>>>>>> > > socket\n"); >>>>>>>> > > > >>>> > | ^ >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>> to >>>>>>>> > > socket\n"); >>>>>>>> > > > >>>> > | ^ >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>> > > > >>>> > ========================================= >>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>> > > > >>>> > ========================================= >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>> > > query=requires >>>>>>>> > > > >>>> queryval=matlab >>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> > > > >>>> > TEST >>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>> > > > >>>> > # ../ex72: >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>> no diff >>>>>>>> > > > >>>> > CC >>>>>>>> > > > >>>> >>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>> > > > >>>> > CLINKER >>>>>>>> > > > >>>> >>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>> > > > >>>> > TEST >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>> > > > >>>> > not ok >>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>> > > code: >>>>>>>> > > > >>>> 1 >>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>> SKIP >>>>>>>> > > Command >>>>>>>> > > > >>>> failed so no diff >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>>> test >>>>>>>> > > query=requires >>>>>>>> > > > >>>> queryval=matlab >>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>> > > > >>>> > TEST >>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>> > > > >>>> > TEST >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>> > > > >>>> > ok >>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > # ------------- >>>>>>>> > > > >>>> > # Summary >>>>>>>> > > > >>>> > # ------------- >>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>> > > > >>>> > # >>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>> 15.190000000000001 >>>>>>>> > > sec >>>>>>>> > > > >>>> > # >>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>> 6.47 sec / >>>>>>>> > > 7.54 >>>>>>>> > > > >>>> sec >>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>> > > > >>>> > >>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>> tried to >>>>>>>> > > > >>>> configure petsc >>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>> successful. After >>>>>>>> > > > >>>> running make >>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>> message. >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> > > not ok >>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>> > > > >>>> code: 124 >>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> > > > >>>> > > >>>>>>>> -------------------------------------------------------------- >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>> 01, 2020 >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>> named >>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>> COPTFLAGS=-O3 >>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>>>>>> 67 in >>>>>>>> > > > >>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error >>>>>>>> Message >>>>>>>> > > -------send >>>>>>>> > > > >>>> entire >>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> > > > >>>> > > # >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>> MPI_COMM_SELF >>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>> > > > >>>> > > # >>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>>>>>> all MPI >>>>>>>> > > > >>>> processes. >>>>>>>> > > > >>>> > > # You may or may not see output from other >>>>>>>> processes, depending >>>>>>>> > > on >>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>> > > > >>>> > > # >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> > > Thanks >>>>>>>> > > > >>>> > > Srinivas >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>>>> > > > >>>> > > >>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> > > > >>>>>>>> > > > >>>> > > > i.e.: >>>>>>>> > > > >>>> > > > >>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> > > > >>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>>>> 20PHD0548 via >>>>>>>> > > > >>>> petsc-users < >>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>>>> > > > >>>> > > > >>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>> > > > >>>> > > >> >>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>>>> balay at mcs.anl.gov> >>>>>>>> > > > >>>> wrote: >>>>>>>> > > > >>>> > > >> >>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre >>>>>>>> will work >>>>>>>> > > > >>>> here]. >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> > > >>> ./configure >>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> > > >>> Satish >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>> > > petsc-users >>>>>>>> > > > >>>> wrote: >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>> > > > >>>> > > >>> > >>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>> > > > >>>> > > >>> > >>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>> > > > >>>> > > >>> > >>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>> > > balay at mcs.anl.gov> >>>>>>>> > > > >>>> wrote: >>>>>>>> > > > >>>> > > >>> > >>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work >>>>>>>> in this mode. >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>>>> dependency/conflicts >>>>>>>> > > across >>>>>>>> > > > >>>> packages] >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>>>> petsc-users wrote: >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit >>>>>>>> integers] conflict >>>>>>>> > > with >>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>>>> blas/lapack with >>>>>>>> > > > >>>> matlab - to >>>>>>>> > > > >>>> > > >>> have a >>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>>>> 20PHD0548 via >>>>>>>> > > > >>>> petsc-users >>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>> > > > >>>> > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>>>> MATLAB is not >>>>>>>> > > > >>>> working. It is >>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 >>>>>>>> versions. >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>>>> cluster with >>>>>>>> > > > >>>> libmesh and >>>>>>>> > > > >>>> > > >>> this is >>>>>>>> > > > >>>> > > >>> > > for >>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I >>>>>>>> tried without >>>>>>>> > > > >>>> linking >>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>> > > > >>>> > > >>> > > with >>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>>>>>> configuring >>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>> > > > >>>> > > >>> that >>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>> > > > >>>> > > >>> > > > > was not found but >>>>>>>> --enable-petsc-required is >>>>>>>> > > specified. >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>>>>>> libmesh with >>>>>>>> > > > >>>> PETSc and >>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for >>>>>>>> complicated >>>>>>>> > > geometries >>>>>>>> > > > >>>> it is >>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh >>>>>>>> construct. >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>>>>>> various >>>>>>>> > > things >>>>>>>> > > > >>>> and ended >>>>>>>> > > > >>>> > > >>> up with >>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further >>>>>>>> to do my >>>>>>>> > > > >>>> research work. >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>>>>>>> possible. >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla >>>>>>>> < >>>>>>>> > > > >>>> mail2amneet at gmail.com> >>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>>>>> libMesh for >>>>>>>> > > the >>>>>>>> > > > >>>> WEC >>>>>>>> > > > >>>> > > >>> application. >>>>>>>> > > > >>>> > > >>> > > You >>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>>>>>> builds with >>>>>>>> > > > >>>> Matlab. >>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for >>>>>>>> wanting to build >>>>>>>> > > > >>>> libMesh? >>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM >>>>>>>> INTURU SRINIVAS >>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>> > > > >>>> > > >>> > > > > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>>>>>>> removing all >>>>>>>> > > > >>>> occurrences >>>>>>>> > > > >>>> > > >>> of >>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I >>>>>>>> ran "make >>>>>>>> > > test" >>>>>>>> > > > >>>> got the >>>>>>>> > > > >>>> > > >>> > > following >>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>> > > > >>>> > > >>> Error >>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>> --------------------- Error >>>>>>>> > > Message >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> >>>>>>>> -------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>>> library >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>> MATLAB engine >>>>>>>> > > on >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > > > >>>> for >>>>>>>> > > > >>>> > > >>> trouble >>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>> Version 3.13.4, >>>>>>>> > > Aug >>>>>>>> > > > >>>> 01, 2020 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test >>>>>>>> on a >>>>>>>> > > linux-debug >>>>>>>> > > > >>>> named >>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>>>>> --download-fblaslapack=1 >>>>>>>> > > > >>>> --with-x=0 >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>> PetscMatlabEngineCreate() >>>>>>>> > > line >>>>>>>> > > > >>>> 67 in >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 >>>>>>>> in >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>>>> entries: >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End >>>>>>>> of Error >>>>>>>> > > > >>>> Message >>>>>>>> > > > >>>> > > >>> -------send >>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>>>> communicator >>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>> Open MPI to >>>>>>>> > > kill >>>>>>>> > > > >>>> all MPI >>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>>>> other >>>>>>>> > > processes, >>>>>>>> > > > >>>> > > >>> depending on >>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>> > > > >>>> # SKIP >>>>>>>> > > > >>>> > > >>> Command >>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>> > > > >>>> > > >>> Error >>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>> --------------------- Error >>>>>>>> > > Message >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> >>>>>>>> -------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>>> library >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>> MATLAB engine >>>>>>>> > > on >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>> > > > >>>> for >>>>>>>> > > > >>>> > > >>> trouble >>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>> Version 3.13.4, >>>>>>>> > > Aug >>>>>>>> > > > >>>> 01, 2020 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test >>>>>>>> on a >>>>>>>> > > linux-opt >>>>>>>> > > > >>>> named >>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>> PetscMatlabEngineCreate() >>>>>>>> > > line >>>>>>>> > > > >>>> 67 in >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 >>>>>>>> in >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>>>> entries: >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End >>>>>>>> of Error >>>>>>>> > > > >>>> Message >>>>>>>> > > > >>>> > > >>> -------send >>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>>>> communicator >>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>> Open MPI to >>>>>>>> > > kill >>>>>>>> > > > >>>> all MPI >>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>>>> other >>>>>>>> > > processes, >>>>>>>> > > > >>>> > > >>> depending on >>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>> > > > >>>> # SKIP >>>>>>>> > > > >>>> > > >>> Command >>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc >>>>>>>> 3.17.5 >>>>>>>> > > version. I >>>>>>>> > > > >>>> am >>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both >>>>>>>> petsc 3.13.4 and >>>>>>>> > > > >>>> petsc >>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM >>>>>>>> Satish Balay < >>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>>>>>> petsc's >>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>> > > > >>>> > > >>> > > for >>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> > > -leng >>>>>>>> > > > >>>> -lmex >>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) >>>>>>>> - we are >>>>>>>> > > seeing: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n >>>>>>>> -licuuc" are not >>>>>>>> > > > >>>> preset here. >>>>>>>> > > > >>>> > > >>> This >>>>>>>> > > > >>>> > > >>> > > might >>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab >>>>>>>> versions. >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>> > > > >>>> > > >>> > > and >>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>>>>> -licudata >>>>>>>> > > -licui18n >>>>>>>> > > > >>>> -licuuc" >>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>>>> 20PHD0548 >>>>>>>> > > via >>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>>>>>> building >>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building >>>>>>>> libmesh with >>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>> > > successfully. >>>>>>>> > > > >>>> But >>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>> > > > >>>> > > >>> > > not >>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>>>>> Satish Balay < >>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log >>>>>>>> from both >>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the >>>>>>>> logs >>>>>>>> > > friendly to >>>>>>>> > > > >>>> mailing >>>>>>>> > > > >>>> > > >>> list - >>>>>>>> > > > >>>> > > >>> > > or >>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with >>>>>>>> 3.17? [or >>>>>>>> > > 3.19?] >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU >>>>>>>> SRINIVAS >>>>>>>> > > 20PHD0548 >>>>>>>> > > > >>>> via >>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file >>>>>>>> while >>>>>>>> > > building >>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>> > > > >>>> > > >>> > > with >>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and >>>>>>>> do the >>>>>>>> > > needful. >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at >>>>>>>> 10:19?AM INTURU >>>>>>>> > > > >>>> SRINIVAS >>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>>>>> > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. >>>>>>>> During >>>>>>>> > > building >>>>>>>> > > > >>>> of >>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>> > > > >>>> > > >>> > > error >>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at >>>>>>>> 9:43?PM Satish >>>>>>>> > > > >>>> Balay < >>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> https://ibamr.github.io/linux says >>>>>>>> > > > >>>> petsc-3.17 >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>>>>> petsc-3.17.5? >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU >>>>>>>> SRINIVAS >>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc >>>>>>>> with MATLAB for >>>>>>>> > > > >>>> working on >>>>>>>> > > > >>>> > > >>> the >>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>>>>> building the >>>>>>>> > > PETSc, >>>>>>>> > > > >>>> using the >>>>>>>> > > > >>>> > > >>> > > following >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export >>>>>>>> PETSC_ARCH=linux-debug >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> --download-fblaslapack=1 \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>> `EvaluateResidual': >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>> `EvaluateJacobian': >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> > > >>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld >>>>>>>> returned 1 exit >>>>>>>> > > > >>>> status >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>>>>> [gmakefile.test:185: >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> >>>>>>>> > > > >>>> >>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>>>>> unfinished >>>>>>>> > > jobs.... >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve >>>>>>>> this issue >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent >>>>>>>> from Vellore >>>>>>>> > > > >>>> Institute of >>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may >>>>>>>> contain legally >>>>>>>> > > > >>>> protected >>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>>>>> Institute of >>>>>>>> > > > >>>> Technology?. >>>>>>>> > > > >>>> > > >>> If >>>>>>>> > > > >>>> > > >>> > > you are >>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you >>>>>>>> should not >>>>>>>> > > > >>>> disseminate, >>>>>>>> > > > >>>> > > >>> distribute >>>>>>>> > > > >>>> > > >>> > > or copy >>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender >>>>>>>> immediately >>>>>>>> > > > >>>> and destroy >>>>>>>> > > > >>>> > > >>> all >>>>>>>> > > > >>>> > > >>> > > copies of >>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. 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The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From carljohanthore at gmail.com Wed Sep 6 03:10:19 2023 From: carljohanthore at gmail.com (Carl-Johan Thore) Date: Wed, 6 Sep 2023 10:10:19 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: <8B433012-D804-4865-9C77-C074BEB68DE9@lip6.fr> References: <8B433012-D804-4865-9C77-C074BEB68DE9@lip6.fr> Message-ID: "Na?ve question, but is your problem really symmetric? For example, if you do FEM, how do you impose Dirichlet boundary conditions?" The structure of the matrix is K = [A B; B^T C] with A and C symmetric, so the problem should be symmetric. Numerically, the maximum relative difference between K and K^T is on the order of, let's say, 1e-18 which I guess is a good as can be expected? I'm using FEM with (homogeneous) Dirichlet boundary conditions imposed by zeroing rows and columns for the fixed DOFs and adding ones to the corresponding diagonal elements, i.e. same as what MatZeroRowsColumns does. MatZeroRowsColumns doesn't work for sbaij but we already have an implementation in which rows and columns are cancelled in the element matrices before assembly which is well-tested for the aij-case. We've also verified numerically that aij and sbaij yields the same upper triangular part, and that the RHS is the same in both cases. "If you can reproduce this on a smaller example and are at liberty to share the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov, I can have a look." Yes, this is reproducible on smaller problems. In case I send you Mat, IS, and RHS, which format is preferable? Kind regards, Carl-Johan On Wed, Sep 6, 2023 at 8:21?AM Pierre Jolivet wrote: > Na?ve question, but is your problem really symmetric? > For example, if you do FEM, how do you impose Dirichlet boundary > conditions? > If you can reproduce this on a smaller example and are at liberty to share > the Mat, IS, and RHS Vec, feel free to send them at > petsc-maint at mcs.anl.gov, I can have a look. > > Thanks, > Pierre > > On 6 Sep 2023, at 8:14 AM, Carl-Johan Thore > wrote: > > ? > Thanks for this! > I now get convergence with sbaij and fieldsplit. However, as can be seen > in the attached file, it requires around three times as many outer > iterations as with aij to reach the same point (to within rtol). Switching > from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct" > choice?) helps quite a bit, but still sbaij takes many more iterations. So > it seems that your sbaij-implementation works but that I'm doing something > wrong when setting up the fieldsplit pc, or that some of the subsolvers > doesn't work properly with sbaij. I've tried bjacobi as you had in your > logs, but not hypre yet. But anyway, one doesn't expect the matrix format > to have this much impact on convergence? Any other suggestions? > /Carl-Johan > > On Mon, Sep 4, 2023 at 9:31?PM Pierre Jolivet > wrote: > >> The branch should now be good to go ( >> https://gitlab.com/petsc/petsc/-/merge_requests/6841). >> Sorry, I made a mistake before, hence the error on PetscObjectQuery(). >> I?m not sure the code will be covered by the pipeline, but I have tested >> this on a Raviart?Thomas discretization with PCFIELDSPLIT. >> You?ll see in the attached logs that: >> 1) the numerics match >> 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} >> block from the global (symmetric) A and we get the A_{10} block cheaply by >> just using MatCreateHermitianTranspose(), instead of calling another time >> MatCreateSubMatrix() >> Please let me know if you have some time to test the branch and whether >> it fails or succeeds on your test cases. >> >> Also, I do not agree with what Hong said. >> Sometimes, the assembly of a coefficient can be more expensive than the >> communication of the said coefficient. >> So they are instances where SBAIJ would be more efficient than AIJ even >> if it would require more communication, it is not a black and white picture. >> >> Thanks, >> Pierre >> >> >> On 28 Aug 2023, at 12:12 PM, Pierre Jolivet >> wrote: >> >> >> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore >> wrote: >> >> I've tried the new files, and with them, PCFIELDSPLIT now gets set up >> without crashes (but the setup is significantly slower than for MATAIJ) >> >> >> I?ll be back from Japan at the end of this week, my schedule is too >> packed to get anything done in the meantime. >> But I?ll let you know when things are working properly (last I checked, I >> think it was working, but I may have forgotten about a corner case or two). >> But yes, though one would except things to be faster and less memory >> intensive with SBAIJ, it?s unfortunately not always the case. >> >> Thanks, >> Pierre >> >> Unfortunately I still get errors later in the process: >> >> [0]PETSC ERROR: Null argument, when expecting valid pointer >> [0]PETSC ERROR: Null Pointer: Parameter # 1 >> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d >> GIT Date: 2023-08-22 20:32:33 -0400 >> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 >> --with-cuda --with-cusp --download-scalapack --download-hdf5 >> --download-zlib --download-mumps --download-parmetis --download-metis >> --download-ptscotch --download-hypre --download-spai >> [0]PETSC ERROR: #1 PetscObjectQuery() at >> /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 >> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at >> /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 >> [0]PETSC ERROR: #3 MatCreateSubMatrix() at >> /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 >> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at >> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 >> [0]PETSC ERROR: #5 PCSetUp() at >> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 >> [0]PETSC ERROR: #6 KSPSetUp() at >> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 >> >> The code I'm running here works without any problems for MATAIJ. To run >> it with MATSBAIJ I've simply used the command-line option >> -dm_mat_type sbaij >> >> >> Kind regards, >> Carl-Johan >> >> >> On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users < >> petsc-users at mcs.anl.gov> wrote: >> >>> >>> >>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore >>> wrote: >>> >>> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up >>> with the same issue.? >>> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices >>> from these blocks, or is there >>> somewhere else in the code that things will go wrong? >>> >>> >>> Ah, no, you are right, in that case it should work. >>> >>> For the MATNEST I was thinking to get some savings from the >>> block-symmetry at least >>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for >>> them would just be a >>> (pretty big) bonus. >>> >>> ?I?ll rebase on top of main and try to get it integrated if it could be >>> useful to you (but I?m traveling >>> right now so everything gets done more slowly, sorry).? >>> Sound great, Thanks again! >>> >>> >>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >>> I need to add a new code path in MatCreateRedundantMatrix() to make sure >>> the resulting Mat is indeed SBAIJ, but that is orthogonal to the >>> PCFIELDSPLIT issue. >>> The branch should be usable in its current state. >>> >>> Thanks, >>> Pierre >>> >>> >>> *From:* Pierre Jolivet >>> *Sent:* Saturday, August 26, 2023 4:36 PM >>> *To:* Carl-Johan Thore >>> *Cc:* Carl-Johan Thore ; >>> petsc-users at mcs.anl.gov >>> *Subject:* Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >>> >>> >>> >>> >>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore >>> wrote: >>> >>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used >>> to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get >>> the A01 and A10 blocks in PCFIELDSPLIT. >>> I have a branch that fixes this, but I haven?t rebased in a while (and >>> I?m AFK right now), would you want me to rebase and give it a go, or must >>> you stick to a release tarball?" >>> >>> Ok, would be great if you could look at this! I don't need to stick to >>> any particular branch. >>> >>> Do you think MATNEST could be an alternative here? >>> >>> >>> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up >>> with the same issue. >>> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was >>> crashing but I think it was thoroughly fixed in >>> https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >>> It is ugly code on top of ugly code, so I didn?t try to get it >>> integrated and just used the branch locally, and then moved to some other >>> stuff. >>> I?ll rebase on top of main and try to get it integrated if it could be >>> useful to you (but I?m traveling right now so everything gets done more >>> slowly, sorry). >>> >>> Thanks, >>> Pierre >>> >>> >>> My matrix is >>> [A00 A01; >>> A01^t A11] >>> so perhaps with MATNEST I can make use of the block-symmetry at least, >>> and then use MATSBAIJ for >>> A00 and A11 if it's possible to combine matrix types which the manual >>> seems to imply. >>> >>> Kind regards >>> Carl-Johan >>> >>> >>> >>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore >>> wrote: >>> ? >>> Hi, >>> >>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >>> According to the manual "[t]he fieldsplit preconditioner cannot >>> currently be used with the MATBAIJ or MATSBAIJ data formats if the >>> blocksize is larger than 1". Since my blocksize is exactly 1 it would >>> seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For >>> symmetric format, iscol must equal isrow" >>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >>> fieldsplit.c at >>> >>> /* extract the A01 and A10 matrices */ ilink = jac->head; >>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >>> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >>> MAT_INITIAL_MATRIX, &jac->B)); } >>> >>> This, since my A01 and A10 are not square, seems to explain why iscol is >>> not equal to isrow. >>> From this I gather that it is in general NOT possible to use >>> PCFIELDSPLIT with MATSBAIJ even with block size 1? >>> >>> Kind regards, >>> Carl-Johan >>> >>> >>> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.jolivet at lip6.fr Wed Sep 6 03:36:31 2023 From: pierre.jolivet at lip6.fr (Pierre Jolivet) Date: Wed, 6 Sep 2023 10:36:31 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: References: Message-ID: <9C4D73AC-458E-47D8-9332-740A99DF7C69@lip6.fr> > On 6 Sep 2023, at 10:10 AM, Carl-Johan Thore wrote: > > ? > "Na?ve question, but is your problem really symmetric? > For example, if you do FEM, how do you impose Dirichlet boundary conditions?" > > The structure of the matrix is K = [A B; B^T C] with A and C symmetric, so the problem should be symmetric. Numerically, the maximum relative difference between K and K^T is > on the order of, let's say, 1e-18 which I guess is a good as can be expected? I'm using FEM with (homogeneous) Dirichlet boundary conditions imposed by zeroing rows and columns > for the fixed DOFs and adding ones to the corresponding diagonal elements, i.e. same as what MatZeroRowsColumns does. MatZeroRowsColumns doesn't work for sbaij but we already have an implementation in which rows and columns are cancelled in the element matrices before assembly which is well-tested for the aij-case. We've also verified numerically that aij and sbaij yields the same upper triangular part, and that the RHS is the same in both cases. > > "If you can reproduce this on a smaller example and are at liberty to share the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov, I can have a look." > > Yes, this is reproducible on smaller problems. In case I send you Mat, IS, and RHS, which format is preferable? If the problem is small, it doesn?t make much difference, as long as you tell me the scalar type and whether you are using 32- or 64-bit indices. Thanks, Pierre > Kind regards, > Carl-Johan > > > On Wed, Sep 6, 2023 at 8:21?AM Pierre Jolivet wrote: >> Na?ve question, but is your problem really symmetric? >> For example, if you do FEM, how do you impose Dirichlet boundary conditions? >> If you can reproduce this on a smaller example and are at liberty to share the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov, I can have a look. >> >> Thanks, >> Pierre >> >>> On 6 Sep 2023, at 8:14 AM, Carl-Johan Thore wrote: >>> >>> ? >>> Thanks for this! >>> I now get convergence with sbaij and fieldsplit. However, as can be seen in the attached file, it requires around three times as many outer iterations as with aij to reach the same point (to within rtol). Switching from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct" choice?) helps quite a bit, but still sbaij takes many more iterations. So it seems that your sbaij-implementation works but that I'm doing something wrong when setting up the fieldsplit pc, or that some of the subsolvers doesn't work properly with sbaij. I've tried bjacobi as you had in your logs, but not hypre yet. But anyway, one doesn't expect the matrix format to have this much impact on convergence? Any other suggestions? >>> /Carl-Johan >>> >>> On Mon, Sep 4, 2023 at 9:31?PM Pierre Jolivet wrote: >>>> The branch should now be good to go (https://gitlab.com/petsc/petsc/-/merge_requests/6841). >>>> Sorry, I made a mistake before, hence the error on PetscObjectQuery(). >>>> I?m not sure the code will be covered by the pipeline, but I have tested this on a Raviart?Thomas discretization with PCFIELDSPLIT. >>>> You?ll see in the attached logs that: >>>> 1) the numerics match >>>> 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} block from the global (symmetric) A and we get the A_{10} block cheaply by just using MatCreateHermitianTranspose(), instead of calling another time MatCreateSubMatrix() >>>> Please let me know if you have some time to test the branch and whether it fails or succeeds on your test cases. >>>> >>>> Also, I do not agree with what Hong said. >>>> Sometimes, the assembly of a coefficient can be more expensive than the communication of the said coefficient. >>>> So they are instances where SBAIJ would be more efficient than AIJ even if it would require more communication, it is not a black and white picture. >>>> >>>> Thanks, >>>> Pierre >>>> >>>> >>>>> On 28 Aug 2023, at 12:12 PM, Pierre Jolivet wrote: >>>>> >>>>> >>>>>>> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore wrote: >>>>>>> >>>>>>> I've tried the new files, and with them, PCFIELDSPLIT now gets set up without crashes (but the setup is significantly slower than for MATAIJ) >>>>>> >>>>>> I?ll be back from Japan at the end of this week, my schedule is too packed to get anything done in the meantime. >>>>>> But I?ll let you know when things are working properly (last I checked, I think it was working, but I may have forgotten about a corner case or two). >>>>>> But yes, though one would except things to be faster and less memory intensive with SBAIJ, it?s unfortunately not always the case. >>>>>> >>>>>> Thanks, >>>>>> Pierre >>>>>> >>>>>> Unfortunately I still get errors later in the process: >>>>>> >>>>>> [0]PETSC ERROR: Null argument, when expecting valid pointer >>>>>> [0]PETSC ERROR: Null Pointer: Parameter # 1 >>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d GIT Date: 2023-08-22 20:32:33 -0400 >>>>>> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 --with-cuda --with-cusp --download-scalapack --download-hdf5 --download-zlib --download-mumps --download-parmetis --download-metis --download-ptscotch --download-hypre --download-spai >>>>>> [0]PETSC ERROR: #1 PetscObjectQuery() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 >>>>>> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 >>>>>> [0]PETSC ERROR: #3 MatCreateSubMatrix() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 >>>>>> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 >>>>>> [0]PETSC ERROR: #5 PCSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 >>>>>> [0]PETSC ERROR: #6 KSPSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 >>>>>> >>>>>> The code I'm running here works without any problems for MATAIJ. To run it with MATSBAIJ I've simply used the command-line option >>>>>> -dm_mat_type sbaij >>>>>> >>>>>> >>>>>> Kind regards, >>>>>> Carl-Johan >>>>>> >>>>>> >>>>>>> On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users wrote: >>>>>>> >>>>>>> >>>>>>>>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore wrote: >>>>>>>>> >>>>>>>>> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue.? >>>>>>>>> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices from these blocks, or is there >>>>>>>>> somewhere else in the code that things will go wrong? >>>>>>>> >>>>>>>> Ah, no, you are right, in that case it should work. >>>>>>>> >>>>>>>> For the MATNEST I was thinking to get some savings from the block-symmetry at least >>>>>>>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for them would just be a >>>>>>>> (pretty big) bonus. >>>>>>>> >>>>>>>> ?I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling >>>>>>>> right now so everything gets done more slowly, sorry).? >>>>>>>> Sound great, Thanks again! >>>>>>> >>>>>>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >>>>>>> I need to add a new code path in MatCreateRedundantMatrix() to make sure the resulting Mat is indeed SBAIJ, but that is orthogonal to the PCFIELDSPLIT issue. >>>>>>> The branch should be usable in its current state. >>>>>>> >>>>>>> Thanks, >>>>>>> Pierre >>>>>>> >>>>>>>> >>>>>>>> From: Pierre Jolivet >>>>>>>> Sent: Saturday, August 26, 2023 4:36 PM >>>>>>>> To: Carl-Johan Thore >>>>>>>> Cc: Carl-Johan Thore ; petsc-users at mcs.anl.gov >>>>>>>> Subject: Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore wrote: >>>>>>>> >>>>>>>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get the A01 and A10 blocks in PCFIELDSPLIT. >>>>>>>> I have a branch that fixes this, but I haven?t rebased in a while (and I?m AFK right now), would you want me to rebase and give it a go, or must you stick to a release tarball?" >>>>>>>> >>>>>>>> Ok, would be great if you could look at this! I don't need to stick to any particular branch. >>>>>>>> >>>>>>>> Do you think MATNEST could be an alternative here? >>>>>>>> >>>>>>>> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue. >>>>>>>> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was crashing but I think it was thoroughly fixed in https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >>>>>>>> It is ugly code on top of ugly code, so I didn?t try to get it integrated and just used the branch locally, and then moved to some other stuff. >>>>>>>> I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling right now so everything gets done more slowly, sorry). >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Pierre >>>>>>>> >>>>>>>> >>>>>>>> My matrix is >>>>>>>> [A00 A01; >>>>>>>> A01^t A11] >>>>>>>> so perhaps with MATNEST I can make use of the block-symmetry at least, and then use MATSBAIJ for >>>>>>>> A00 and A11 if it's possible to combine matrix types which the manual seems to imply. >>>>>>>> >>>>>>>> Kind regards >>>>>>>> Carl-Johan >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore wrote: >>>>>>>> ? >>>>>>>> Hi, >>>>>>>> >>>>>>>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >>>>>>>> According to the manual "[t]he fieldsplit preconditioner cannot >>>>>>>> currently be used with the MATBAIJ or MATSBAIJ data formats if the >>>>>>>> blocksize is larger than 1". Since my blocksize is exactly 1 it would seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For symmetric format, iscol must equal isrow" >>>>>>>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >>>>>>>> fieldsplit.c at >>>>>>>> >>>>>>>> /* extract the A01 and A10 matrices */ ilink = jac->head; >>>>>>>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >>>>>>>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >>>>>>>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >>>>>>>> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >>>>>>>> MAT_INITIAL_MATRIX, &jac->B)); } >>>>>>>> >>>>>>>> This, since my A01 and A10 are not square, seems to explain why iscol is not equal to isrow. >>>>>>>> From this I gather that it is in general NOT possible to use >>>>>>>> PCFIELDSPLIT with MATSBAIJ even with block size 1? >>>>>>>> >>>>>>>> Kind regards, >>>>>>>> Carl-Johan >>>>>>> >>>>> >>>> >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.jolivet at lip6.fr Wed Sep 6 07:16:16 2023 From: pierre.jolivet at lip6.fr (Pierre Jolivet) Date: Wed, 6 Sep 2023 14:16:16 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: References: <8B433012-D804-4865-9C77-C074BEB68DE9@lip6.fr> Message-ID: (switching back to petsc-users with the previous attachment striped) I?m assuming your problem is kind of ill-posed? PCICC and PCILU have different default parameters, and thus can yield different convergence curves, especially for difficult problems. When switching from AIJ to SBAIJ, ILU will switch to ICC. If I switch to something more ?robust? (PCCHOLESKY from MUMPS), then I get the same convergence (up to machine precision). I think this highlight there is no issue with the new PCFIELDSPLIT/MatCreateSubMatri[x,ces]() code, but merely that you need to be a bit careful with the inner solvers. Thanks, Pierre ?? > On 6 Sep 2023, at 11:27 AM, Carl-Johan Thore wrote: > > Ok, here's data from a small instance of my problem. It's in Matlab-format which is what I usually use, but let me know if you want something else. > I can send smaller versions of the problem if you prefer that (really small versions will take a bit of time to code so that one doesn't just get the solution > 0 everywhere). > > One IS, ISO, is included because in my code PETSc computes the other IS as the complement. Also included is the output from PETSc for aij and > sbaij, and a Matlab-script to check the data. > > Kind regards, > Carl-Johan > > On Wed, Sep 6, 2023 at 10:10?AM Carl-Johan Thore > wrote: >> "Na?ve question, but is your problem really symmetric? >> For example, if you do FEM, how do you impose Dirichlet boundary conditions?" >> >> The structure of the matrix is K = [A B; B^T C] with A and C symmetric, so the problem should be symmetric. Numerically, the maximum relative difference between K and K^T is >> on the order of, let's say, 1e-18 which I guess is a good as can be expected? I'm using FEM with (homogeneous) Dirichlet boundary conditions imposed by zeroing rows and columns >> for the fixed DOFs and adding ones to the corresponding diagonal elements, i.e. same as what MatZeroRowsColumns does. MatZeroRowsColumns doesn't work for sbaij but we already have an implementation in which rows and columns are cancelled in the element matrices before assembly which is well-tested for the aij-case. We've also verified numerically that aij and sbaij yields the same upper triangular part, and that the RHS is the same in both cases. >> >> "If you can reproduce this on a smaller example and are at liberty to share the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov , I can have a look." >> >> Yes, this is reproducible on smaller problems. In case I send you Mat, IS, and RHS, which format is preferable? >> >> Kind regards, >> Carl-Johan >> >> >> On Wed, Sep 6, 2023 at 8:21?AM Pierre Jolivet > wrote: >>> Na?ve question, but is your problem really symmetric? >>> For example, if you do FEM, how do you impose Dirichlet boundary conditions? >>> If you can reproduce this on a smaller example and are at liberty to share the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov , I can have a look. >>> >>> Thanks, >>> Pierre >>> >>>> On 6 Sep 2023, at 8:14 AM, Carl-Johan Thore > wrote: >>>> >>>> ? >>>> Thanks for this! >>>> I now get convergence with sbaij and fieldsplit. However, as can be seen in the attached file, it requires around three times as many outer iterations as with aij to reach the same point (to within rtol). Switching from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct" choice?) helps quite a bit, but still sbaij takes many more iterations. So it seems that your sbaij-implementation works but that I'm doing something wrong when setting up the fieldsplit pc, or that some of the subsolvers doesn't work properly with sbaij. I've tried bjacobi as you had in your logs, but not hypre yet. But anyway, one doesn't expect the matrix format to have this much impact on convergence? Any other suggestions? >>>> /Carl-Johan >>>> >>>> On Mon, Sep 4, 2023 at 9:31?PM Pierre Jolivet > wrote: >>>>> The branch should now be good to go (https://gitlab.com/petsc/petsc/-/merge_requests/6841). >>>>> Sorry, I made a mistake before, hence the error on PetscObjectQuery(). >>>>> I?m not sure the code will be covered by the pipeline, but I have tested this on a Raviart?Thomas discretization with PCFIELDSPLIT. >>>>> You?ll see in the attached logs that: >>>>> 1) the numerics match >>>>> 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} block from the global (symmetric) A and we get the A_{10} block cheaply by just using MatCreateHermitianTranspose(), instead of calling another time MatCreateSubMatrix() >>>>> Please let me know if you have some time to test the branch and whether it fails or succeeds on your test cases. >>>>> >>>>> Also, I do not agree with what Hong said. >>>>> Sometimes, the assembly of a coefficient can be more expensive than the communication of the said coefficient. >>>>> So they are instances where SBAIJ would be more efficient than AIJ even if it would require more communication, it is not a black and white picture. >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>> >>>>>> On 28 Aug 2023, at 12:12 PM, Pierre Jolivet > wrote: >>>>>> >>>>>> >>>>>>> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore > wrote: >>>>>>> >>>>>>> I've tried the new files, and with them, PCFIELDSPLIT now gets set up without crashes (but the setup is significantly slower than for MATAIJ) >>>>>> >>>>>> I?ll be back from Japan at the end of this week, my schedule is too packed to get anything done in the meantime. >>>>>> But I?ll let you know when things are working properly (last I checked, I think it was working, but I may have forgotten about a corner case or two). >>>>>> But yes, though one would except things to be faster and less memory intensive with SBAIJ, it?s unfortunately not always the case. >>>>>> >>>>>> Thanks, >>>>>> Pierre >>>>>> >>>>>>> Unfortunately I still get errors later in the process: >>>>>>> >>>>>>> [0]PETSC ERROR: Null argument, when expecting valid pointer >>>>>>> [0]PETSC ERROR: Null Pointer: Parameter # 1 >>>>>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d GIT Date: 2023-08-22 20:32:33 -0400 >>>>>>> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 --with-cuda --with-cusp --download-scalapack --download-hdf5 --download-zlib --download-mumps --download-parmetis --download-metis --download-ptscotch --download-hypre --download-spai >>>>>>> [0]PETSC ERROR: #1 PetscObjectQuery() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 >>>>>>> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 >>>>>>> [0]PETSC ERROR: #3 MatCreateSubMatrix() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 >>>>>>> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 >>>>>>> [0]PETSC ERROR: #5 PCSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 >>>>>>> [0]PETSC ERROR: #6 KSPSetUp() at /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 >>>>>>> >>>>>>> The code I'm running here works without any problems for MATAIJ. To run it with MATSBAIJ I've simply used the command-line option >>>>>>> -dm_mat_type sbaij >>>>>>> >>>>>>> >>>>>>> Kind regards, >>>>>>> Carl-Johan >>>>>>> >>>>>>> >>>>>>> On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users > wrote: >>>>>>>> >>>>>>>> >>>>>>>>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore > wrote: >>>>>>>>> >>>>>>>>> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue.? >>>>>>>>> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices from these blocks, or is there >>>>>>>>> somewhere else in the code that things will go wrong? >>>>>>>> >>>>>>>> Ah, no, you are right, in that case it should work. >>>>>>>> >>>>>>>>> For the MATNEST I was thinking to get some savings from the block-symmetry at least >>>>>>>>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for them would just be a >>>>>>>>> (pretty big) bonus. >>>>>>>>> >>>>>>>>> ?I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling >>>>>>>>> right now so everything gets done more slowly, sorry).? >>>>>>>>> Sound great, Thanks again! >>>>>>>> >>>>>>>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >>>>>>>> I need to add a new code path in MatCreateRedundantMatrix() to make sure the resulting Mat is indeed SBAIJ, but that is orthogonal to the PCFIELDSPLIT issue. >>>>>>>> The branch should be usable in its current state. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Pierre >>>>>>>> >>>>>>>>> >>>>>>>>> From: Pierre Jolivet > >>>>>>>>> Sent: Saturday, August 26, 2023 4:36 PM >>>>>>>>> To: Carl-Johan Thore > >>>>>>>>> Cc: Carl-Johan Thore >; petsc-users at mcs.anl.gov >>>>>>>>> Subject: Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore > wrote: >>>>>>>>> >>>>>>>>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get the A01 and A10 blocks in PCFIELDSPLIT. >>>>>>>>> I have a branch that fixes this, but I haven?t rebased in a while (and I?m AFK right now), would you want me to rebase and give it a go, or must you stick to a release tarball?" >>>>>>>>> >>>>>>>>> Ok, would be great if you could look at this! I don't need to stick to any particular branch. >>>>>>>>> >>>>>>>>> Do you think MATNEST could be an alternative here? >>>>>>>>> >>>>>>>>> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up with the same issue. >>>>>>>>> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was crashing but I think it was thoroughly fixed in https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >>>>>>>>> It is ugly code on top of ugly code, so I didn?t try to get it integrated and just used the branch locally, and then moved to some other stuff. >>>>>>>>> I?ll rebase on top of main and try to get it integrated if it could be useful to you (but I?m traveling right now so everything gets done more slowly, sorry). >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Pierre >>>>>>>>> >>>>>>>>> >>>>>>>>> My matrix is >>>>>>>>> [A00 A01; >>>>>>>>> A01^t A11] >>>>>>>>> so perhaps with MATNEST I can make use of the block-symmetry at least, and then use MATSBAIJ for >>>>>>>>> A00 and A11 if it's possible to combine matrix types which the manual seems to imply. >>>>>>>>> >>>>>>>>> Kind regards >>>>>>>>> Carl-Johan >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore > wrote: >>>>>>>>> ? >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >>>>>>>>> According to the manual "[t]he fieldsplit preconditioner cannot >>>>>>>>> currently be used with the MATBAIJ or MATSBAIJ data formats if the >>>>>>>>> blocksize is larger than 1". Since my blocksize is exactly 1 it would seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For symmetric format, iscol must equal isrow" >>>>>>>>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >>>>>>>>> fieldsplit.c at >>>>>>>>> >>>>>>>>> /* extract the A01 and A10 matrices */ ilink = jac->head; >>>>>>>>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >>>>>>>>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >>>>>>>>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >>>>>>>>> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >>>>>>>>> MAT_INITIAL_MATRIX, &jac->B)); } >>>>>>>>> >>>>>>>>> This, since my A01 and A10 are not square, seems to explain why iscol is not equal to isrow. >>>>>>>>> From this I gather that it is in general NOT possible to use >>>>>>>>> PCFIELDSPLIT with MATSBAIJ even with block size 1? >>>>>>>>> >>>>>>>>> Kind regards, >>>>>>>>> Carl-Johan >>>>>>>> >>>>>> >>>>> >>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: asm_sbaij.log Type: application/octet-stream Size: 23970 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: asm_aij.log Type: application/octet-stream Size: 24238 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From carljohanthore at gmail.com Wed Sep 6 10:00:21 2023 From: carljohanthore at gmail.com (Carl-Johan Thore) Date: Wed, 6 Sep 2023 17:00:21 +0200 Subject: [petsc-users] PCFIELDSPLIT with MATSBAIJ In-Reply-To: References: <8B433012-D804-4865-9C77-C074BEB68DE9@lip6.fr> Message-ID: Great, that's as I suspected then. The matrix comes from density-based topology optimization using an FE-model for Stokes-Brinkman with pressure jump stabilization, so it's a difficult problem I would say. I'll experiment with the inner solvers and see what works. Thanks again for the help, Carl-Johan On Wed, Sep 6, 2023 at 2:16?PM Pierre Jolivet wrote: > (switching back to petsc-users with the previous attachment striped) > I?m assuming your problem is kind of ill-posed? > PCICC and PCILU have different default parameters, and thus can yield > different convergence curves, especially for difficult problems. > When switching from AIJ to SBAIJ, ILU will switch to ICC. > If I switch to something more ?robust? (PCCHOLESKY from MUMPS), then I get > the same convergence (up to machine precision). > I think this highlight there is no issue with the new > PCFIELDSPLIT/MatCreateSubMatri[x,ces]() code, but merely that you need to > be a bit careful with the inner solvers. > > Thanks, > Pierre > > > > On 6 Sep 2023, at 11:27 AM, Carl-Johan Thore > wrote: > > Ok, here's data from a small instance of my problem. It's in Matlab-format > which is what I usually use, but let me know if you want something else. > I can send smaller versions of the problem if you prefer that (really > small versions will take a bit of time to code so that one doesn't just get > the solution > 0 everywhere). > > One IS, ISO, is included because in my code PETSc computes the other IS as > the complement. Also included is the output from PETSc for aij and > sbaij, and a Matlab-script to check the data. > > Kind regards, > Carl-Johan > > On Wed, Sep 6, 2023 at 10:10?AM Carl-Johan Thore > wrote: > >> "Na?ve question, but is your problem really symmetric? >> For example, if you do FEM, how do you impose Dirichlet boundary >> conditions?" >> >> The structure of the matrix is K = [A B; B^T C] with A and C symmetric, >> so the problem should be symmetric. Numerically, the maximum relative >> difference between K and K^T is >> on the order of, let's say, 1e-18 which I guess is a good as can be >> expected? I'm using FEM with (homogeneous) Dirichlet boundary conditions >> imposed by zeroing rows and columns >> for the fixed DOFs and adding ones to the corresponding diagonal >> elements, i.e. same as what MatZeroRowsColumns does. MatZeroRowsColumns >> doesn't work for sbaij but we already have an implementation in which rows >> and columns are cancelled in the element matrices before assembly which is >> well-tested for the aij-case. We've also verified numerically that aij and >> sbaij yields the same upper triangular part, and that the RHS is the same >> in both cases. >> >> "If you can reproduce this on a smaller example and are at liberty to >> share the Mat, IS, and RHS Vec, feel free to send them at >> petsc-maint at mcs.anl.gov, I can have a look." >> >> Yes, this is reproducible on smaller problems. In case I send you Mat, >> IS, and RHS, which format is preferable? >> >> Kind regards, >> Carl-Johan >> >> >> On Wed, Sep 6, 2023 at 8:21?AM Pierre Jolivet >> wrote: >> >>> Na?ve question, but is your problem really symmetric? >>> For example, if you do FEM, how do you impose Dirichlet boundary >>> conditions? >>> If you can reproduce this on a smaller example and are at liberty to >>> share the Mat, IS, and RHS Vec, feel free to send them at >>> petsc-maint at mcs.anl.gov, I can have a look. >>> >>> Thanks, >>> Pierre >>> >>> On 6 Sep 2023, at 8:14 AM, Carl-Johan Thore >>> wrote: >>> >>> ? >>> Thanks for this! >>> I now get convergence with sbaij and fieldsplit. However, as can be seen >>> in the attached file, it requires around three times as many outer >>> iterations as with aij to reach the same point (to within rtol). Switching >>> from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct" >>> choice?) helps quite a bit, but still sbaij takes many more iterations. So >>> it seems that your sbaij-implementation works but that I'm doing something >>> wrong when setting up the fieldsplit pc, or that some of the subsolvers >>> doesn't work properly with sbaij. I've tried bjacobi as you had in your >>> logs, but not hypre yet. But anyway, one doesn't expect the matrix format >>> to have this much impact on convergence? Any other suggestions? >>> /Carl-Johan >>> >>> On Mon, Sep 4, 2023 at 9:31?PM Pierre Jolivet >>> wrote: >>> >>>> The branch should now be good to go ( >>>> https://gitlab.com/petsc/petsc/-/merge_requests/6841). >>>> Sorry, I made a mistake before, hence the error on PetscObjectQuery(). >>>> I?m not sure the code will be covered by the pipeline, but I have >>>> tested this on a Raviart?Thomas discretization with PCFIELDSPLIT. >>>> You?ll see in the attached logs that: >>>> 1) the numerics match >>>> 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01} >>>> block from the global (symmetric) A and we get the A_{10} block cheaply by >>>> just using MatCreateHermitianTranspose(), instead of calling another time >>>> MatCreateSubMatrix() >>>> Please let me know if you have some time to test the branch and whether >>>> it fails or succeeds on your test cases. >>>> >>>> Also, I do not agree with what Hong said. >>>> Sometimes, the assembly of a coefficient can be more expensive than the >>>> communication of the said coefficient. >>>> So they are instances where SBAIJ would be more efficient than AIJ even >>>> if it would require more communication, it is not a black and white picture. >>>> >>>> Thanks, >>>> Pierre >>>> >>>> >>>> On 28 Aug 2023, at 12:12 PM, Pierre Jolivet >>>> wrote: >>>> >>>> >>>> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore >>>> wrote: >>>> >>>> I've tried the new files, and with them, PCFIELDSPLIT now gets set up >>>> without crashes (but the setup is significantly slower than for MATAIJ) >>>> >>>> >>>> I?ll be back from Japan at the end of this week, my schedule is too >>>> packed to get anything done in the meantime. >>>> But I?ll let you know when things are working properly (last I checked, >>>> I think it was working, but I may have forgotten about a corner case or >>>> two). >>>> But yes, though one would except things to be faster and less memory >>>> intensive with SBAIJ, it?s unfortunately not always the case. >>>> >>>> Thanks, >>>> Pierre >>>> >>>> Unfortunately I still get errors later in the process: >>>> >>>> [0]PETSC ERROR: Null argument, when expecting valid pointer >>>> [0]PETSC ERROR: Null Pointer: Parameter # 1 >>>> [0]PETSC ERROR: Petsc Development GIT revision: >>>> v3.19.4-1023-ga6d78fcba1d GIT Date: 2023-08-22 20:32:33 -0400 >>>> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0 >>>> --with-cuda --with-cusp --download-scalapack --download-hdf5 >>>> --download-zlib --download-mumps --download-parmetis --download-metis >>>> --download-ptscotch --download-hypre --download-spai >>>> [0]PETSC ERROR: #1 PetscObjectQuery() at >>>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742 >>>> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at >>>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414 >>>> [0]PETSC ERROR: #3 MatCreateSubMatrix() at >>>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476 >>>> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at >>>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826 >>>> [0]PETSC ERROR: #5 PCSetUp() at >>>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069 >>>> [0]PETSC ERROR: #6 KSPSetUp() at >>>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415 >>>> >>>> The code I'm running here works without any problems for MATAIJ. To run >>>> it with MATSBAIJ I've simply used the command-line option >>>> -dm_mat_type sbaij >>>> >>>> >>>> Kind regards, >>>> Carl-Johan >>>> >>>> >>>> On Sat, Aug 26, 2023 at 5:21?PM Pierre Jolivet via petsc-users < >>>> petsc-users at mcs.anl.gov> wrote: >>>> >>>>> >>>>> >>>>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore >>>>> wrote: >>>>> >>>>> ?Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up >>>>> with the same issue.? >>>>> I?m not sure I follow. Does PCFIELDSPLIT extract further submatrices >>>>> from these blocks, or is there >>>>> somewhere else in the code that things will go wrong? >>>>> >>>>> >>>>> Ah, no, you are right, in that case it should work. >>>>> >>>>> For the MATNEST I was thinking to get some savings from the >>>>> block-symmetry at least >>>>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for >>>>> them would just be a >>>>> (pretty big) bonus. >>>>> >>>>> ?I?ll rebase on top of main and try to get it integrated if it could >>>>> be useful to you (but I?m traveling >>>>> right now so everything gets done more slowly, sorry).? >>>>> Sound great, Thanks again! >>>>> >>>>> >>>>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841. >>>>> I need to add a new code path in MatCreateRedundantMatrix() to make >>>>> sure the resulting Mat is indeed SBAIJ, but that is orthogonal to the >>>>> PCFIELDSPLIT issue. >>>>> The branch should be usable in its current state. >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>> >>>>> *From:* Pierre Jolivet >>>>> *Sent:* Saturday, August 26, 2023 4:36 PM >>>>> *To:* Carl-Johan Thore >>>>> *Cc:* Carl-Johan Thore ; >>>>> petsc-users at mcs.anl.gov >>>>> *Subject:* Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ >>>>> >>>>> >>>>> >>>>> >>>>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore >>>>> wrote: >>>>> >>>>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be >>>>> used to retrieve rectangular blocks in MatCreateSubMatrices, thus you >>>>> cannot get the A01 and A10 blocks in PCFIELDSPLIT. >>>>> I have a branch that fixes this, but I haven?t rebased in a while (and >>>>> I?m AFK right now), would you want me to rebase and give it a go, or must >>>>> you stick to a release tarball?" >>>>> >>>>> Ok, would be great if you could look at this! I don't need to stick to >>>>> any particular branch. >>>>> >>>>> Do you think MATNEST could be an alternative here? >>>>> >>>>> >>>>> Well, your A00 and A11 will possibly be SBAIJ also, so you?ll end up >>>>> with the same issue. >>>>> I?m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was >>>>> crashing but I think it was thoroughly fixed in >>>>> https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/ >>>>> It is ugly code on top of ugly code, so I didn?t try to get it >>>>> integrated and just used the branch locally, and then moved to some other >>>>> stuff. >>>>> I?ll rebase on top of main and try to get it integrated if it could be >>>>> useful to you (but I?m traveling right now so everything gets done more >>>>> slowly, sorry). >>>>> >>>>> Thanks, >>>>> Pierre >>>>> >>>>> >>>>> My matrix is >>>>> [A00 A01; >>>>> A01^t A11] >>>>> so perhaps with MATNEST I can make use of the block-symmetry at least, >>>>> and then use MATSBAIJ for >>>>> A00 and A11 if it's possible to combine matrix types which the manual >>>>> seems to imply. >>>>> >>>>> Kind regards >>>>> Carl-Johan >>>>> >>>>> >>>>> >>>>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore < >>>>> carljohanthore at gmail.com> wrote: >>>>> ? >>>>> Hi, >>>>> >>>>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4. >>>>> According to the manual "[t]he fieldsplit preconditioner cannot >>>>> currently be used with the MATBAIJ or MATSBAIJ data formats if the >>>>> blocksize is larger than 1". Since my blocksize is exactly 1 it would >>>>> seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For >>>>> symmetric format, iscol must equal isrow" >>>>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in >>>>> fieldsplit.c at >>>>> >>>>> /* extract the A01 and A10 matrices */ ilink = jac->head; >>>>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if >>>>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat, >>>>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else { >>>>> PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis, >>>>> MAT_INITIAL_MATRIX, &jac->B)); } >>>>> >>>>> This, since my A01 and A10 are not square, seems to explain why iscol >>>>> is not equal to isrow. >>>>> From this I gather that it is in general NOT possible to use >>>>> PCFIELDSPLIT with MATSBAIJ even with block size 1? >>>>> >>>>> Kind regards, >>>>> Carl-Johan >>>>> >>>>> >>>>> >>>> >>>> >>> >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Wed Sep 6 13:17:30 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 6 Sep 2023 14:17:30 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Ok, so the C++ binding for Matlab engine is working on your machine. PETSc uses the C binding which links against different libraries but, one would think the C binding would work for sure if the C++ binding works. Can you try a Matlab Engine C example provided by Matlab? > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 wrote: > > Hi Amneet, > > I repeated the same procedure again and this time it is working. > $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp -lMatlabDataArray -lMatlabEngine > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > $export LD_LIBRARY_PATH > $./a.out > Square root of -2 is 0 + 1.41421i > Square root of 2 is 1.41421 + 0i > Square root of 6 is 2.44949 + 0i > Square root of 8 is 2.82843 + 0i > I don't know how it is working this time? > > Thanks and regards > Srinivas > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 > wrote: >> Hi Amneet, >> I tried the following example to run a matlab engine. >> >> #include "MatlabDataArray.hpp" >> #include "MatlabEngine.hpp" >> #include >> void callSQRT() { >> >> using namespace matlab::engine; >> >> // Start MATLAB engine synchronously >> std::unique_ptr matlabPtr = startMATLAB(); >> >> //Create MATLAB data array factory >> matlab::data::ArrayFactory factory; >> >> // Define a four-element typed array >> matlab::data::TypedArray const argArray = >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >> >> // Call MATLAB sqrt function on the data array >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", argArray); >> >> // Display results >> for (int i = 0; i < results.getNumberOfElements(); i++) { >> double a = argArray[i]; >> std::complex v = results[i]; >> double realPart = v.real(); >> double imgPart = v.imag(); >> std::cout << "Square root of " << a << " is " << >> realPart << " + " << imgPart << "i" << std::endl; >> } >> } >> >> int main() { >> callSQRT(); >> return 0; >> } >> >> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> $export LD_LIBRARY_PATH >> $./a.out >> Starting >> Error: The import statement 'import matlab.internal.engine.input' cannot be found or cannot be imported. Imported names must end with '.*' or be fully qualified. >> >> terminate called after throwing an instance of 'matlab::engine::EngineException' >> what(): MATLAB process cannot be created. >> Aborted (core dumped) >> >> I got the above error for Matlab R2020b. Please help me to sort out this. >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: >>> BTW, what Barry is suggesting is the following: >>> >>> Compile a sample code with a command line this: >>> >>> g++ -std=c++11 -I matlabroot/extern/include/ -L matlabroot/extern/bin/glnxa64/ >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>> >>> This command is provided here: >>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>> >>> A sample MATLAB code is here: >>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>> >>> (You can just pick a few lines of code from here to create a barebone example) >>> >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: >>>> Srinivas --- Do you have a different version of MATLAB that you can install? If your organization has a MATLAB license, you can install recent versions of MATLAB from mathworks.com >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > wrote: >>>>> >>>>> Ok, I have no suggestions. It seems to be more an issue with the Matlab than PETSc. You could find a pure Matlab example of using the engine (in the Matlab documentation) and try it to see if it works. >>>>> >>>>> Barry >>>>> >>>>> >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 > wrote: >>>>>> >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>> I got the same errors for petsc 3.17.5 >>>>>> >>>>>> make all >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> ========================================= >>>>>> ========================================= >>>>>> Now to check if the libraries are working do: >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>> >>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>> # [0]PETSC ERROR: Error in external library >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 >>>>>> # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> # -------------------------------------------------------------------------- >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> # with errorcode 85. >>>>>> # >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> # You may or may not see output from other processes, depending on >>>>>> # exactly when Open MPI kills them. >>>>>> # -------------------------------------------------------------------------- >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> >>>>>> >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> # >>>>>> # To rerun failed tests: >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: >>>>>>> >>>>>>> The error is occuring during >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. >>>>>>> >>>>>>> You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> replace it with >>>>>>> >>>>>>> e->ep = engOpen(""); >>>>>>> >>>>>>> Now in the PETSc directory do make all (it should recompile one file) and then run the >>>>>>> >>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>> >>>>>>> again >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>> >>>>>>>> Hi Amneeth, >>>>>>>> >>>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>>> >>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> The version of PETSc you are using is out-of-date, we recommend updating to the new release >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>>> https://petsc.org/release/download/ >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> ============================================================================================= >>>>>>>> Configuring PETSc to compile on your system >>>>>>>> ============================================================================================= >>>>>>>> Compilers: >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> Linkers: >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>> BlasLapack: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads >>>>>>>> uses 8 byte integers >>>>>>>> MPI: >>>>>>>> Version: 3 >>>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>>> Implementation: openmpi >>>>>>>> OMPI_VERSION: 4.0.3 >>>>>>>> pthread: >>>>>>>> cmake: >>>>>>>> Version: 3.16.3 >>>>>>>> /usr/bin/cmake >>>>>>>> regex: >>>>>>>> Matlab: >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> /usr/local/MATLAB/R2020b >>>>>>>> MatlabEngine: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>>> Language used to compile PETSc: C >>>>>>>> PETSc: >>>>>>>> PETSC_ARCH: linux-opt >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>> Prefix: >>>>>>>> Scalar type: real >>>>>>>> Precision: double >>>>>>>> Support for __float128 >>>>>>>> Integer size: 4 bytes >>>>>>>> Single library: yes >>>>>>>> Shared libraries: yes >>>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>>> Using GNU make: /usr/bin/make >>>>>>>> xxx=========================================================================xxx >>>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all >>>>>>>> xxx=========================================================================xxx >>>>>>>> >>>>>>>> $make >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> ========================================= >>>>>>>> ========================================= >>>>>>>> Now to check if the libraries are working do: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>>> >>>>>>>> $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> # -------------------------------------------------------------------------- >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>> # with errorcode 85. >>>>>>>> # >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>> # exactly when Open MPI kills them. >>>>>>>> # -------------------------------------------------------------------------- >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>> >>>>>>>> >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> # >>>>>>>> # To rerun failed tests: >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> >>>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>>> >>>>>>>> How to check error info and proceed further? >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? >>>>>>>>> >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>>>> Sorry for missing that. >>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>> >>>>>>>>>> < M A T L A B (R) > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>>> November 23, 2020 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> To get started, type doc. >>>>>>>>>> For product information, visit www.mathworks.com . >>>>>>>>>> >>>>>>>>>> Thanks and regards >>>>>>>>>> Srinivas >>>>>>>>>> >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: >>>>>>>>>>> You are missing one more step: >>>>>>>>>>> >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>> >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>>> >>>>>>>>>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>>> >>>>>>>>>>> Satish >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>>>>>> >>>>>>>>>>> > Hi Sathish, >>>>>>>>>>> > >>>>>>>>>>> > I tried the following procedure >>>>>>>>>>> > >>>>>>>>>>> > *$make * >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > ========================================= >>>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>> > >>>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>>>>>>>> > query=requires >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > ------------------------------------------------------------------------ >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>>>>>>>>> > probably memory access out of range >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS >>>>>>>>>>> > X to find memory corruption errors >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, >>>>>>>>>>> > and run >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > CC >>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > CLINKER >>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > TEST >>>>>>>>>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>>>>>>>>>> > # Running problem 5 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > # with errorcode 126076. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed >>>>>>>>>>> > so no diff >>>>>>>>>>> > >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # Summary >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>>> > # >>>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>>> > # >>>>>>>>>>> > # To rerun failed tests: >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > # >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec >>>>>>>>>>> > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > Running problem 5 >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > -------------------------------------------------------------------------- >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > with errorcode 126076. >>>>>>>>>>> > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>>> > >>>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>>> > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: >>>>>>>>>>> > >>>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>>> > > >>>>>>>>>>> > > cd $HOME >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>>> > > >>>>>>>>>> > > manually with make> >>>>>>>>>>> > > >>>>>>>>>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles >>>>>>>>>>> > > >>>>>>>>>>> > > Satish >>>>>>>>>>> > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>>> > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have >>>>>>>>>>> > > any >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please help me how to >>>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we point to >>>>>>>>>>> > > this >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those >>>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>>> > > > is why I suggested just using a different matrix, or running a problem >>>>>>>>>>> > > you >>>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>>> > > > >>>>>>>>>>> > > > Thanks, >>>>>>>>>>> > > > >>>>>>>>>>> > > > Matt >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Thanks and regards >>>>>>>>>>> > > > > Srinivas. >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > petsc-users < >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you are giving me >>>>>>>>>>> > > to >>>>>>>>>>> > > > >>> sort this out. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed to build >>>>>>>>>>> > > Petsc >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> It appears you do not have >>>>>>>>>>> > > valgrind >>>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>>>>>>> > > > >>> Or install >>>>>>>>>>> > > valgrind-devel or >>>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> Compilers: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -fPIC >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> Linkers: >>>>>>>>>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>> > > > >>> make: >>>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>> > >

to >>>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>>> > > > >>> MPI: >>>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>>> > > --oversubscribe >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>>> > > > >>> pthread: >>>>>>>>>>> > > > >>> cmake: >>>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>>> > > > >>> regex: >>>>>>>>>>> > > > >>> Matlab: >>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>> Library: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>>>>>> > > -lut >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>>> > > > >>> PETSc: >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>>> > > > >>> Precision: double >>>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make* >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> ========================================= >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>> =============================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Thanks, >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Matt >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>> > > Sun >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > > > >>> CC >>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>> CLINKER >>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>> TEST >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: 124 >>>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # Summary >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / >>>>>>>>>>> > > 0.02 sec >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>> > > -Wwrite-strings >>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>>>>>> > > -lmx >>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>>>>> > > -lquadmath >>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please find the >>>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>>> > > > >>> Srinivas >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional info - and debug >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Satish >>>>>>>>>>> > > > >>>> ---------- >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng >>>>>>>>>>> > > -lmex >>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort >>>>>>>>>>> > > -lmpi >>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>>> > > processors >>>>>>>>>>> > > > >>>> = 1 >>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> 5 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you >>>>>>>>>>> > > - on >>>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com . >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>>>>>>>>>> > > thread >>>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>>>> > > corresponding >>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>>>>> > > > >>>> > main >>>>>>>>>>> > > > >>>> > release >>>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>>>>>> > > matlab/R2021a >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>>>>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>> > > > >>>> > make: >>>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>> > >

>>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>>> > > > >>>> > regex: >>>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: >>>>>>>>>>> > > > >>>> 1 >>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>> > > Command >>>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 >>>>>>>>>>> > > sec >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>>> > > 7.54 >>>>>>>>>>> > > > >>>> sec >>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>>>>>>>>> > > > >>>> running make >>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error message. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>>> > > -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> > > -------send >>>>>>>>>>> > > > >>>> entire >>>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> > > > >>>> processes. >>>>>>>>>>> > > > >>>> > > # You may or may not see output from other processes, depending >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > Thanks >>>>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > wrote: >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > > >>>> petsc-users < >>>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>>>>>>>>> > > > >>>> here]. >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > petsc-users >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>>>> > > balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts >>>>>>>>>>> > > across >>>>>>>>>>> > > > >>>> packages] >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict >>>>>>>>>>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>>>>>>>>> > > > >>>> matlab - to >>>>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > > >>>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>>>>>>>>> > > > >>>> working. It is >>>>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>>>>>>>>> > > > >>>> libmesh and >>>>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>>>>>>>>> > > > >>>> linking >>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>>>> > > > >>>> > > >>> that >>>>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>>>>>>>>> > > specified. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>>>>>>>>> > > > >>>> PETSc and >>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>>>>>>>>> > > geometries >>>>>>>>>>> > > > >>>> it is >>>>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>>>>>>>>>> > > things >>>>>>>>>>> > > > >>>> and ended >>>>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>>>>>>>>> > > > >>>> research work. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for >>>>>>>>>>> > > the >>>>>>>>>>> > > > >>>> WEC >>>>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>>>>>>>>> > > > >>>> Matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>>>>>>>>> > > > >>>> libMesh? >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > > > > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>>>>>>>>> > > > >>>> occurrences >>>>>>>>>>> > > > >>>> > > >>> of >>>>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make >>>>>>>>>>> > > test" >>>>>>>>>>> > > > >>>> got the >>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>> > > Message >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> for >>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>> > > Aug >>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>> > > linux-debug >>>>>>>>>>> > > > >>>> named >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>> > > line >>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>> > > > >>>> Message >>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>> > > kill >>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>> > > processes, >>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>> > > Message >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> for >>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>> > > Aug >>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>> > > linux-opt >>>>>>>>>>> > > > >>>> named >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>> > > line >>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>> > > > >>>> Message >>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>> > > kill >>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>> > > processes, >>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>>>>>>>>> > > version. I >>>>>>>>>>> > > > >>>> am >>>>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>>>>>>>>> > > > >>>> petsc >>>>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > -leng >>>>>>>>>>> > > > >>>> -lmex >>>>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are >>>>>>>>>>> > > seeing: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>>>>>>>>> > > > >>>> preset here. >>>>>>>>>>> > > > >>>> > > >>> This >>>>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>>>>>>>>> > > -licui18n >>>>>>>>>>> > > > >>>> -licuuc" >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>>>> > > via >>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>>>>> > > successfully. >>>>>>>>>>> > > > >>>> But >>>>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>>>>>>>> > > friendly to >>>>>>>>>>> > > > >>>> mailing >>>>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or >>>>>>>>>>> > > 3.19?] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>>>>>>> > > 20PHD0548 >>>>>>>>>>> > > > >>>> via >>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>>>>>>>>>> > > building >>>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the >>>>>>>>>>> > > needful. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>>>>>>>>> > > building >>>>>>>>>>> > > > >>>> of >>>>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>>>>>>>>> > > > >>>> Balay < >>>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>>>>>>>>> > > > >>>> working on >>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the >>>>>>>>>>> > > PETSc, >>>>>>>>>>> > > > >>>> using the >>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>>>>>>>>> > > > >>>> status >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished >>>>>>>>>>> > > jobs.... >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>>>>>>>>>> > > > >>>> Institute of >>>>>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain legally >>>>>>>>>>> > > > >>>> protected >>>>>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>>>>>>>>>> > > > >>>> Technology?. >>>>>>>>>>> > > > >>>> > > >>> If >>>>>>>>>>> > > > >>>> > > >>> > > you are >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should not >>>>>>>>>>> > > > >>>> disseminate, >>>>>>>>>>> > > > >>>> > > >>> distribute >>>>>>>>>>> > > > >>>> > > >>> > > or copy >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately >>>>>>>>>>> > > > >>>> and destroy >>>>>>>>>>> > > > >>>> > > >>> all >>>>>>>>>>> > > > >>>> > > >>> > > copies of >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you have >>>>>>>>>>> > > > >>>> received this >>>>>>>>>>> > > > >>>> > > >>> email >>>>>>>>>>> > > > >>>> > > >>> > > in error, >>>>>>>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by reply email >>>>>>>>>>> > > and >>>>>>>>>>> > > > >>>> delete >>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>> > > > >>>> > > >>> > > original >>>>>>>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without reading >>>>>>>>>>> > > them.* >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>>> > > > >>>> Technology. >>>>>>>>>>> > > > >>>> > > >> The contents of this email may contain legally protected >>>>>>>>>>> > > > >>>> confidential or >>>>>>>>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>>>>>>>> > > Technology?. If >>>>>>>>>>> > > > >>>> you are >>>>>>>>>>> > > > >>>> > > >> not the intended recipient, you should not disseminate, >>>>>>>>>>> > > > >>>> distribute or copy >>>>>>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy >>>>>>>>>>> > > > >>>> all copies of >>>>>>>>>>> > > > >>>> > > >> this message and any attachments. If you have received this >>>>>>>>>>> > > > >>>> email in error, >>>>>>>>>>> > > > >>>> > > >> please promptly notify the sender by reply email and delete >>>>>>>>>>> > > the >>>>>>>>>>> > > > >>>> original >>>>>>>>>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > -- >>>>>>>>>>> > > > >>>> > > > --Amneet >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>>> > > Technology. >>>>>>>>>>> > > > >>> The contents of this email may contain legally protected >>>>>>>>>>> > > confidential or >>>>>>>>>>> > > > >>> privileged information of ?Vellore Institute of Technology?. If you >>>>>>>>>>> > > are >>>>>>>>>>> > > > >>> not the intended recipient, you should not disseminate, distribute >>>>>>>>>>> > > or copy >>>>>>>>>>> > > > >>> this e-mail. Please notify the sender immediately and destroy all >>>>>>>>>>> > > copies of >>>>>>>>>>> > > > >>> this message and any attachments. 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Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> --Amneet >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> Disclaimer: >>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. 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URL: From bsmith at petsc.dev Wed Sep 6 13:17:30 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 6 Sep 2023 14:17:30 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> Message-ID: <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Ok, so the C++ binding for Matlab engine is working on your machine. PETSc uses the C binding which links against different libraries but, one would think the C binding would work for sure if the C++ binding works. Can you try a Matlab Engine C example provided by Matlab? > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 wrote: > > Hi Amneet, > > I repeated the same procedure again and this time it is working. > $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp -lMatlabDataArray -lMatlabEngine > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > $export LD_LIBRARY_PATH > $./a.out > Square root of -2 is 0 + 1.41421i > Square root of 2 is 1.41421 + 0i > Square root of 6 is 2.44949 + 0i > Square root of 8 is 2.82843 + 0i > I don't know how it is working this time? > > Thanks and regards > Srinivas > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 > wrote: >> Hi Amneet, >> I tried the following example to run a matlab engine. >> >> #include "MatlabDataArray.hpp" >> #include "MatlabEngine.hpp" >> #include >> void callSQRT() { >> >> using namespace matlab::engine; >> >> // Start MATLAB engine synchronously >> std::unique_ptr matlabPtr = startMATLAB(); >> >> //Create MATLAB data array factory >> matlab::data::ArrayFactory factory; >> >> // Define a four-element typed array >> matlab::data::TypedArray const argArray = >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >> >> // Call MATLAB sqrt function on the data array >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", argArray); >> >> // Display results >> for (int i = 0; i < results.getNumberOfElements(); i++) { >> double a = argArray[i]; >> std::complex v = results[i]; >> double realPart = v.real(); >> double imgPart = v.imag(); >> std::cout << "Square root of " << a << " is " << >> realPart << " + " << imgPart << "i" << std::endl; >> } >> } >> >> int main() { >> callSQRT(); >> return 0; >> } >> >> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> $export LD_LIBRARY_PATH >> $./a.out >> Starting >> Error: The import statement 'import matlab.internal.engine.input' cannot be found or cannot be imported. Imported names must end with '.*' or be fully qualified. >> >> terminate called after throwing an instance of 'matlab::engine::EngineException' >> what(): MATLAB process cannot be created. >> Aborted (core dumped) >> >> I got the above error for Matlab R2020b. Please help me to sort out this. >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: >>> BTW, what Barry is suggesting is the following: >>> >>> Compile a sample code with a command line this: >>> >>> g++ -std=c++11 -I matlabroot/extern/include/ -L matlabroot/extern/bin/glnxa64/ >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>> >>> This command is provided here: >>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>> >>> A sample MATLAB code is here: >>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>> >>> (You can just pick a few lines of code from here to create a barebone example) >>> >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: >>>> Srinivas --- Do you have a different version of MATLAB that you can install? If your organization has a MATLAB license, you can install recent versions of MATLAB from mathworks.com >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > wrote: >>>>> >>>>> Ok, I have no suggestions. It seems to be more an issue with the Matlab than PETSc. You could find a pure Matlab example of using the engine (in the Matlab documentation) and try it to see if it works. >>>>> >>>>> Barry >>>>> >>>>> >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 > wrote: >>>>>> >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>> I got the same errors for petsc 3.17.5 >>>>>> >>>>>> make all >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> ========================================= >>>>>> ========================================= >>>>>> Now to check if the libraries are working do: >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>> >>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>> # [0]PETSC ERROR: Error in external library >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 >>>>>> # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> # -------------------------------------------------------------------------- >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> # with errorcode 85. >>>>>> # >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> # You may or may not see output from other processes, depending on >>>>>> # exactly when Open MPI kills them. >>>>>> # -------------------------------------------------------------------------- >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> >>>>>> >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> # >>>>>> # To rerun failed tests: >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: >>>>>>> >>>>>>> The error is occuring during >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. >>>>>>> >>>>>>> You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> replace it with >>>>>>> >>>>>>> e->ep = engOpen(""); >>>>>>> >>>>>>> Now in the PETSc directory do make all (it should recompile one file) and then run the >>>>>>> >>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>> >>>>>>> again >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>> >>>>>>>> Hi Amneeth, >>>>>>>> >>>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>>> >>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> The version of PETSc you are using is out-of-date, we recommend updating to the new release >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>>> https://petsc.org/release/download/ >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> ============================================================================================= >>>>>>>> Configuring PETSc to compile on your system >>>>>>>> ============================================================================================= >>>>>>>> Compilers: >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> Linkers: >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>> BlasLapack: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads >>>>>>>> uses 8 byte integers >>>>>>>> MPI: >>>>>>>> Version: 3 >>>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>>> Implementation: openmpi >>>>>>>> OMPI_VERSION: 4.0.3 >>>>>>>> pthread: >>>>>>>> cmake: >>>>>>>> Version: 3.16.3 >>>>>>>> /usr/bin/cmake >>>>>>>> regex: >>>>>>>> Matlab: >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> /usr/local/MATLAB/R2020b >>>>>>>> MatlabEngine: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>>> Language used to compile PETSc: C >>>>>>>> PETSc: >>>>>>>> PETSC_ARCH: linux-opt >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>> Prefix: >>>>>>>> Scalar type: real >>>>>>>> Precision: double >>>>>>>> Support for __float128 >>>>>>>> Integer size: 4 bytes >>>>>>>> Single library: yes >>>>>>>> Shared libraries: yes >>>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>>> Using GNU make: /usr/bin/make >>>>>>>> xxx=========================================================================xxx >>>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all >>>>>>>> xxx=========================================================================xxx >>>>>>>> >>>>>>>> $make >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> ========================================= >>>>>>>> ========================================= >>>>>>>> Now to check if the libraries are working do: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>>> >>>>>>>> $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> # -------------------------------------------------------------------------- >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>> # with errorcode 85. >>>>>>>> # >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>> # exactly when Open MPI kills them. >>>>>>>> # -------------------------------------------------------------------------- >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>> >>>>>>>> >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> # >>>>>>>> # To rerun failed tests: >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> >>>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>>> >>>>>>>> How to check error info and proceed further? >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? >>>>>>>>> >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>>>> Sorry for missing that. >>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>> >>>>>>>>>> < M A T L A B (R) > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>>> November 23, 2020 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> To get started, type doc. >>>>>>>>>> For product information, visit www.mathworks.com . >>>>>>>>>> >>>>>>>>>> Thanks and regards >>>>>>>>>> Srinivas >>>>>>>>>> >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: >>>>>>>>>>> You are missing one more step: >>>>>>>>>>> >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>> >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>>> >>>>>>>>>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>>> >>>>>>>>>>> Satish >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>>>>>> >>>>>>>>>>> > Hi Sathish, >>>>>>>>>>> > >>>>>>>>>>> > I tried the following procedure >>>>>>>>>>> > >>>>>>>>>>> > *$make * >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > ========================================= >>>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>> > >>>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>>>>>>>> > query=requires >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > ------------------------------------------------------------------------ >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>>>>>>>>> > probably memory access out of range >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS >>>>>>>>>>> > X to find memory corruption errors >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, >>>>>>>>>>> > and run >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > CC >>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > CLINKER >>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > TEST >>>>>>>>>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>>>>>>>>>> > # Running problem 5 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > # with errorcode 126076. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed >>>>>>>>>>> > so no diff >>>>>>>>>>> > >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # Summary >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>>> > # >>>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>>> > # >>>>>>>>>>> > # To rerun failed tests: >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > # >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec >>>>>>>>>>> > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > Running problem 5 >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > -------------------------------------------------------------------------- >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > with errorcode 126076. >>>>>>>>>>> > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>>> > >>>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>>> > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: >>>>>>>>>>> > >>>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>>> > > >>>>>>>>>>> > > cd $HOME >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>>> > > >>>>>>>>>> > > manually with make> >>>>>>>>>>> > > >>>>>>>>>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles >>>>>>>>>>> > > >>>>>>>>>>> > > Satish >>>>>>>>>>> > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>>> > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have >>>>>>>>>>> > > any >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please help me how to >>>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we point to >>>>>>>>>>> > > this >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those >>>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>>> > > > is why I suggested just using a different matrix, or running a problem >>>>>>>>>>> > > you >>>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>>> > > > >>>>>>>>>>> > > > Thanks, >>>>>>>>>>> > > > >>>>>>>>>>> > > > Matt >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Thanks and regards >>>>>>>>>>> > > > > Srinivas. >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > petsc-users < >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you are giving me >>>>>>>>>>> > > to >>>>>>>>>>> > > > >>> sort this out. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed to build >>>>>>>>>>> > > Petsc >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> It appears you do not have >>>>>>>>>>> > > valgrind >>>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>>>>>>> > > > >>> Or install >>>>>>>>>>> > > valgrind-devel or >>>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > =============================================================================== >>>>>>>>>>> > > > >>> Compilers: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -fPIC >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> Linkers: >>>>>>>>>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>> > > > >>> make: >>>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>> > >

to >>>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>>> > > > >>> MPI: >>>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>>> > > --oversubscribe >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>>> > > > >>> pthread: >>>>>>>>>>> > > > >>> cmake: >>>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>>> > > > >>> regex: >>>>>>>>>>> > > > >>> Matlab: >>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>> Library: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>>>>>> > > -lut >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>>> > > > >>> PETSc: >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>>> > > > >>> Precision: double >>>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make* >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> ========================================= >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>> =============================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Thanks, >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Matt >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>> > > Sun >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > > > >>> CC >>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>> CLINKER >>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>> TEST >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: 124 >>>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # Summary >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / >>>>>>>>>>> > > 0.02 sec >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>> > > -Wwrite-strings >>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>>>>>> > > -lmx >>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>>>>> > > -lquadmath >>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please find the >>>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>>> > > > >>> Srinivas >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional info - and debug >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Satish >>>>>>>>>>> > > > >>>> ---------- >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng >>>>>>>>>>> > > -lmex >>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort >>>>>>>>>>> > > -lmpi >>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>>> > > processors >>>>>>>>>>> > > > >>>> = 1 >>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> 5 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you >>>>>>>>>>> > > - on >>>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com . >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>>>>>>>>>> > > thread >>>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>>>> > > corresponding >>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>>>>> > > > >>>> > main >>>>>>>>>>> > > > >>>> > release >>>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>>>>>> > > matlab/R2021a >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>>>>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>> > > > >>>> > make: >>>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>> > >

>>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>>> > > > >>>> > regex: >>>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: >>>>>>>>>>> > > > >>>> 1 >>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>> > > Command >>>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 >>>>>>>>>>> > > sec >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>>> > > 7.54 >>>>>>>>>>> > > > >>>> sec >>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>>>>>>>>> > > > >>>> running make >>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error message. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>>> > > -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> > > -------send >>>>>>>>>>> > > > >>>> entire >>>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> > > > >>>> processes. >>>>>>>>>>> > > > >>>> > > # You may or may not see output from other processes, depending >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > Thanks >>>>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > wrote: >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > > >>>> petsc-users < >>>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>>>>>>>>> > > > >>>> here]. >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > petsc-users >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>>>> > > balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts >>>>>>>>>>> > > across >>>>>>>>>>> > > > >>>> packages] >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict >>>>>>>>>>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>>>>>>>>> > > > >>>> matlab - to >>>>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>> > > > >>>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>>>>>>>>> > > > >>>> working. It is >>>>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>>>>>>>>> > > > >>>> libmesh and >>>>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>>>>>>>>> > > > >>>> linking >>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>>>> > > > >>>> > > >>> that >>>>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>>>>>>>>> > > specified. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>>>>>>>>> > > > >>>> PETSc and >>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>>>>>>>>> > > geometries >>>>>>>>>>> > > > >>>> it is >>>>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>>>>>>>>>> > > things >>>>>>>>>>> > > > >>>> and ended >>>>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>>>>>>>>> > > > >>>> research work. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for >>>>>>>>>>> > > the >>>>>>>>>>> > > > >>>> WEC >>>>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>>>>>>>>> > > > >>>> Matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>>>>>>>>> > > > >>>> libMesh? >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > > > > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>>>>>>>>> > > > >>>> occurrences >>>>>>>>>>> > > > >>>> > > >>> of >>>>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make >>>>>>>>>>> > > test" >>>>>>>>>>> > > > >>>> got the >>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>> > > Message >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> for >>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>> > > Aug >>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>> > > linux-debug >>>>>>>>>>> > > > >>>> named >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>> > > line >>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>> > > > >>>> Message >>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>> > > kill >>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>> > > processes, >>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>> > > Message >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> for >>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>> > > Aug >>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>> > > linux-opt >>>>>>>>>>> > > > >>>> named >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>> > > line >>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>> > > > >>>> Message >>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>> > > kill >>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>> > > processes, >>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>>>>>>>>> > > version. I >>>>>>>>>>> > > > >>>> am >>>>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>>>>>>>>> > > > >>>> petsc >>>>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > -leng >>>>>>>>>>> > > > >>>> -lmex >>>>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are >>>>>>>>>>> > > seeing: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>>>>>>>>> > > > >>>> preset here. >>>>>>>>>>> > > > >>>> > > >>> This >>>>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>>>>>>>>> > > -licui18n >>>>>>>>>>> > > > >>>> -licuuc" >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>>>> > > via >>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>>>>> > > successfully. >>>>>>>>>>> > > > >>>> But >>>>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>>>>>>>> > > friendly to >>>>>>>>>>> > > > >>>> mailing >>>>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or >>>>>>>>>>> > > 3.19?] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>>>>>>> > > 20PHD0548 >>>>>>>>>>> > > > >>>> via >>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>>>>>>>>>> > > building >>>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the >>>>>>>>>>> > > needful. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>>>>>>>>> > > building >>>>>>>>>>> > > > >>>> of >>>>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>>>>>>>>> > > > >>>> Balay < >>>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>>>>>>>>> > > > >>>> working on >>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the >>>>>>>>>>> > > PETSc, >>>>>>>>>>> > > > >>>> using the >>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>>>>>>>>> > > > >>>> status >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished >>>>>>>>>>> > > jobs.... >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>>>>>>>>>> > > > >>>> Institute of >>>>>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain legally >>>>>>>>>>> > > > >>>> protected >>>>>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>>>>>>>>>> > > > >>>> Technology?. >>>>>>>>>>> > > > >>>> > > >>> If >>>>>>>>>>> > > > >>>> > > >>> > > you are >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should not >>>>>>>>>>> > > > >>>> disseminate, >>>>>>>>>>> > > > >>>> > > >>> distribute >>>>>>>>>>> > > > >>>> > > >>> > > or copy >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately >>>>>>>>>>> > > > >>>> and destroy >>>>>>>>>>> > > > >>>> > > >>> all >>>>>>>>>>> > > > >>>> > > >>> > > copies of >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you have >>>>>>>>>>> > > > >>>> received this >>>>>>>>>>> > > > >>>> > > >>> email >>>>>>>>>>> > > > >>>> > > >>> > > in error, >>>>>>>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by reply email >>>>>>>>>>> > > and >>>>>>>>>>> > > > >>>> delete >>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>> > > > >>>> > > >>> > > original >>>>>>>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without reading >>>>>>>>>>> > > them.* >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>>> > > > >>>> Technology. >>>>>>>>>>> > > > >>>> > > >> The contents of this email may contain legally protected >>>>>>>>>>> > > > >>>> confidential or >>>>>>>>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>>>>>>>> > > Technology?. If >>>>>>>>>>> > > > >>>> you are >>>>>>>>>>> > > > >>>> > > >> not the intended recipient, you should not disseminate, >>>>>>>>>>> > > > >>>> distribute or copy >>>>>>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy >>>>>>>>>>> > > > >>>> all copies of >>>>>>>>>>> > > > >>>> > > >> this message and any attachments. If you have received this >>>>>>>>>>> > > > >>>> email in error, >>>>>>>>>>> > > > >>>> > > >> please promptly notify the sender by reply email and delete >>>>>>>>>>> > > the >>>>>>>>>>> > > > >>>> original >>>>>>>>>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > -- >>>>>>>>>>> > > > >>>> > > > --Amneet >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>>> > > Technology. >>>>>>>>>>> > > > >>> The contents of this email may contain legally protected >>>>>>>>>>> > > confidential or >>>>>>>>>>> > > > >>> privileged information of ?Vellore Institute of Technology?. If you >>>>>>>>>>> > > are >>>>>>>>>>> > > > >>> not the intended recipient, you should not disseminate, distribute >>>>>>>>>>> > > or copy >>>>>>>>>>> > > > >>> this e-mail. Please notify the sender immediately and destroy all >>>>>>>>>>> > > copies of >>>>>>>>>>> > > > >>> this message and any attachments. 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Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> --Amneet >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> Disclaimer: >>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>>>> >>>>>> >>>>>> Disclaimer: >>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>> >>>> >>>> >>>> -- >>>> --Amneet >>>> >>>> >>>> >>> >>> >>> -- >>> --Amneet >>> >>> >>> > > Disclaimer: > This message was sent from Vellore Institute of Technology. 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URL: From balay at mcs.anl.gov Wed Sep 6 13:54:47 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Wed, 6 Sep 2023 13:54:47 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: I'm still curios why the first [c++] attempt failed but the second one succeeded. The only difference I can spot is myEngineApp.cpp vs myEngineApp2.cpp. What is the difference here between these 2 source files? Or is it some random error [the same source code worked failed before - but works now - and might fail again later?] Maybe there is some issue with matlab license here - that prevents some usages (or usage patterns) to fail? Satish On Wed, 6 Sep 2023, Barry Smith wrote: > > Ok, so the C++ binding for Matlab engine is working on your machine. PETSc uses the C binding which links against different libraries but, one would think the C binding would work for sure if the C++ binding works. Can you try a Matlab Engine C example provided by Matlab? > > > > > > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 wrote: > > > > Hi Amneet, > > > > I repeated the same procedure again and this time it is working. > > $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp -lMatlabDataArray -lMatlabEngine > > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > $export LD_LIBRARY_PATH > > $./a.out > > Square root of -2 is 0 + 1.41421i > > Square root of 2 is 1.41421 + 0i > > Square root of 6 is 2.44949 + 0i > > Square root of 8 is 2.82843 + 0i > > I don't know how it is working this time? > > > > Thanks and regards > > Srinivas > > > > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 > wrote: > >> Hi Amneet, > >> I tried the following example to run a matlab engine. > >> > >> #include "MatlabDataArray.hpp" > >> #include "MatlabEngine.hpp" > >> #include > >> void callSQRT() { > >> > >> using namespace matlab::engine; > >> > >> // Start MATLAB engine synchronously > >> std::unique_ptr matlabPtr = startMATLAB(); > >> > >> //Create MATLAB data array factory > >> matlab::data::ArrayFactory factory; > >> > >> // Define a four-element typed array > >> matlab::data::TypedArray const argArray = > >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); > >> > >> // Call MATLAB sqrt function on the data array > >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", argArray); > >> > >> // Display results > >> for (int i = 0; i < results.getNumberOfElements(); i++) { > >> double a = argArray[i]; > >> std::complex v = results[i]; > >> double realPart = v.real(); > >> double imgPart = v.imag(); > >> std::cout << "Square root of " << a << " is " << > >> realPart << " + " << imgPart << "i" << std::endl; > >> } > >> } > >> > >> int main() { > >> callSQRT(); > >> return 0; > >> } > >> > >> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine > >> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >> $export LD_LIBRARY_PATH > >> $./a.out > >> Starting > >> Error: The import statement 'import matlab.internal.engine.input' cannot be found or cannot be imported. Imported names must end with '.*' or be fully qualified. > >> > >> terminate called after throwing an instance of 'matlab::engine::EngineException' > >> what(): MATLAB process cannot be created. > >> Aborted (core dumped) > >> > >> I got the above error for Matlab R2020b. Please help me to sort out this. > >> > >> Thanks and regards > >> Srinivas > >> > >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: > >>> BTW, what Barry is suggesting is the following: > >>> > >>> Compile a sample code with a command line this: > >>> > >>> g++ -std=c++11 -I matlabroot/extern/include/ -L matlabroot/extern/bin/glnxa64/ > >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine > >>> > >>> This command is provided here: > >>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html > >>> > >>> A sample MATLAB code is here: > >>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html > >>> > >>> (You can just pick a few lines of code from here to create a barebone example) > >>> > >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: > >>>> Srinivas --- Do you have a different version of MATLAB that you can install? If your organization has a MATLAB license, you can install recent versions of MATLAB from mathworks.com > >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > wrote: > >>>>> > >>>>> Ok, I have no suggestions. It seems to be more an issue with the Matlab than PETSc. You could find a pure Matlab example of using the engine (in the Matlab documentation) and try it to see if it works. > >>>>> > >>>>> Barry > >>>>> > >>>>> > >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 > wrote: > >>>>>> > >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); > >>>>>> I got the same errors for petsc 3.17.5 > >>>>>> > >>>>>> make all > >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o > >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 > >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE > >>>>>> Building with 'gcc'. > >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>> | ^ > >>>>>> > >>>>>> MEX completed successfully. > >>>>>> Building with 'gcc'. > >>>>>> MEX completed successfully. > >>>>>> Building with 'gcc'. > >>>>>> MEX completed successfully. > >>>>>> Building with 'gcc'. > >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>> | ^ > >>>>>> > >>>>>> MEX completed successfully. > >>>>>> ========================================= > >>>>>> ========================================= > >>>>>> Now to check if the libraries are working do: > >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check > >>>>>> > >>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ > >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires > >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > >>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > >>>>>> # [0]PETSC ERROR: Error in external library > >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 > >>>>>> # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 > >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 > >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 > >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 > >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > >>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 > >>>>>> # [0]PETSC ERROR: -error_output_stdout > >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > >>>>>> # [0]PETSC ERROR: -malloc_dump > >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > >>>>>> # [0]PETSC ERROR: -pc_type lu > >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- > >>>>>> # -------------------------------------------------------------------------- > >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > >>>>>> # with errorcode 85. > >>>>>> # > >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>> # You may or may not see output from other processes, depending on > >>>>>> # exactly when Open MPI kills them. > >>>>>> # -------------------------------------------------------------------------- > >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>>>>> > >>>>>> > >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 > >>>>>> # > >>>>>> # To rerun failed tests: > >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 > >>>>>> > >>>>>> Thanks and regards > >>>>>> Srinivas > >>>>>> > >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: > >>>>>>> > >>>>>>> The error is occuring during > >>>>>>> > >>>>>>> e->ep = engOpen(buffer); > >>>>>>> > >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. > >>>>>>> > >>>>>>> You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line > >>>>>>> > >>>>>>> e->ep = engOpen(buffer); > >>>>>>> > >>>>>>> replace it with > >>>>>>> > >>>>>>> e->ep = engOpen(""); > >>>>>>> > >>>>>>> Now in the PETSc directory do make all (it should recompile one file) and then run the > >>>>>>> > >>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ > >>>>>>> > >>>>>>> again > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > >>>>>>>> > >>>>>>>> Hi Amneeth, > >>>>>>>> > >>>>>>>> I think the errors are different with petsc 3.17.5 > >>>>>>>> > >>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >>>>>>>> The version of PETSc you are using is out-of-date, we recommend updating to the new release > >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 > >>>>>>>> https://petsc.org/release/download/ > >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > >>>>>>>> ============================================================================================= > >>>>>>>> Configuring PETSc to compile on your system > >>>>>>>> ============================================================================================= > >>>>>>>> Compilers: > >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 > >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC > >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 > >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>> Linkers: > >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 > >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 > >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl > >>>>>>>> BlasLapack: > >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread > >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads > >>>>>>>> uses 8 byte integers > >>>>>>>> MPI: > >>>>>>>> Version: 3 > >>>>>>>> mpiexec: /usr/bin/mpiexec > >>>>>>>> Implementation: openmpi > >>>>>>>> OMPI_VERSION: 4.0.3 > >>>>>>>> pthread: > >>>>>>>> cmake: > >>>>>>>> Version: 3.16.3 > >>>>>>>> /usr/bin/cmake > >>>>>>>> regex: > >>>>>>>> Matlab: > >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > >>>>>>>> /usr/local/MATLAB/R2020b > >>>>>>>> MatlabEngine: > >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c > >>>>>>>> Language used to compile PETSc: C > >>>>>>>> PETSc: > >>>>>>>> PETSC_ARCH: linux-opt > >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 > >>>>>>>> Prefix: > >>>>>>>> Scalar type: real > >>>>>>>> Precision: double > >>>>>>>> Support for __float128 > >>>>>>>> Integer size: 4 bytes > >>>>>>>> Single library: yes > >>>>>>>> Shared libraries: yes > >>>>>>>> Memory alignment from malloc(): 16 bytes > >>>>>>>> Using GNU make: /usr/bin/make > >>>>>>>> xxx=========================================================================xxx > >>>>>>>> Configure stage complete. Now build PETSc libraries with: > >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all > >>>>>>>> xxx=========================================================================xxx > >>>>>>>> > >>>>>>>> $make > >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 > >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE > >>>>>>>> Building with 'gcc'. > >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>>>> | ^ > >>>>>>>> > >>>>>>>> MEX completed successfully. > >>>>>>>> Building with 'gcc'. > >>>>>>>> MEX completed successfully. > >>>>>>>> Building with 'gcc'. > >>>>>>>> MEX completed successfully. > >>>>>>>> Building with 'gcc'. > >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: > >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] > >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>>>> | ^ > >>>>>>>> > >>>>>>>> MEX completed successfully. > >>>>>>>> ========================================= > >>>>>>>> ========================================= > >>>>>>>> Now to check if the libraries are working do: > >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check > >>>>>>>> > >>>>>>>> $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ > >>>>>>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests > >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires > >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > >>>>>>>> # [0]PETSC ERROR: Error in external library > >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 > >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 > >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 > >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 > >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > >>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 > >>>>>>>> # [0]PETSC ERROR: -error_output_stdout > >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > >>>>>>>> # [0]PETSC ERROR: -malloc_dump > >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > >>>>>>>> # [0]PETSC ERROR: -pc_type lu > >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- > >>>>>>>> # -------------------------------------------------------------------------- > >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > >>>>>>>> # with errorcode 85. > >>>>>>>> # > >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>>>> # You may or may not see output from other processes, depending on > >>>>>>>> # exactly when Open MPI kills them. > >>>>>>>> # -------------------------------------------------------------------------- > >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>>>>>>> > >>>>>>>> > >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 > >>>>>>>> # > >>>>>>>> # To rerun failed tests: > >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 > >>>>>>>> > >>>>>>>> To get the info of the error there is no specific probe id reported. > >>>>>>>> > >>>>>>>> How to check error info and proceed further? > >>>>>>>> > >>>>>>>> Thanks and regards > >>>>>>>> Srinivas > >>>>>>>> > >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: > >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? > >>>>>>>>> > >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: > >>>>>>>>>> Sorry for missing that. > >>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > >>>>>>>>>> > >>>>>>>>>> < M A T L A B (R) > > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. > >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) > >>>>>>>>>> November 23, 2020 > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> To get started, type doc. > >>>>>>>>>> For product information, visit www.mathworks.com . > >>>>>>>>>> > >>>>>>>>>> Thanks and regards > >>>>>>>>>> Srinivas > >>>>>>>>>> > >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: > >>>>>>>>>>> You are missing one more step: > >>>>>>>>>>> > >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 > >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > >>>>>>>>>>> > >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" > >>>>>>>>>>> > >>>>>>>>>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. > >>>>>>>>>>> > >>>>>>>>>>> Satish > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > >>>>>>>>>>> > >>>>>>>>>>> > Hi Sathish, > >>>>>>>>>>> > > >>>>>>>>>>> > I tried the following procedure > >>>>>>>>>>> > > >>>>>>>>>>> > *$make * > >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE > >>>>>>>>>>> > Building with 'gcc'. > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > >>>>>>>>>>> > In function ?PetscBinaryWrite?: > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function > >>>>>>>>>>> > [-Wmaybe-uninitialized] > >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>>>>>>> > | ^ > >>>>>>>>>>> > > >>>>>>>>>>> > MEX completed successfully. > >>>>>>>>>>> > Building with 'gcc'. > >>>>>>>>>>> > MEX completed successfully. > >>>>>>>>>>> > Building with 'gcc'. > >>>>>>>>>>> > MEX completed successfully. > >>>>>>>>>>> > Building with 'gcc'. > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > >>>>>>>>>>> > In function ?PetscBinaryWrite?: > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function > >>>>>>>>>>> > [-Wmaybe-uninitialized] > >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>>>>>>> > | ^ > >>>>>>>>>>> > > >>>>>>>>>>> > MEX completed successfully. > >>>>>>>>>>> > ========================================= > >>>>>>>>>>> > Now to check if the libraries are working do: > >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > >>>>>>>>>>> > > >>>>>>>>>>> > *$make test query=requires queryval=matlab > >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* > >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab > >>>>>>>>>>> > query=requires > >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>>>>>>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > -------------------------------------------------------------- > >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > for trouble shooting. > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > >>>>>>>>>>> > 4 10:02:32 2023 > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > -------------------------------------------------------------- > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data > >>>>>>>>>>> > # [0]PETSC ERROR: > >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > for trouble shooting. > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > >>>>>>>>>>> > 4 10:02:32 2023 > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > # [0]PETSC ERROR: > >>>>>>>>>>> > ------------------------------------------------------------------------ > >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > >>>>>>>>>>> > probably memory access out of range > >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > >>>>>>>>>>> > # [0]PETSC ERROR: or see > >>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS > >>>>>>>>>>> > X to find memory corruption errors > >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > >>>>>>>>>>> > and run > >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > -------------------------------------------------------------- > >>>>>>>>>>> > # [0]PETSC ERROR: Signal received > >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > for trouble shooting. > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > >>>>>>>>>>> > 4 10:02:32 2023 > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file > >>>>>>>>>>> > # -------------------------------------------------------------------------- > >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > >>>>>>>>>>> > # with errorcode 50162059. > >>>>>>>>>>> > # > >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>>>>>>> > # You may or may not see output from other processes, depending on > >>>>>>>>>>> > # exactly when Open MPI kills them. > >>>>>>>>>>> > # -------------------------------------------------------------------------- > >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>>>>>>>>>> > CC > >>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > >>>>>>>>>>> > CLINKER > >>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>>>>>>>>>> > TEST > >>>>>>>>>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > >>>>>>>>>>> > # Running problem 5 > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > -------------------------------------------------------------- > >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > for trouble shooting. > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 > >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor > >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > # -------------------------------------------------------------------------- > >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>>>>>>>>>> > # with errorcode 126076. > >>>>>>>>>>> > # > >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>>>>>>> > # You may or may not see output from other processes, depending on > >>>>>>>>>>> > # exactly when Open MPI kills them. > >>>>>>>>>>> > # -------------------------------------------------------------------------- > >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed > >>>>>>>>>>> > so no diff > >>>>>>>>>>> > > >>>>>>>>>>> > # ------------- > >>>>>>>>>>> > # Summary > >>>>>>>>>>> > # ------------- > >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 > >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>>>>>>>>> > # success 0/2 tests (0.0%) > >>>>>>>>>>> > # failed 2/2 tests (100.0%) > >>>>>>>>>>> > # todo 0/2 tests (0.0%) > >>>>>>>>>>> > # skip 0/2 tests (0.0%) > >>>>>>>>>>> > # > >>>>>>>>>>> > # Wall clock time for tests: 4 sec > >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec > >>>>>>>>>>> > # > >>>>>>>>>>> > # To rerun failed tests: > >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 > >>>>>>>>>>> > # > >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): > >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec > >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec > >>>>>>>>>>> > > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* > >>>>>>>>>>> > *$make matlab_ls_test* > >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include > >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include > >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath > >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test > >>>>>>>>>>> > > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* > >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 > >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > >>>>>>>>>>> > MB108SMEC028.(none) > >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 > >>>>>>>>>>> > Running problem 5 > >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 > >>>>>>>>>>> > 94202473157392 max tags = 2147483647 > >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > -------------------------------------------------------------- > >>>>>>>>>>> > [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on > >>>>>>>>>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > for trouble shooting. > >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit > >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 > >>>>>>>>>>> > [0]PETSC ERROR: Configure options > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c > >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > [0]PETSC ERROR: -info > >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 > >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor > >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire > >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > -------------------------------------------------------------------------- > >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>>>>>>>>>> > with errorcode 126076. > >>>>>>>>>>> > > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>>>>>>> > You may or may not see output from other processes, depending on > >>>>>>>>>>> > exactly when Open MPI kills them. > >>>>>>>>>>> > > >>>>>>>>>>> > Please find the attachment for configure.log and make.log files > >>>>>>>>>>> > > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: > >>>>>>>>>>> > > >>>>>>>>>>> > > To use datafiles in the test suite: > >>>>>>>>>>> > > > >>>>>>>>>>> > > cd $HOME > >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles > >>>>>>>>>>> > > >>>>>>>>>>> > > manually with make> > >>>>>>>>>>> > > > >>>>>>>>>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles > >>>>>>>>>>> > > > >>>>>>>>>>> > > Satish > >>>>>>>>>>> > > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: > >>>>>>>>>>> > > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < > >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > Hi Matthew, > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have > >>>>>>>>>>> > > any > >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please help me how to > >>>>>>>>>>> > > > > define this DATAFILESPATH? > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we point to > >>>>>>>>>>> > > this > >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those > >>>>>>>>>>> > > > matrices, since they are just for testing here. That > >>>>>>>>>>> > > > is why I suggested just using a different matrix, or running a problem > >>>>>>>>>>> > > you > >>>>>>>>>>> > > > care about in IBAMR. > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > Thanks, > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > Matt > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > Thanks and regards > >>>>>>>>>>> > > > > Srinivas. > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > > >>>>>>>>>>> > > wrote: > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via > >>>>>>>>>>> > > petsc-users < > >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov > wrote: > >>>>>>>>>>> > > > >> > >>>>>>>>>>> > > > >>> Hi Sathish, > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you are giving me > >>>>>>>>>>> > > to > >>>>>>>>>>> > > > >>> sort this out. > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed to build > >>>>>>>>>>> > > Petsc > >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 > >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* > >>>>>>>>>>> > > > >>> Using python3 for Python > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > =============================================================================== > >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your system > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > =============================================================================== > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > =============================================================================== > >>>>>>>>>>> > > > >>> It appears you do not have > >>>>>>>>>>> > > valgrind > >>>>>>>>>>> > > > >>> installed on your system. > >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org > >>>>>>>>>>> > > > >>> Or install > >>>>>>>>>>> > > valgrind-devel or > >>>>>>>>>>> > > > >>> equivalent using your package manager. > >>>>>>>>>>> > > > >>> Then rerun ./configure > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > =============================================================================== > >>>>>>>>>>> > > > >>> Compilers: > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>>>>>>>>> > > -fPIC > >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>>>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > >>>>>>>>>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>>>>> > > > >>> Linkers: > >>>>>>>>>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>>>>>>>>> > > -shared > >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > >>>>>>>>>>> > > -Wno-unknown-pragmas > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>>>>>>>>> > > -shared > >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > >>>>>>>>>>> > > -Wno-unknown-pragmas > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl > >>>>>>>>>>> > > > >>> make: > >>>>>>>>>>> > > > >>> Version: 4.2 > >>>>>>>>>>> > > > >>> /usr/bin/make > >>>>>>>>>>> > > > >>> BlasLapack: > >>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread > >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads > >>>>>>>>>>> > >

to > >>>>>>>>>>> > > > >>> control the number of threads > >>>>>>>>>>> > > > >>> uses 8 byte integers > >>>>>>>>>>> > > > >>> MPI: > >>>>>>>>>>> > > > >>> Version: 3 > >>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include > >>>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec > >>>>>>>>>>> > > --oversubscribe > >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 > >>>>>>>>>>> > > > >>> pthread: > >>>>>>>>>>> > > > >>> cmake: > >>>>>>>>>>> > > > >>> Version: 3.16.3 > >>>>>>>>>>> > > > >>> /usr/bin/cmake > >>>>>>>>>>> > > > >>> regex: > >>>>>>>>>>> > > > >>> Matlab: > >>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> MatlabEngine: > >>>>>>>>>>> > > > >>> Library: > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat > >>>>>>>>>>> > > -lut > >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc > >>>>>>>>>>> > > > >>> Language used to compile PETSc: C > >>>>>>>>>>> > > > >>> PETSc: > >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt > >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > >>>>>>>>>>> > > > >>> Scalar type: real > >>>>>>>>>>> > > > >>> Precision: double > >>>>>>>>>>> > > > >>> Support for __float128 > >>>>>>>>>>> > > > >>> Integer size: 4 bytes > >>>>>>>>>>> > > > >>> shared libraries: enabled > >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > xxx=========================================================================xxx > >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: > >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > xxx=========================================================================xxx > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as > >>>>>>>>>>> > > > >>> you suggested earlier. > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> *$make* > >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE > >>>>>>>>>>> > > > >>> Building with 'gcc'. > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function > >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] > >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>>>>>>> > > > >>> | ^ > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> MEX completed successfully. > >>>>>>>>>>> > > > >>> Building with 'gcc'. > >>>>>>>>>>> > > > >>> MEX completed successfully. > >>>>>>>>>>> > > > >>> Building with 'gcc'. > >>>>>>>>>>> > > > >>> MEX completed successfully. > >>>>>>>>>>> > > > >>> Building with 'gcc'. > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function > >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] > >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > >>>>>>>>>>> > > > >>> | ^ > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> MEX completed successfully. > >>>>>>>>>>> > > > >>> ========================================= > >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: > >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > >>>>>>>>>>> > > > >>> =============================================== > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* > >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > >>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>>>>>>>>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > > > >>> -------------------------------------------------------------- > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >> > >>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it > >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of yours. > >>>>>>>>>>> > > > >> > >>>>>>>>>>> > > > >> Thanks, > >>>>>>>>>>> > > > >> > >>>>>>>>>>> > > > >> Matt > >>>>>>>>>>> > > > >> > >>>>>>>>>>> > > > >> > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See > >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > >>>>>>>>>>> > > > >>> shooting. > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit > >>>>>>>>>>> > > Sun > >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > >>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>>>>>>>>>> > > > >>> # with errorcode 113065. > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on > >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>>>>>>>>>> > > > >>> CC > >>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > >>>>>>>>>>> > > > >>> CLINKER > >>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>>>>>>>>>> > > > >>> TEST > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > >>>>>>>>>>> > > code: 124 > >>>>>>>>>>> > > > >>> # Running problem 5 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > > > >>> -------------------------------------------------------------- > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See > >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > >>>>>>>>>>> > > > >>> shooting. > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > >>>>>>>>>>> > > MB108SMEC028 by > >>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send > >>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>>>>>>>>>> > > > >>> # with errorcode 126076. > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on > >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command > >>>>>>>>>>> > > > >>> failed so no diff > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> # ------------- > >>>>>>>>>>> > > > >>> # Summary > >>>>>>>>>>> > > > >>> # ------------- > >>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 > >>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) > >>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) > >>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) > >>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec > >>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> # To rerun failed tests: > >>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 > >>>>>>>>>>> > > > >>> # > >>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): > >>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec > >>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / > >>>>>>>>>>> > > 0.02 sec > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> *How to sort out this error?* > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* > >>>>>>>>>>> > > > >>> *$make matlab_ls_test* > >>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall > >>>>>>>>>>> > > -Wwrite-strings > >>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > >>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > >>>>>>>>>>> > > -Wno-strict-aliasing > >>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include > >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > >>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include > >>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > >>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > >>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib > >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > >>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > >>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > >>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex > >>>>>>>>>>> > > -lmx > >>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr > >>>>>>>>>>> > > -lmpi_mpifh > >>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread > >>>>>>>>>>> > > -lquadmath > >>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. > >>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please find the > >>>>>>>>>>> > > > >>> attachment and do the needful. > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> Thanks and regards > >>>>>>>>>>> > > > >>> Srinivas > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > > >>>>>>>>>>> > > wrote: > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional info - and debug > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> Satish > >>>>>>>>>>> > > > >>>> ---------- > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd > >>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ > >>>>>>>>>>> > > > >>>> balay at compute-386-07 > >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > >>>>>>>>>>> > > > >>>> make matlab_ls_test > >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > >>>>>>>>>>> > > -Wall > >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > -fstack-protector > >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > >>>>>>>>>>> > > -Wno-strict-aliasing > >>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include > >>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > >>>>>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > >>>>>>>>>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib > >>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > >>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib > >>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > >>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 > >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > >>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > >>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng > >>>>>>>>>>> > > -lmex > >>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort > >>>>>>>>>>> > > -lmpi > >>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o > >>>>>>>>>>> > > > >>>> matlab_ls_test > >>>>>>>>>>> > > > >>>> balay at compute-386-07 > >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > >>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info > >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of > >>>>>>>>>>> > > processors > >>>>>>>>>>> > > > >>>> = 1 > >>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS > >>>>>>>>>>> > > > >>>> compute-386-07.(none) > >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 > >>>>>>>>>>> > > > >>>> Running problem 5 > >>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 > >>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 > >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash > >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine > >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: > >>>>>>>>>>> > > > >>>> TestingInitialize > >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: > >>>>>>>>>>> > > > >>>> TestingInitialize > >>>>>>>>>>> > > > >>>> 5 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you > >>>>>>>>>>> > > - on > >>>>>>>>>>> > > > >>>> this machine..>>>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> balay at compute-386-07 > >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> < M A T L A B (R) > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> February 17, 2021 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> To get started, type doc. > >>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com . > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting > >>>>>>>>>>> > > thread > >>>>>>>>>>> > > > >>>> to petsc-users only] > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the > >>>>>>>>>>> > > corresponding > >>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, > >>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch > >>>>>>>>>>> > > > >>>> > main > >>>>>>>>>>> > > > >>>> > release > >>>>>>>>>>> > > > >>>> > * release-3.13 > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load > >>>>>>>>>>> > > matlab/R2021a > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure > >>>>>>>>>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ > >>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > Compilers: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > C Compiler: > >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC > >>>>>>>>>>> > > -Wall > >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > -fstack-protector > >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>>>>> > > > >>>> > C++ Compiler: > >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall > >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > -fstack-protector > >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC > >>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>>>>> > > > >>>> > Fortran Compiler: > >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC > >>>>>>>>>>> > > -Wall > >>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 > >>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > >>>>>>>>>>> > > > >>>> > Linkers: > >>>>>>>>>>> > > > >>>> > Shared linker: > >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > >>>>>>>>>>> > > -shared -fPIC > >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>>> > Dynamic linker: > >>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc > >>>>>>>>>>> > > -shared -fPIC > >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas > >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 > >>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl > >>>>>>>>>>> > > > >>>> > make: > >>>>>>>>>>> > > > >>>> > Version: 4.2 > >>>>>>>>>>> > > > >>>> > /usr/bin/make > >>>>>>>>>>> > > > >>>> > BlasLapack: > >>>>>>>>>>> > > > >>>> > Library: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 > >>>>>>>>>>> > > > >>>> -liomp5 -lpthread > >>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads > >>>>>>>>>>> > >

> >>>>>>>>>>> > > > >>>> to control the number of threads > >>>>>>>>>>> > > > >>>> > uses 8 byte integers > >>>>>>>>>>> > > > >>>> > MPI: > >>>>>>>>>>> > > > >>>> > Version: 4 > >>>>>>>>>>> > > > >>>> > Includes: > >>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include > >>>>>>>>>>> > > > >>>> > Mpiexec: > >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec > >>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 > >>>>>>>>>>> > > > >>>> > pthread: > >>>>>>>>>>> > > > >>>> > Library: -lpthread > >>>>>>>>>>> > > > >>>> > cmake: > >>>>>>>>>>> > > > >>>> > Version: 3.16.3 > >>>>>>>>>>> > > > >>>> > /usr/bin/cmake > >>>>>>>>>>> > > > >>>> > regex: > >>>>>>>>>>> > > > >>>> > Matlab: > >>>>>>>>>>> > > > >>>> > Includes: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include > >>>>>>>>>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a > >>>>>>>>>>> > > > >>>> > MatlabEngine: > >>>>>>>>>>> > > > >>>> > Library: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc > >>>>>>>>>>> > > > >>>> > sowing: > >>>>>>>>>>> > > > >>>> > Version: 1.1.25 > >>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort > >>>>>>>>>>> > > > >>>> > valgrind: > >>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C > >>>>>>>>>>> > > > >>>> > PETSc: > >>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt > >>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc > >>>>>>>>>>> > > > >>>> > Scalar type: real > >>>>>>>>>>> > > > >>>> > Precision: double > >>>>>>>>>>> > > > >>>> > Support for __float128 > >>>>>>>>>>> > > > >>>> > Integer size: 4 bytes > >>>>>>>>>>> > > > >>>> > shared libraries: enabled > >>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > xxx=========================================================================xxx > >>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: > >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > xxx=========================================================================xxx > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o > >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 > >>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE > >>>>>>>>>>> > > > >>>> > Building with 'gcc'. > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function > >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] > >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > >>>>>>>>>>> > > socket\n"); > >>>>>>>>>>> > > > >>>> > | ^ > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > MEX completed successfully. > >>>>>>>>>>> > > > >>>> > Building with 'gcc'. > >>>>>>>>>>> > > > >>>> > MEX completed successfully. > >>>>>>>>>>> > > > >>>> > Building with 'gcc'. > >>>>>>>>>>> > > > >>>> > MEX completed successfully. > >>>>>>>>>>> > > > >>>> > Building with 'gcc'. > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In > >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function > >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] > >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > >>>>>>>>>>> > > socket\n"); > >>>>>>>>>>> > > > >>>> > | ^ > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > MEX completed successfully. > >>>>>>>>>>> > > > >>>> > ========================================= > >>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: > >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check > >>>>>>>>>>> > > > >>>> > ========================================= > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test > >>>>>>>>>>> > > query=requires > >>>>>>>>>>> > > > >>>> queryval=matlab > >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > >>>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > >>>>>>>>>>> > > > >>>> > TEST > >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 > >>>>>>>>>>> > > > >>>> > # ../ex72: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > >>>>>>>>>>> > > > >>>> > CC > >>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > >>>>>>>>>>> > > > >>>> > CLINKER > >>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>>>>>>>>>> > > > >>>> > TEST > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>>>>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > >>>>>>>>>>> > > code: > >>>>>>>>>>> > > > >>>> 1 > >>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: > >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) > >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP > >>>>>>>>>>> > > Command > >>>>>>>>>>> > > > >>>> failed so no diff > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test > >>>>>>>>>>> > > query=requires > >>>>>>>>>>> > > > >>>> queryval=matlab > >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires > >>>>>>>>>>> > > > >>>> > TEST > >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 > >>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 > >>>>>>>>>>> > > > >>>> > TEST > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>>>>>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > # ------------- > >>>>>>>>>>> > > > >>>> > # Summary > >>>>>>>>>>> > > > >>>> > # ------------- > >>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) > >>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) > >>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) > >>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) > >>>>>>>>>>> > > > >>>> > # > >>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec > >>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 > >>>>>>>>>>> > > sec > >>>>>>>>>>> > > > >>>> > # > >>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): > >>>>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / > >>>>>>>>>>> > > 7.54 > >>>>>>>>>>> > > > >>>> sec > >>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to > >>>>>>>>>>> > > > >>>> configure petsc > >>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After > >>>>>>>>>>> > > > >>>> running make > >>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error message. > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > >>>>>>>>>>> > > > >>>> code: 124 > >>>>>>>>>>> > > > >>>> > > # Running problem 5 > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message > >>>>>>>>>>> > > > >>>> > > -------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See > >>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > > > >>>> > > for trouble shooting. > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > >>>>>>>>>>> > > > >>>> MB108SMEC028 by > >>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > >>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > >>>>>>>>>>> > > > >>>> --with-debugging=0 > >>>>>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 > >>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > >>>>>>>>>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor > >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message > >>>>>>>>>>> > > -------send > >>>>>>>>>>> > > > >>>> entire > >>>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > > > >>>> > > # > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF > >>>>>>>>>>> > > > >>>> > > # with errorcode 126076. > >>>>>>>>>>> > > > >>>> > > # > >>>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > >>>>>>>>>>> > > > >>>> processes. > >>>>>>>>>>> > > > >>>> > > # You may or may not see output from other processes, depending > >>>>>>>>>>> > > on > >>>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. > >>>>>>>>>>> > > > >>>> > > # > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > Thanks > >>>>>>>>>>> > > > >>>> > > Srinivas > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < > >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > wrote: > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in > >>>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > i.e.: > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via > >>>>>>>>>>> > > > >>>> petsc-users < > >>>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this > >>>>>>>>>>> > > > >>>> > > >> > >>>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > > >>>>>>>>>>> > > > >>>> wrote: > >>>>>>>>>>> > > > >>>> > > >> > >>>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work > >>>>>>>>>>> > > > >>>> here]. > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> i.e: > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > >>>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > >>>>>>>>>>> > > PETSC_ARCH=linux-opt > >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ > >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> --with-matlab-engine=1 > >>>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> Satish > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > >>>>>>>>>>> > > petsc-users > >>>>>>>>>>> > > > >>>> wrote: > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > Hi Satish, > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir > >>>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < > >>>>>>>>>>> > > balay at mcs.anl.gov > > >>>>>>>>>>> > > > >>>> wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Also: > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts > >>>>>>>>>>> > > across > >>>>>>>>>>> > > > >>>> packages] > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > Satish > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict > >>>>>>>>>>> > > with > >>>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring > >>>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with > >>>>>>>>>>> > > > >>>> matlab - to > >>>>>>>>>>> > > > >>>> > > >>> have a > >>>>>>>>>>> > > > >>>> > > >>> > > compatible build > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Satish > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via > >>>>>>>>>>> > > > >>>> petsc-users > >>>>>>>>>>> > > > >>>> > > >>> wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not > >>>>>>>>>>> > > > >>>> working. It is > >>>>>>>>>>> > > > >>>> > > >>> > > showing > >>>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with > >>>>>>>>>>> > > > >>>> libmesh and > >>>>>>>>>>> > > > >>>> > > >>> this is > >>>>>>>>>>> > > > >>>> > > >>> > > for > >>>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without > >>>>>>>>>>> > > > >>>> linking > >>>>>>>>>>> > > > >>>> > > >>> Matlab > >>>>>>>>>>> > > > >>>> > > >>> > > with > >>>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring > >>>>>>>>>>> > > > >>>> libmesh 1.6.2 > >>>>>>>>>>> > > > >>>> > > >>> that > >>>>>>>>>>> > > > >>>> > > >>> > > PETSc > >>>>>>>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is > >>>>>>>>>>> > > specified. > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with > >>>>>>>>>>> > > > >>>> PETSc and > >>>>>>>>>>> > > > >>>> > > >>> Matlab > >>>>>>>>>>> > > > >>>> > > >>> > > is in > >>>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated > >>>>>>>>>>> > > geometries > >>>>>>>>>>> > > > >>>> it is > >>>>>>>>>>> > > > >>>> > > >>> > > mentioned to > >>>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various > >>>>>>>>>>> > > things > >>>>>>>>>>> > > > >>>> and ended > >>>>>>>>>>> > > > >>>> > > >>> up with > >>>>>>>>>>> > > > >>>> > > >>> > > > > errors. > >>>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my > >>>>>>>>>>> > > > >>>> research work. > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards > >>>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < > >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, > >>>>>>>>>>> > > > >>>> > > >>> > > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for > >>>>>>>>>>> > > the > >>>>>>>>>>> > > > >>>> WEC > >>>>>>>>>>> > > > >>>> > > >>> application. > >>>>>>>>>>> > > > >>>> > > >>> > > You > >>>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with > >>>>>>>>>>> > > > >>>> Matlab. > >>>>>>>>>>> > > > >>>> > > >>> > > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build > >>>>>>>>>>> > > > >>>> libMesh? > >>>>>>>>>>> > > > >>>> > > >>> > > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, > >>>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet > >>>>>>>>>>> > > > >>>> > > >>> > > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS > >>>>>>>>>>> > > > >>>> 20PHD0548 via > >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users > >>>>>>>>>>> > > > >>>> > > >>> > > > > > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all > >>>>>>>>>>> > > > >>>> occurrences > >>>>>>>>>>> > > > >>>> > > >>> of > >>>>>>>>>>> > > > >>>> > > >>> > > "-lut > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make > >>>>>>>>>>> > > test" > >>>>>>>>>>> > > > >>>> got the > >>>>>>>>>>> > > > >>>> > > >>> > > following > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> errors > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok > >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > >>>>>>>>>>> > > > >>>> > > >>> Error > >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > >>>>>>>>>>> > > Message > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> -------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine > >>>>>>>>>>> > > on > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > > > >>>> for > >>>>>>>>>>> > > > >>>> > > >>> trouble > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > >>>>>>>>>>> > > Aug > >>>>>>>>>>> > > > >>>> 01, 2020 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > >>>>>>>>>>> > > linux-debug > >>>>>>>>>>> > > > >>>> named > >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 > >>>>>>>>>>> > > > >>>> --with-x=0 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() > >>>>>>>>>>> > > line > >>>>>>>>>>> > > > >>>> 67 in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > >>>>>>>>>>> > > > >>>> Message > >>>>>>>>>>> > > > >>>> > > >>> -------send > >>>>>>>>>>> > > > >>>> > > >>> > > entire > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to > >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > >>>>>>>>>>> > > kill > >>>>>>>>>>> > > > >>>> all MPI > >>>>>>>>>>> > > > >>>> > > >>> > > processes. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other > >>>>>>>>>>> > > processes, > >>>>>>>>>>> > > > >>>> > > >>> depending on > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok > >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>>>>>>>>> > > > >>>> # SKIP > >>>>>>>>>>> > > > >>>> > > >>> Command > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok > >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # > >>>>>>>>>>> > > > >>>> > > >>> Error > >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error > >>>>>>>>>>> > > Message > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> -------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine > >>>>>>>>>>> > > on > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html > >>>>>>>>>>> > > > >>>> for > >>>>>>>>>>> > > > >>>> > > >>> trouble > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > >>>>>>>>>>> > > Aug > >>>>>>>>>>> > > > >>>> 01, 2020 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a > >>>>>>>>>>> > > linux-opt > >>>>>>>>>>> > > > >>>> named > >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > >>>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 > >>>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt > >>>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 > >>>>>>>>>>> > > > >>>> --download-fblaslapack=1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() > >>>>>>>>>>> > > line > >>>>>>>>>>> > > > >>>> 67 in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error > >>>>>>>>>>> > > > >>>> Message > >>>>>>>>>>> > > > >>>> > > >>> -------send > >>>>>>>>>>> > > > >>>> > > >>> > > entire > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to > >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator > >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to > >>>>>>>>>>> > > kill > >>>>>>>>>>> > > > >>>> all MPI > >>>>>>>>>>> > > > >>>> > > >>> > > processes. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other > >>>>>>>>>>> > > processes, > >>>>>>>>>>> > > > >>>> > > >>> depending on > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -------------------------------------------------------------------------- > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok > >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test > >>>>>>>>>>> > > > >>>> # SKIP > >>>>>>>>>>> > > > >>>> > > >>> Command > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 > >>>>>>>>>>> > > version. I > >>>>>>>>>>> > > > >>>> am > >>>>>>>>>>> > > > >>>> > > >>> sharing the > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and > >>>>>>>>>>> > > > >>>> petsc > >>>>>>>>>>> > > > >>>> > > >>> 3.17.5. > >>>>>>>>>>> > > > >>>> > > >>> > > Please find > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < > >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's > >>>>>>>>>>> > > > >>>> > > >>> configure.log/make.log > >>>>>>>>>>> > > > >>>> > > >>> > > for > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: > >>>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > >>>>>>>>>>> > > -leng > >>>>>>>>>>> > > > >>>> -lmex > >>>>>>>>>>> > > > >>>> > > >>> -lmx > >>>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are > >>>>>>>>>>> > > seeing: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not > >>>>>>>>>>> > > > >>>> preset here. > >>>>>>>>>>> > > > >>>> > > >>> This > >>>>>>>>>>> > > > >>>> > > >>> > > might > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables > >>>>>>>>>>> > > > >>>> > > >>> > > and > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata > >>>>>>>>>>> > > -licui18n > >>>>>>>>>>> > > > >>>> -licuuc" > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in > >>>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 > >>>>>>>>>>> > > via > >>>>>>>>>>> > > > >>>> > > >>> petsc-users > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building > >>>>>>>>>>> > > > >>>> petsc3.13.4 with > >>>>>>>>>>> > > > >>>> > > >>> > > matlab and > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> also > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with > >>>>>>>>>>> > > > >>>> petsc3.17.5 and > >>>>>>>>>>> > > > >>>> > > >>> matlab. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done > >>>>>>>>>>> > > successfully. > >>>>>>>>>>> > > > >>>> But > >>>>>>>>>>> > > > >>>> > > >>> libmesh is > >>>>>>>>>>> > > > >>>> > > >>> > > not > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < > >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both > >>>>>>>>>>> > > > >>>> petsc-3.13 and > >>>>>>>>>>> > > > >>>> > > >>> 3.17 [or > >>>>>>>>>>> > > > >>>> > > >>> > > 3.19]. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs > >>>>>>>>>>> > > friendly to > >>>>>>>>>>> > > > >>>> mailing > >>>>>>>>>>> > > > >>>> > > >>> list - > >>>>>>>>>>> > > > >>>> > > >>> > > or > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> send > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or > >>>>>>>>>>> > > 3.19?] > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS > >>>>>>>>>>> > > 20PHD0548 > >>>>>>>>>>> > > > >>>> via > >>>>>>>>>>> > > > >>>> > > >>> petsc-users > >>>>>>>>>>> > > > >>>> > > >>> > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while > >>>>>>>>>>> > > building > >>>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 > >>>>>>>>>>> > > > >>>> > > >>> > > with > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the > >>>>>>>>>>> > > needful. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU > >>>>>>>>>>> > > > >>>> SRINIVAS > >>>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > > >>>>>>>>>>> > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During > >>>>>>>>>>> > > building > >>>>>>>>>>> > > > >>>> of > >>>>>>>>>>> > > > >>>> > > >>> libmesh, the > >>>>>>>>>>> > > > >>>> > > >>> > > error > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish > >>>>>>>>>>> > > > >>>> Balay < > >>>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says > >>>>>>>>>>> > > > >>>> petsc-3.17 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS > >>>>>>>>>>> > > > >>>> 20PHD0548 via > >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for > >>>>>>>>>>> > > > >>>> working on > >>>>>>>>>>> > > > >>>> > > >>> the > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the > >>>>>>>>>>> > > PETSc, > >>>>>>>>>>> > > > >>>> using the > >>>>>>>>>>> > > > >>>> > > >>> > > following > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to > >>>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit > >>>>>>>>>>> > > > >>>> status > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished > >>>>>>>>>>> > > jobs.... > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore > >>>>>>>>>>> > > > >>>> Institute of > >>>>>>>>>>> > > > >>>> > > >>> > > Technology. > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain legally > >>>>>>>>>>> > > > >>>> protected > >>>>>>>>>>> > > > >>>> > > >>> > > confidential or > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of > >>>>>>>>>>> > > > >>>> Technology?. > >>>>>>>>>>> > > > >>>> > > >>> If > >>>>>>>>>>> > > > >>>> > > >>> > > you are > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should not > >>>>>>>>>>> > > > >>>> disseminate, > >>>>>>>>>>> > > > >>>> > > >>> distribute > >>>>>>>>>>> > > > >>>> > > >>> > > or copy > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately > >>>>>>>>>>> > > > >>>> and destroy > >>>>>>>>>>> > > > >>>> > > >>> all > >>>>>>>>>>> > > > >>>> > > >>> > > copies of > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. 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If > >>>>>>>>>>> > > > >>>> you are > >>>>>>>>>>> > > > >>>> > > >> not the intended recipient, you should not disseminate, > >>>>>>>>>>> > > > >>>> distribute or copy > >>>>>>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy > >>>>>>>>>>> > > > >>>> all copies of > >>>>>>>>>>> > > > >>>> > > >> this message and any attachments. If you have received this > >>>>>>>>>>> > > > >>>> email in error, > >>>>>>>>>>> > > > >>>> > > >> please promptly notify the sender by reply email and delete > >>>>>>>>>>> > > the > >>>>>>>>>>> > > > >>>> original > >>>>>>>>>>> > > > >>>> > > >> email and any backup copies without reading them.* > >>>>>>>>>>> > > > >>>> > > >> > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > -- > >>>>>>>>>>> > > > >>>> > > > --Amneet > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> > >>>>>>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of > >>>>>>>>>>> > > Technology. > >>>>>>>>>>> > > > >>> The contents of this email may contain legally protected > >>>>>>>>>>> > > confidential or > >>>>>>>>>>> > > > >>> privileged information of ?Vellore Institute of Technology?. If you > >>>>>>>>>>> > > are > >>>>>>>>>>> > > > >>> not the intended recipient, you should not disseminate, distribute > >>>>>>>>>>> > > or copy > >>>>>>>>>>> > > > >>> this e-mail. Please notify the sender immediately and destroy all > >>>>>>>>>>> > > copies of > >>>>>>>>>>> > > > >>> this message and any attachments. 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If you > >>>>>>>>>>> > > are > >>>>>>>>>>> > > > > not the intended recipient, you should not disseminate, distribute or > >>>>>>>>>>> > > copy > >>>>>>>>>>> > > > > this e-mail. Please notify the sender immediately and destroy all > >>>>>>>>>>> > > copies of > >>>>>>>>>>> > > > > this message and any attachments. If you have received this email in > >>>>>>>>>>> > > error, > >>>>>>>>>>> > > > > please promptly notify the sender by reply email and delete the > >>>>>>>>>>> > > original > >>>>>>>>>>> > > > > email and any backup copies without reading them.* > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>> > >>>>>>>>>> Disclaimer: > >>>>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> -- > >>>>>>>>> --Amneet > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>>>> Disclaimer: > >>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. > >>>>>>> > >>>>>> > >>>>>> Disclaimer: > >>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. > >>>>> > >>>> > >>>> > >>>> -- > >>>> --Amneet > >>>> > >>>> > >>>> > >>> > >>> > >>> -- > >>> --Amneet > >>> > >>> > >>> > > > > Disclaimer: > > This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. > > From inturu.srinivas2020 at vitstudent.ac.in Wed Sep 6 13:59:42 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Thu, 7 Sep 2023 00:29:42 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: I tried with different examples and all are working later. As you said there may be a license issue. I will try with latest matlab version. Thanks and regards Srinivas On Thu, Sep 7, 2023, 00:24 Satish Balay wrote: > I'm still curios why the first [c++] attempt failed but the second one > succeeded. > > The only difference I can spot is myEngineApp.cpp vs myEngineApp2.cpp. > What is the difference here between these 2 source files? > > Or is it some random error [the same source code worked failed before - > but works now - and might fail again later?] > > Maybe there is some issue with matlab license here - that prevents some > usages (or usage patterns) to fail? > > Satish > > On Wed, 6 Sep 2023, Barry Smith wrote: > > > > > Ok, so the C++ binding for Matlab engine is working on your machine. > PETSc uses the C binding which links against different libraries but, one > would think the C binding would work for sure if the C++ binding works. Can > you try a Matlab Engine C example provided by Matlab? > > > > > > > > > > > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > > Hi Amneet, > > > > > > I repeated the same procedure again and this time it is working. > > > $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp > -lMatlabDataArray -lMatlabEngine > > > > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > $export LD_LIBRARY_PATH > > > $./a.out > > > Square root of -2 is 0 + 1.41421i > > > Square root of 2 is 1.41421 + 0i > > > Square root of 6 is 2.44949 + 0i > > > Square root of 8 is 2.82843 + 0i > > > I don't know how it is working this time? > > > > > > Thanks and regards > > > Srinivas > > > > > > > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in inturu.srinivas2020 at vitstudent.ac.in>> wrote: > > >> Hi Amneet, > > >> I tried the following example to run a matlab engine. > > >> > > >> #include "MatlabDataArray.hpp" > > >> #include "MatlabEngine.hpp" > > >> #include > > >> void callSQRT() { > > >> > > >> using namespace matlab::engine; > > >> > > >> // Start MATLAB engine synchronously > > >> std::unique_ptr matlabPtr = startMATLAB(); > > >> > > >> //Create MATLAB data array factory > > >> matlab::data::ArrayFactory factory; > > >> > > >> // Define a four-element typed array > > >> matlab::data::TypedArray const argArray = > > >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); > > >> > > >> // Call MATLAB sqrt function on the data array > > >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", > argArray); > > >> > > >> // Display results > > >> for (int i = 0; i < results.getNumberOfElements(); i++) { > > >> double a = argArray[i]; > > >> std::complex v = results[i]; > > >> double realPart = v.real(); > > >> double imgPart = v.imag(); > > >> std::cout << "Square root of " << a << " is " << > > >> realPart << " + " << imgPart << "i" << std::endl; > > >> } > > >> } > > >> > > >> int main() { > > >> callSQRT(); > > >> return 0; > > >> } > > >> > > >> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp > -lMatlabDataArray -lMatlabEngine > > >> > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >> $export LD_LIBRARY_PATH > > >> $./a.out > > >> Starting > > >> Error: The import statement 'import matlab.internal.engine.input' > cannot be found or cannot be imported. Imported names must end with '.*' or > be fully qualified. > > >> > > >> terminate called after throwing an instance of > 'matlab::engine::EngineException' > > >> what(): MATLAB process cannot be created. > > >> Aborted (core dumped) > > >> > > >> I got the above error for Matlab R2020b. Please help me to sort out > this. > > >> > > >> Thanks and regards > > >> Srinivas > > >> > > >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: > > >>> BTW, what Barry is suggesting is the following: > > >>> > > >>> Compile a sample code with a command line this: > > >>> > > >>> g++ -std=c++11 -I matlabroot/extern/include/ -L > matlabroot/extern/bin/glnxa64/ > > >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine > > >>> > > >>> This command is provided here: > > >>> > https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html > > >>> > > >>> A sample MATLAB code is here: > > >>> > https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html > > >>> > > >>> (You can just pick a few lines of code from here to create a > barebone example) > > >>> > > >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: > > >>>> Srinivas --- Do you have a different version of MATLAB that you can > install? If your organization has a MATLAB license, you can install recent > versions of MATLAB from mathworks.com > > >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > wrote: > > >>>>> > > >>>>> Ok, I have no suggestions. It seems to be more an issue with > the Matlab than PETSc. You could find a pure Matlab example of using the > engine (in the Matlab documentation) and try it to see if it works. > > >>>>> > > >>>>> Barry > > >>>>> > > >>>>> > > >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in inturu.srinivas2020 at vitstudent.ac.in>> wrote: > > >>>>>> > > >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); > > >>>>>> I got the same errors for petsc 3.17.5 > > >>>>>> > > >>>>>> make all > > >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o > > >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 > > >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE > > >>>>>> Building with 'gcc'. > > >>>>>> > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > > >>>>>> > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > > >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>>>> | ^ > > >>>>>> > > >>>>>> MEX completed successfully. > > >>>>>> Building with 'gcc'. > > >>>>>> MEX completed successfully. > > >>>>>> Building with 'gcc'. > > >>>>>> MEX completed successfully. > > >>>>>> Building with 'gcc'. > > >>>>>> > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > > >>>>>> > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > > >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>>>> | ^ > > >>>>>> > > >>>>>> MEX completed successfully. > > >>>>>> ========================================= > > >>>>>> ========================================= > > >>>>>> Now to check if the libraries are working do: > > >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt > check > > >>>>>> > > >>>>>> make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/ > > >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ > queryval=matlab query=requires > > >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > >>>>>> TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > > >>>>>> # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > >>>>>> # [0]PETSC ERROR: Error in external library > > >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble > shooting. > > >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > > >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by > vit Tue Sep 5 21:39:22 2023 > > >>>>>> # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 > > >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 > > >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 > > >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 > > >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at > /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > > >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at > /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > > >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at > /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > > >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at > /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > > >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at > /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > > >>>>>> # [0]PETSC ERROR: #9 main() at > /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > > >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: > > >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 > > >>>>>> # [0]PETSC ERROR: -error_output_stdout > > >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > > >>>>>> # [0]PETSC ERROR: -malloc_dump > > >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > >>>>>> # [0]PETSC ERROR: -pc_type lu > > >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > > >>>>>> # [0]PETSC ERROR: ----------------End of Error Message > -------send entire error message to petsc-maint at mcs.anl.gov---------- > > >>>>>> # > -------------------------------------------------------------------------- > > >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > >>>>>> # with errorcode 85. > > >>>>>> # > > >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > >>>>>> # You may or may not see output from other processes, depending on > > >>>>>> # exactly when Open MPI kills them. > > >>>>>> # > -------------------------------------------------------------------------- > > >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > >>>>>> > > >>>>>> > > >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 > > >>>>>> # > > >>>>>> # To rerun failed tests: > > >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 > > >>>>>> > > >>>>>> Thanks and regards > > >>>>>> Srinivas > > >>>>>> > > >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: > > >>>>>>> > > >>>>>>> The error is occuring during > > >>>>>>> > > >>>>>>> e->ep = engOpen(buffer); > > >>>>>>> > > >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab > -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to > assume the problem is occuring when engOpen() is attempting to connect the > stdout and stdin from the Matlab session that is launched to the > executable. > > >>>>>>> > > >>>>>>> You can try the following. In 3.17.5 edit the file > src/sys/classes/matlabengine/matlab.c and locate the line > > >>>>>>> > > >>>>>>> e->ep = engOpen(buffer); > > >>>>>>> > > >>>>>>> replace it with > > >>>>>>> > > >>>>>>> e->ep = engOpen(""); > > >>>>>>> > > >>>>>>> Now in the PETSc directory do make all (it should recompile one > file) and then run the > > >>>>>>> > > >>>>>>> make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/ > > >>>>>>> > > >>>>>>> again > > >>>>>>> > > >>>>>>> > > >>>>>>> > > >>>>>>> > > >>>>>>> > > >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via > petsc-users > > wrote: > > >>>>>>>> > > >>>>>>>> Hi Amneeth, > > >>>>>>>> > > >>>>>>>> I think the errors are different with petsc 3.17.5 > > >>>>>>>> > > >>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx > --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > >>>>>>>> The version of PETSc you are using is out-of-date, we recommend > updating to the new release > > >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 > > >>>>>>>> https://petsc.org/release/download/ > > >>>>>>>> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > >>>>>>>> > ============================================================================================= > > >>>>>>>> Configuring PETSc to compile on your > system > > >>>>>>>> > ============================================================================================= > > >>>>>>>> Compilers: > > > >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall > -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch > -fstack-protector -fvisibility=hidden -O3 > > >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch > -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC > > >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > > >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall > -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 > > >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>>>>>>> Linkers: > > >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall > -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch > -fstack-protector -fvisibility=hidden -O3 > > >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall > -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch > -fstack-protector -fvisibility=hidden -O3 > > >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl > > >>>>>>>> BlasLapack: > > >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread > > >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or > -omp_num_threads

to control the number of threads > > >>>>>>>> uses 8 byte integers > > >>>>>>>> MPI: > > >>>>>>>> Version: 3 > > >>>>>>>> mpiexec: /usr/bin/mpiexec > > >>>>>>>> Implementation: openmpi > > >>>>>>>> OMPI_VERSION: 4.0.3 > > >>>>>>>> pthread: > > >>>>>>>> cmake: > > >>>>>>>> Version: 3.16.3 > > >>>>>>>> /usr/bin/cmake > > >>>>>>>> regex: > > >>>>>>>> Matlab: > > >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > >>>>>>>> /usr/local/MATLAB/R2020b > > >>>>>>>> MatlabEngine: > > >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat > -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher > -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c > > >>>>>>>> Language used to compile PETSc: C > > >>>>>>>> PETSc: > > >>>>>>>> PETSC_ARCH: linux-opt > > >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 > > >>>>>>>> Prefix: > > >>>>>>>> Scalar type: real > > >>>>>>>> Precision: double > > >>>>>>>> Support for __float128 > > >>>>>>>> Integer size: 4 bytes > > >>>>>>>> Single library: yes > > >>>>>>>> Shared libraries: yes > > >>>>>>>> Memory alignment from malloc(): 16 bytes > > >>>>>>>> Using GNU make: /usr/bin/make > > >>>>>>>> > xxx=========================================================================xxx > > >>>>>>>> Configure stage complete. Now build PETSc libraries with: > > >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 > PETSC_ARCH=linux-opt all > > >>>>>>>> > xxx=========================================================================xxx > > >>>>>>>> > > >>>>>>>> $make > > >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 > > >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE > > >>>>>>>> Building with 'gcc'. > > >>>>>>>> > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > > >>>>>>>> > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > > >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>>>>>> | ^ > > >>>>>>>> > > >>>>>>>> MEX completed successfully. > > >>>>>>>> Building with 'gcc'. > > >>>>>>>> MEX completed successfully. > > >>>>>>>> Building with 'gcc'. > > >>>>>>>> MEX completed successfully. > > >>>>>>>> Building with 'gcc'. > > >>>>>>>> > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ?PetscBinaryWrite?: > > >>>>>>>> > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > warning: ?err? may be used uninitialized in this function > [-Wmaybe-uninitialized] > > >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>>>>>> | ^ > > >>>>>>>> > > >>>>>>>> MEX completed successfully. > > >>>>>>>> ========================================= > > >>>>>>>> ========================================= > > >>>>>>>> Now to check if the libraries are working do: > > >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 > PETSC_ARCH=linux-opt check > > >>>>>>>> > > >>>>>>>> $make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/ > > >>>>>>>> /usr/bin/python3 > /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py > --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt > --testdir=./linux-opt/tests > > >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ > queryval=matlab query=requires > > >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > >>>>>>>> TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > > >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > >>>>>>>> # [0]PETSC ERROR: Error in external library > > >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for > trouble shooting. > > >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > > >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by > vit Tue Sep 5 10:15:57 2023 > > >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc > --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 > FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 > > >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 > > >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 > > >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at > /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > > >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at > /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > > >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > > >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > > >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > > >>>>>>>> # [0]PETSC ERROR: #9 main() at > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > > >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: > > >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 > > >>>>>>>> # [0]PETSC ERROR: -error_output_stdout > > >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > > >>>>>>>> # [0]PETSC ERROR: -malloc_dump > > >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > >>>>>>>> # [0]PETSC ERROR: -pc_type lu > > >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > > >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message > -------send entire error message to petsc-maint at mcs.anl.gov---------- > > >>>>>>>> # > -------------------------------------------------------------------------- > > >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > >>>>>>>> # with errorcode 85. > > >>>>>>>> # > > >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > >>>>>>>> # You may or may not see output from other processes, depending > on > > >>>>>>>> # exactly when Open MPI kills them. > > >>>>>>>> # > -------------------------------------------------------------------------- > > >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > >>>>>>>> > > >>>>>>>> > > >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 > > >>>>>>>> # > > >>>>>>>> # To rerun failed tests: > > >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 > > >>>>>>>> > > >>>>>>>> To get the info of the error there is no specific probe id > reported. > > >>>>>>>> > > >>>>>>>> How to check error info and proceed further? > > >>>>>>>> > > >>>>>>>> Thanks and regards > > >>>>>>>> Srinivas > > >>>>>>>> > > >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla < > mail2amneet at gmail.com > wrote: > > >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new > configure options that Satish mentioned? > > >>>>>>>>> > > >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via > petsc-users > > wrote: > > >>>>>>>>>> Sorry for missing that. > > >>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay > -nosplash > > >>>>>>>>>> > > >>>>>>>>>> < M A T L A B (R) > > > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. > > >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) > > >>>>>>>>>> November 23, 2020 > > >>>>>>>>>> > > >>>>>>>>>> > > >>>>>>>>>> To get started, type doc. > > >>>>>>>>>> For product information, visit www.mathworks.com < > http://www.mathworks.com/>. > > >>>>>>>>>> > > >>>>>>>>>> Thanks and regards > > >>>>>>>>>> Srinivas > > >>>>>>>>>> > > >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay < > balay at mcs.anl.gov > wrote: > > >>>>>>>>>>> You are missing one more step: > > >>>>>>>>>>> > > >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 > > >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with > command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > >>>>>>>>>>> > > >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command > "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" > > >>>>>>>>>>> > > >>>>>>>>>>> Does this work for you? As the message indicates this > command is invoked by "matlab_ls_test" - and that is failing. > > >>>>>>>>>>> > > >>>>>>>>>>> Satish > > >>>>>>>>>>> > > >>>>>>>>>>> > > >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via > petsc-users wrote: > > >>>>>>>>>>> > > >>>>>>>>>>> > Hi Sathish, > > >>>>>>>>>>> > > > >>>>>>>>>>> > I tried the following procedure > > >>>>>>>>>>> > > > >>>>>>>>>>> > *$make * > > >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE > > >>>>>>>>>>> > Building with 'gcc'. > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > >>>>>>>>>>> > In function ?PetscBinaryWrite?: > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function > > >>>>>>>>>>> > [-Wmaybe-uninitialized] > > >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>>>>>>>>> > | ^ > > >>>>>>>>>>> > > > >>>>>>>>>>> > MEX completed successfully. > > >>>>>>>>>>> > Building with 'gcc'. > > >>>>>>>>>>> > MEX completed successfully. > > >>>>>>>>>>> > Building with 'gcc'. > > >>>>>>>>>>> > MEX completed successfully. > > >>>>>>>>>>> > Building with 'gcc'. > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > >>>>>>>>>>> > In function ?PetscBinaryWrite?: > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function > > >>>>>>>>>>> > [-Wmaybe-uninitialized] > > >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > socket\n"); > > >>>>>>>>>>> > | ^ > > >>>>>>>>>>> > > > >>>>>>>>>>> > MEX completed successfully. > > >>>>>>>>>>> > ========================================= > > >>>>>>>>>>> > Now to check if the libraries are working do: > > >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > PETSC_ARCH=linux-opt check > > >>>>>>>>>>> > > > >>>>>>>>>>> > *$make test query=requires queryval=matlab > > >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* > > >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ > queryval=matlab > > >>>>>>>>>>> > query=requires > > >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > >>>>>>>>>>> > TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > >>>>>>>>>>> > > -------------------------------------------------------------- > > >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library > > >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on > > >>>>>>>>>>> > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>>>>>>>>> > for trouble shooting. > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > 2020 > > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named > MB108SMEC028 by vit Mon Sep > > >>>>>>>>>>> > 4 10:02:32 2023 > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > >>>>>>>>>>> > > -------------------------------------------------------------- > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data > > >>>>>>>>>>> > # [0]PETSC ERROR: > > >>>>>>>>>>> > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>>>>>>>>> > for trouble shooting. > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > 2020 > > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named > MB108SMEC028 by vit Mon Sep > > >>>>>>>>>>> > 4 10:02:32 2023 > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>>>>>>>>> > # [0]PETSC ERROR: > > >>>>>>>>>>> > > ------------------------------------------------------------------------ > > >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: > Segmentation Violation, > > >>>>>>>>>>> > probably memory access out of range > > >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or > -on_error_attach_debugger > > >>>>>>>>>>> > # [0]PETSC ERROR: or see > > >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org < > http://valgrind.org/> on GNU/linux and Apple Mac OS > > >>>>>>>>>>> > X to find memory corruption errors > > >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, > recompile, link, > > >>>>>>>>>>> > and run > > >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > >>>>>>>>>>> > > -------------------------------------------------------------- > > >>>>>>>>>>> > # [0]PETSC ERROR: Signal received > > >>>>>>>>>>> > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>>>>>>>>> > for trouble shooting. > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > 2020 > > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named > MB108SMEC028 by vit Mon Sep > > >>>>>>>>>>> > 4 10:02:32 2023 > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in > unknown file > > >>>>>>>>>>> > # > -------------------------------------------------------------------------- > > >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator > MPI_COMM_WORLD > > >>>>>>>>>>> > # with errorcode 50162059. > > >>>>>>>>>>> > # > > >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > >>>>>>>>>>> > # You may or may not see output from other processes, > depending on > > >>>>>>>>>>> > # exactly when Open MPI kills them. > > >>>>>>>>>>> > # > -------------------------------------------------------------------------- > > >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no > diff > > >>>>>>>>>>> > CC > > >>>>>>>>>>> > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > >>>>>>>>>>> > CLINKER > > >>>>>>>>>>> > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>>>>>>>>>> > TEST > > >>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > Error code: 124 > > >>>>>>>>>>> > # Running problem 5 > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > >>>>>>>>>>> > > -------------------------------------------------------------- > > >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library > > >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on > > >>>>>>>>>>> > # [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>>>>>>>>> > for trouble shooting. > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > 2020 > > >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > MB108SMEC028 by > > >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: > > >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 > > >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor > > >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message > -------send entire > > >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- > > >>>>>>>>>>> > # > -------------------------------------------------------------------------- > > >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator > MPI_COMM_SELF > > >>>>>>>>>>> > # with errorcode 126076. > > >>>>>>>>>>> > # > > >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > >>>>>>>>>>> > # You may or may not see output from other processes, > depending on > > >>>>>>>>>>> > # exactly when Open MPI kills them. > > >>>>>>>>>>> > # > -------------------------------------------------------------------------- > > >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > SKIP Command failed > > >>>>>>>>>>> > so no diff > > >>>>>>>>>>> > > > >>>>>>>>>>> > # ------------- > > >>>>>>>>>>> > # Summary > > >>>>>>>>>>> > # ------------- > > >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 > > >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test > > >>>>>>>>>>> > # success 0/2 tests (0.0%) > > >>>>>>>>>>> > # failed 2/2 tests (100.0%) > > >>>>>>>>>>> > # todo 0/2 tests (0.0%) > > >>>>>>>>>>> > # skip 0/2 tests (0.0%) > > >>>>>>>>>>> > # > > >>>>>>>>>>> > # Wall clock time for tests: 4 sec > > >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec > > >>>>>>>>>>> > # > > >>>>>>>>>>> > # To rerun failed tests: > > >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 > > >>>>>>>>>>> > # > > >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): > > >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec > > >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 > sec / 0.01 sec > > >>>>>>>>>>> > > > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* > > >>>>>>>>>>> > *$make matlab_ls_test* > > >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall > -Wwrite-strings > > >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing > > >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden > -O3 > > >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include > > >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > > >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include > > >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include > matlab_ls_test.c > > >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > > >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > > >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu > -Wl,-rpath,/lib/x86_64-linux-gnu > > >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm > -leng -lmex -lmx > > >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 > -lmpi_usempi_ignore_tkr -lmpi_mpifh > > >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath > -lpthread -lquadmath > > >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test > > >>>>>>>>>>> > > > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 > ./matlab_ls_test > > >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* > > >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number > of processors = 1 > > >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > >>>>>>>>>>> > MB108SMEC028.(none) > > >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 > > >>>>>>>>>>> > Running problem 5 > > >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator > 140155238476992 > > >>>>>>>>>>> > 94202473157392 max tags = 2147483647 > > >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with > command > > >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay > -nosplash > > >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message > > >>>>>>>>>>> > > -------------------------------------------------------------- > > >>>>>>>>>>> > [0]PETSC ERROR: Error in external library > > >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on > > >>>>>>>>>>> > [0]PETSC ERROR: See > https://www.mcs.anl.gov/petsc/documentation/faq.html > > >>>>>>>>>>> > for trouble shooting. > > >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named > MB108SMEC028 by vit > > >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 > > >>>>>>>>>>> > [0]PETSC ERROR: Configure options > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > >>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c > > >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: > > >>>>>>>>>>> > [0]PETSC ERROR: -info > > >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 > > >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor > > >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message > -------send entire > > >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- > > >>>>>>>>>>> > > -------------------------------------------------------------------------- > > >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator > MPI_COMM_SELF > > >>>>>>>>>>> > with errorcode 126076. > > >>>>>>>>>>> > > > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > processes. > > >>>>>>>>>>> > You may or may not see output from other processes, > depending on > > >>>>>>>>>>> > exactly when Open MPI kills them. > > >>>>>>>>>>> > > > >>>>>>>>>>> > Please find the attachment for configure.log and make.log > files > > >>>>>>>>>>> > > > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay < > balay at mcs.anl.gov > wrote: > > >>>>>>>>>>> > > > >>>>>>>>>>> > > To use datafiles in the test suite: > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > cd $HOME > > >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles > > >>>>>>>>>>> > > DATAFILESPATH - or set > > >>>>>>>>>>> > > manually with make> > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > make test query=requires queryval=matlab > DATAFILESPATH=$HOME/datafiles > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > Satish > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS > 20PHD0548 < > > >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in inturu.srinivas2020 at vitstudent.ac.in>> wrote: > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > Hi Matthew, > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using > IBAMR. I do not have > > >>>>>>>>>>> > > any > > >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you > please help me how to > > >>>>>>>>>>> > > > > define this DATAFILESPATH? > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our > machine, we point to > > >>>>>>>>>>> > > this > > >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. > You don't have those > > >>>>>>>>>>> > > > matrices, since they are just for testing here. That > > >>>>>>>>>>> > > > is why I suggested just using a different matrix, or > running a problem > > >>>>>>>>>>> > > you > > >>>>>>>>>>> > > > care about in IBAMR. > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > Thanks, > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > Matt > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > > Thanks and regards > > >>>>>>>>>>> > > > > Srinivas. > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < > knepley at gmail.com > > > >>>>>>>>>>> > > wrote: > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS > 20PHD0548 via > > >>>>>>>>>>> > > petsc-users < > > >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov petsc-users at mcs.anl.gov>> wrote: > > >>>>>>>>>>> > > > >> > > >>>>>>>>>>> > > > >>> Hi Sathish, > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support > you are giving me > > >>>>>>>>>>> > > to > > >>>>>>>>>>> > > > >>> sort this out. > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you > followed to build > > >>>>>>>>>>> > > Petsc > > >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> *$./configure > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > PETSC_ARCH=linux-opt > > >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 > > >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 > --with-matlab-engine=1* > > >>>>>>>>>>> > > > >>> Using python3 for Python > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > =============================================================================== > > >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your > system > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > =============================================================================== > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > =============================================================================== > > >>>>>>>>>>> > > > >>> It appears > you do not have > > >>>>>>>>>>> > > valgrind > > >>>>>>>>>>> > > > >>> installed on your system. > > >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from > www.valgrind.org > > >>>>>>>>>>> > > > >>> Or > install > > >>>>>>>>>>> > > valgrind-devel or > > >>>>>>>>>>> > > > >>> equivalent using your package manager. > > >>>>>>>>>>> > > > >>> Then rerun ./configure > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > =============================================================================== > > >>>>>>>>>>> > > > >>> Compilers: > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> C Compiler: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>>>>>>>>>> > > -fPIC > > >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > > >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) > 9.4.0 > > >>>>>>>>>>> > > > >>> C++ Compiler: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > > >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) > 11.4.0 > > >>>>>>>>>>> > > > >>> Fortran Compiler: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 > -Wno-unused-dummy-argument -O3 > > >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu > 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > >>>>>>>>>>> > > > >>> Linkers: > > >>>>>>>>>>> > > > >>> Shared linker: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>>>>>>>>>> > > -shared > > >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > >>>>>>>>>>> > > -Wno-unknown-pragmas > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > > >>>>>>>>>>> > > > >>> Dynamic linker: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > >>>>>>>>>>> > > -shared > > >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > >>>>>>>>>>> > > -Wno-unknown-pragmas > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > > >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ > -ldl > > >>>>>>>>>>> > > > >>> make: > > >>>>>>>>>>> > > > >>> Version: 4.2 > > >>>>>>>>>>> > > > >>> /usr/bin/make > > >>>>>>>>>>> > > > >>> BlasLapack: > > >>>>>>>>>>> > > > >>> Library: > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 > -lpthread > > >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or > -omp_num_threads > > >>>>>>>>>>> > >

to > > >>>>>>>>>>> > > > >>> control the number of threads > > >>>>>>>>>>> > > > >>> uses 8 byte integers > > >>>>>>>>>>> > > > >>> MPI: > > >>>>>>>>>>> > > > >>> Version: 3 > > >>>>>>>>>>> > > > >>> Includes: > -I/home/vit/sfw/linux/openmpi/4.1.4/include > > >>>>>>>>>>> > > > >>> Mpiexec: > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec > > >>>>>>>>>>> > > --oversubscribe > > >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 > > >>>>>>>>>>> > > > >>> pthread: > > >>>>>>>>>>> > > > >>> cmake: > > >>>>>>>>>>> > > > >>> Version: 3.16.3 > > >>>>>>>>>>> > > > >>> /usr/bin/cmake > > >>>>>>>>>>> > > > >>> regex: > > >>>>>>>>>>> > > > >>> Matlab: > > >>>>>>>>>>> > > > >>> Includes: > -I/usr/local/MATLAB/R2020b/extern/include > > >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b > > >>>>>>>>>>> > > > >>> MatlabEngine: > > >>>>>>>>>>> > > > >>> Library: > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -leng -lmex -lmx -lmat > > >>>>>>>>>>> > > -lut > > >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc > > >>>>>>>>>>> > > > >>> Language used to compile PETSc: C > > >>>>>>>>>>> > > > >>> PETSc: > > >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt > > >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > > >>>>>>>>>>> > > > >>> Scalar type: real > > >>>>>>>>>>> > > > >>> Precision: double > > >>>>>>>>>>> > > > >>> Support for __float128 > > >>>>>>>>>>> > > > >>> Integer size: 4 bytes > > >>>>>>>>>>> > > > >>> shared libraries: enabled > > >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > xxx=========================================================================xxx > > >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc > libraries with: > > >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > PETSC_ARCH=linux-opt all > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > xxx=========================================================================xxx > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata > -licui18n -licuuc as > > >>>>>>>>>>> > > > >>> you suggested earlier. > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> *$make* > > >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this > function > > >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] > > >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error > writing to socket\n"); > > >>>>>>>>>>> > > > >>> | ^ > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this > function > > >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] > > >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error > writing to socket\n"); > > >>>>>>>>>>> > > > >>> | ^ > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > >>>>>>>>>>> > > > >>> ========================================= > > >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: > > >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > PETSC_ARCH=linux-opt check > > >>>>>>>>>>> > > > >>> =============================================== > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* > > >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > > >>>>>>>>>>> > > > >>> CC > linux-opt/tests/ksp/ksp/tutorials/ex72.o > > >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > >>>>>>>>>>> > > > >>> TEST > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error > Message > > >>>>>>>>>>> > > > >>> > -------------------------------------------------------------- > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: > /matrices/arco1 > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > >> > > >>>>>>>>>>> > > > >> No, the problem is that you do not have > DATAFILESPATH defined, so it > > >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some > test of yours. > > >>>>>>>>>>> > > > >> > > >>>>>>>>>>> > > > >> Thanks, > > >>>>>>>>>>> > > > >> > > >>>>>>>>>>> > > > >> Matt > > >>>>>>>>>>> > > > >> > > >>>>>>>>>>> > > > >> > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See > > >>>>>>>>>>> > > > >>> > https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > >>>>>>>>>>> > > > >>> shooting. > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > Aug 01, 2020 > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named > MB108SMEC028 by vit > > >>>>>>>>>>> > > Sun > > >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options > > >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > COPTFLAGS=-O3 > > >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > --with-debugging=0 > > >>>>>>>>>>> > > > >>> --with-x=0 > --with-matlab-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 > --with-matlab-engine=1 > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 > PetscViewerFileSetUp_BinarySTDIO() line 1444 in > > >>>>>>>>>>> > > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() > line 1511 in > > >>>>>>>>>>> > > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > > >>>>>>>>>>> > > > >>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > > >>>>>>>>>>> > > > >>> > /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > > >>>>>>>>>>> > > > >>> > /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in > > >>>>>>>>>>> > > > >>> > /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error > Message -------send > > >>>>>>>>>>> > > > >>> entire error message to > petsc-maint at mcs.anl.gov---------- > > >>>>>>>>>>> > > > >>> # > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > -------------------------------------------------------------------------- > > >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator > MPI_COMM_SELF > > >>>>>>>>>>> > > > >>> # with errorcode 113065. > > >>>>>>>>>>> > > > >>> # > > >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill > all MPI processes. > > >>>>>>>>>>> > > > >>> # You may or may not see output from other > processes, depending on > > >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. > > >>>>>>>>>>> > > > >>> # > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > -------------------------------------------------------------------------- > > >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command > failed so no diff > > >>>>>>>>>>> > > > >>> CC > > >>>>>>>>>>> > > > >>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > >>>>>>>>>>> > > > >>> CLINKER > > >>>>>>>>>>> > > > >>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > >>>>>>>>>>> > > > >>> TEST > > >>>>>>>>>>> > > > >>> > > >>>>>>>>>>> > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > >>>>>>>>>>> > > > >>> not ok > tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > >>>>>>>>>>> > > code: 124 > > >>>>>>>>>>> > > > >>> # Running problem 5 > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error > Message > > >>>>>>>>>>> > > > >>> > -------------------------------------------------------------- > > >>>>>>> -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? 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URL: From inturu.srinivas2020 at vitstudent.ac.in Wed Sep 6 14:01:58 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Thu, 7 Sep 2023 00:31:58 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: I will try and let you know. Thanks and regards Srinivas On Wed, Sep 6, 2023, 23:47 Barry Smith wrote: > > Ok, so the C++ binding for Matlab engine is working on your machine. > PETSc uses the C binding which links against different libraries but, one > would think the C binding would work for sure if the C++ binding works. Can > you try a Matlab Engine C example provided by Matlab? > > > > > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > Hi Amneet, > > I repeated the same procedure again and this time it is working. > *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp > -lMatlabDataArray -lMatlabEngine* > > *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* > *$export LD_LIBRARY_PATH* > *$./a.out* > Square root of -2 is 0 + 1.41421i > Square root of 2 is 1.41421 + 0i > Square root of 6 is 2.44949 + 0i > Square root of 8 is 2.82843 + 0i > I don't know how it is working this time? > > Thanks and regards > Srinivas > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > >> Hi Amneet, >> I tried the following example to run a matlab engine. >> >> #include "MatlabDataArray.hpp" >> #include "MatlabEngine.hpp" >> #include >> void callSQRT() { >> >> using namespace matlab::engine; >> >> // Start MATLAB engine synchronously >> std::unique_ptr matlabPtr = startMATLAB(); >> >> //Create MATLAB data array factory >> matlab::data::ArrayFactory factory; >> >> // Define a four-element typed array >> matlab::data::TypedArray const argArray = >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >> >> // Call MATLAB sqrt function on the data array >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", >> argArray); >> >> // Display results >> for (int i = 0; i < results.getNumberOfElements(); i++) { >> double a = argArray[i]; >> std::complex v = results[i]; >> double realPart = v.real(); >> double imgPart = v.imag(); >> std::cout << "Square root of " << a << " is " << >> realPart << " + " << imgPart << "i" << std::endl; >> } >> } >> >> int main() { >> callSQRT(); >> return 0; >> } >> >> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp >> -lMatlabDataArray -lMatlabEngine* >> >> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >> *$export LD_LIBRARY_PATH* >> *$./a.out* >> Starting >> Error: The import statement 'import matlab.internal.engine.input' cannot >> be found or cannot be imported. Imported names must end with '.*' or be >> fully qualified. >> >> terminate called after throwing an instance of >> 'matlab::engine::EngineException' >> what(): MATLAB process cannot be created. >> Aborted (core dumped) >> >> I got the above error for Matlab R2020b. Please help me to sort out this. >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla >> wrote: >> >>> BTW, what Barry is suggesting is the following: >>> >>> Compile a sample code with a command line this: >>> >>> >>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>> >>> >>> This command is provided here: >>> >>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>> >>> >>> A sample MATLAB code is here: >>> >>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>> >>> >>> (You can just pick a few lines of code from here to create a barebone example) >>> >>> >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >>> wrote: >>> >>>> Srinivas --- Do you have a different version of MATLAB that you can >>>> install? If your organization has a MATLAB license, you can install recent >>>> versions of MATLAB from mathworks.com >>>> >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>>> >>>>> >>>>> Ok, I have no suggestions. It seems to be more an issue with the >>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>>> (in the Matlab documentation) and try it to see if it works. >>>>> >>>>> Barry >>>>> >>>>> >>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>> >>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>> I got the same errors for petsc 3.17.5 >>>>> >>>>> >>>>> *make all* >>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>> Building with 'gcc'. >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> In function ?PetscBinaryWrite?: >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>> warning: ?err? may be used uninitialized in this function >>>>> [-Wmaybe-uninitialized] >>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> | ^ >>>>> >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> In function ?PetscBinaryWrite?: >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>> warning: ?err? may be used uninitialized in this function >>>>> [-Wmaybe-uninitialized] >>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> | ^ >>>>> >>>>> MEX completed successfully. >>>>> ========================================= >>>>> ========================================= >>>>> Now to check if the libraries are working do: >>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>> >>>>> *make test query=requires queryval=matlab >>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>> query=requires >>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> # [0]PETSC ERROR: Error in external library >>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>> shooting. >>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>>>> Sep 5 21:39:22 2023 >>>>> # [0]PETSC ERROR: Configure options >>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> --known-64-bit-blas-indices=1 >>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>> # [0]PETSC ERROR: #9 main() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>> # [0]PETSC ERROR: -error_output_stdout >>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>> # [0]PETSC ERROR: -malloc_dump >>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>> # [0]PETSC ERROR: -pc_type lu >>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>> # >>>>> -------------------------------------------------------------------------- >>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>> # with errorcode 85. >>>>> # >>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> # You may or may not see output from other processes, depending on >>>>> # exactly when Open MPI kills them. >>>>> # >>>>> -------------------------------------------------------------------------- >>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>> >>>>> >>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>> # >>>>> # To rerun failed tests: >>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>>> >>>>>> >>>>>> The error is occuring during >>>>>> >>>>>> e->ep = engOpen(buffer); >>>>>> >>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>>> stdout and stdin from the Matlab session that is launched to the >>>>>> executable. >>>>>> >>>>>> You can try the following. In 3.17.5 edit the >>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>> >>>>>> e->ep = engOpen(buffer); >>>>>> >>>>>> replace it with >>>>>> >>>>>> e->ep = engOpen(""); >>>>>> >>>>>> Now in the PETSc directory do make all (it should recompile one file) >>>>>> and then run the >>>>>> >>>>>> make test query=requires queryval=matlab >>>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>>> >>>>>> again >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>> wrote: >>>>>> >>>>>> Hi Amneeth, >>>>>> >>>>>> I think the errors are different with petsc 3.17.5 >>>>>> >>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>> >>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>> The version of PETSc you are using is out-of-date, we recommend >>>>>> updating to the new release >>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>> https://petsc.org/release/download/ >>>>>> >>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>> >>>>>> ============================================================================================= >>>>>> Configuring PETSc to compile on your system >>>>>> >>>>>> >>>>>> ============================================================================================= >>>>>> Compilers: >>>>>> >>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>>> -fvisibility=hidden -O3 >>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> Linkers: >>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> BlasLapack: >>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>>>>> to control the number of threads >>>>>> uses 8 byte integers >>>>>> MPI: >>>>>> Version: 3 >>>>>> mpiexec: /usr/bin/mpiexec >>>>>> Implementation: openmpi >>>>>> OMPI_VERSION: 4.0.3 >>>>>> pthread: >>>>>> cmake: >>>>>> Version: 3.16.3 >>>>>> /usr/bin/cmake >>>>>> regex: >>>>>> Matlab: >>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>> /usr/local/MATLAB/R2020b >>>>>> MatlabEngine: >>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>> Language used to compile PETSc: C >>>>>> PETSc: >>>>>> PETSC_ARCH: linux-opt >>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>> Prefix: >>>>>> Scalar type: real >>>>>> Precision: double >>>>>> Support for __float128 >>>>>> Integer size: 4 bytes >>>>>> Single library: yes >>>>>> Shared libraries: yes >>>>>> Memory alignment from malloc(): 16 bytes >>>>>> Using GNU make: /usr/bin/make >>>>>> >>>>>> xxx=========================================================================xxx >>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 >>>>>> PETSC_ARCH=linux-opt all >>>>>> >>>>>> xxx=========================================================================xxx >>>>>> >>>>>> *$make* >>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> Building with 'gcc'. >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> ========================================= >>>>>> ========================================= >>>>>> Now to check if the libraries are working do: >>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>>> check >>>>>> >>>>>> *$make test query=requires queryval=matlab >>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>> /usr/bin/python3 >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>>> --testdir=./linux-opt/tests >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>> queryval=matlab query=requires >>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> -------------------------------------------------------------- >>>>>> # [0]PETSC ERROR: Error in external library >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>> shooting. >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Tue Sep 5 10:15:57 2023 >>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>> # [0]PETSC ERROR: #9 main() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> # with errorcode 85. >>>>>> # >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> # You may or may not see output from other processes, depending on >>>>>> # exactly when Open MPI kills them. >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> >>>>>> >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> # >>>>>> # To rerun failed tests: >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> >>>>>> To get the info of the error there is no specific probe id reported. >>>>>> >>>>>> How to check error info and proceed further? >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>>> wrote: >>>>>> >>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>>>> options that Satish mentioned? >>>>>>> >>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>>> petsc-users wrote: >>>>>>> >>>>>>>> Sorry for missing that. >>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>>>>> >>>>>>>> < M A T L A B (R) > >>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>> November 23, 2020 >>>>>>>> >>>>>>>> >>>>>>>> To get started, type doc. >>>>>>>> For product information, visit www.mathworks.com. >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>>> wrote: >>>>>>>> >>>>>>>>> You are missing one more step: >>>>>>>>> >>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>> >>>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>> >>>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>>> >>>>>>>>> Satish >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> > Hi Sathish, >>>>>>>>> > >>>>>>>>> > I tried the following procedure >>>>>>>>> > >>>>>>>>> > *$make * >>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > | ^ >>>>>>>>> > >>>>>>>>> > MEX completed successfully. >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > MEX completed successfully. >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > MEX completed successfully. >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > | ^ >>>>>>>>> > >>>>>>>>> > MEX completed successfully. >>>>>>>>> > ========================================= >>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>>> check >>>>>>>>> > >>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>> queryval=matlab >>>>>>>>> > query=requires >>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>> > TEST >>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>> vit Mon Sep >>>>>>>>> > 4 10:02:32 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>> vit Mon Sep >>>>>>>>> > 4 10:02:32 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>> > >>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>>> Violation, >>>>>>>>> > probably memory access out of range >>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>>> -on_error_attach_debugger >>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>>> Apple Mac OS >>>>>>>>> > X to find memory corruption errors >>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>>> recompile, link, >>>>>>>>> > and run >>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>> vit Mon Sep >>>>>>>>> > 4 10:02:32 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>>>>> file >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>> > # with errorcode 50162059. >>>>>>>>> > # >>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>> processes. >>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>> on >>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>> > CC >>>>>>>>> > >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>> > CLINKER >>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > TEST >>>>>>>>> > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>> code: 124 >>>>>>>>> > # Running problem 5 >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>> MB108SMEC028 by >>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>> -------send entire >>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>> > # with errorcode 126076. >>>>>>>>> > # >>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>> processes. >>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>> on >>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>> Command failed >>>>>>>>> > so no diff >>>>>>>>> > >>>>>>>>> > # ------------- >>>>>>>>> > # Summary >>>>>>>>> > # ------------- >>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>> > # >>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>> > # >>>>>>>>> > # To rerun failed tests: >>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>> > # >>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>>>>> 0.01 sec >>>>>>>>> > >>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>> > *$make matlab_ls_test* >>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>> -Wwrite-strings >>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>> -Wno-strict-aliasing >>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>>>>> -lmex -lmx >>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>> -lmpi_mpifh >>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>>> -lquadmath >>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>> > >>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>> ./matlab_ls_test >>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>> processors = 1 >>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>> > MB108SMEC028.(none) >>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>> > Running problem 5 >>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>> 140155238476992 >>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>> command >>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>> -nosplash >>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>>> MB108SMEC028 by vit >>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>> entire >>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>> > with errorcode 126076. >>>>>>>>> > >>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>> processes. >>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>> > >>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>> > >>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>>> wrote: >>>>>>>>> > >>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>> > > >>>>>>>>> > > cd $HOME >>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>> > > >>>>>>>> DATAFILESPATH - or set >>>>>>>>> > > manually with make> >>>>>>>>> > > >>>>>>>>> > > make test query=requires queryval=matlab >>>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>>> > > >>>>>>>>> > > Satish >>>>>>>>> > > >>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>> > > >>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>>> > > > >>>>>>>>> > > > > Hi Matthew, >>>>>>>>> > > > > >>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I >>>>>>>>> do not have >>>>>>>>> > > any >>>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>>> help me how to >>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>> > > > > >>>>>>>>> > > > >>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, >>>>>>>>> we point to >>>>>>>>> > > this >>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>>> don't have those >>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>> > > > is why I suggested just using a different matrix, or running >>>>>>>>> a problem >>>>>>>>> > > you >>>>>>>>> > > > care about in IBAMR. >>>>>>>>> > > > >>>>>>>>> > > > Thanks, >>>>>>>>> > > > >>>>>>>>> > > > Matt >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > > > Thanks and regards >>>>>>>>> > > > > Srinivas. >>>>>>>>> > > > > >>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>>> knepley at gmail.com> >>>>>>>>> > > wrote: >>>>>>>>> > > > > >>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 >>>>>>>>> via >>>>>>>>> > > petsc-users < >>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>>> > > > >> >>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>>> are giving me >>>>>>>>> > > to >>>>>>>>> > > > >>> sort this out. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> I tried to follow the same procedure which you followed >>>>>>>>> to build >>>>>>>>> > > Petsc >>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$./configure >>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> It appears you >>>>>>>>> do not have >>>>>>>>> > > valgrind >>>>>>>>> > > > >>> installed on your system. >>>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>>> www.valgrind.org >>>>>>>>> > > > >>> Or install >>>>>>>>> > > valgrind-devel or >>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> Compilers: >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> C Compiler: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > -fPIC >>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>> C++ Compiler: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>> > > > >>> Fortran Compiler: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>> 9.4.0 >>>>>>>>> > > > >>> Linkers: >>>>>>>>> > > > >>> Shared linker: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > -shared >>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>> Dynamic linker: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > -shared >>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>> > > > >>> make: >>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>> > > > >>> BlasLapack: >>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>>> -lpthread >>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>> -omp_num_threads >>>>>>>>> > >

to >>>>>>>>> > > > >>> control the number of threads >>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>> > > > >>> MPI: >>>>>>>>> > > > >>> Version: 3 >>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>> > > --oversubscribe >>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>> > > > >>> pthread: >>>>>>>>> > > > >>> cmake: >>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>> > > > >>> regex: >>>>>>>>> > > > >>> Matlab: >>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>> > > > >>> Library: >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>>>>>>> -lmex -lmx -lmat >>>>>>>>> > > -lut >>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>> > > > >>> PETSc: >>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>> > > > >>> Scalar type: real >>>>>>>>> > > > >>> Precision: double >>>>>>>>> > > > >>> Support for __float128 >>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries >>>>>>>>> with: >>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>>> -licui18n -licuuc as >>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$make* >>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > > > >>> | ^ >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > > > >>> | ^ >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> ========================================= >>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>> > > > >>> =============================================== >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>> > > > >>> TEST >>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > > > >>> >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>> > > > >>> >>>>>>>>> > > > >> >>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>>> defined, so it >>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>>>> yours. >>>>>>>>> > > > >> >>>>>>>>> > > > >> Thanks, >>>>>>>>> > > > >> >>>>>>>>> > > > >> Matt >>>>>>>>> > > > >> >>>>>>>>> > > > >> >>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> for trouble >>>>>>>>> > > > >>> shooting. >>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>> 2020 >>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>>> MB108SMEC028 by vit >>>>>>>>> > > Sun >>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> COPTFLAGS=-O3 >>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>>>> line 1444 in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 >>>>>>>>> in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>> -------send >>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>> MPI_COMM_SELF >>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>> MPI processes. >>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>> depending on >>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>>> no diff >>>>>>>>> > > > >>> CC >>>>>>>>> > > > >>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>> > > > >>> CLINKER >>>>>>>>> > > > >>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > > > >>> TEST >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> # Error >>>>>>>>> > > code: 124 >>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > > > >>> >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> for trouble >>>>>>>>> > > > >>> shooting. >>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>> 2020 >>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>> > > MB108SMEC028 by >>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> COPTFLAGS=-O3 >>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>> -------send >>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>> MPI_COMM_SELF >>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>> MPI processes. >>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>> depending on >>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>> SKIP Command >>>>>>>>> > > > >>> failed so no diff >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> # ------------- >>>>>>>>> > > > >>> # Summary >>>>>>>>> > > > >>> # ------------- >>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>> 0.02 sec / >>>>>>>>> > > 0.02 sec >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>> > > -Wwrite-strings >>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>> -fstack-protector >>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>> matlab_ls_test.c >>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>>> -leng -lmex >>>>>>>>> > > -lmx >>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>>> > > -lmpi_mpifh >>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>> -lpthread >>>>>>>>> > > -lquadmath >>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b >>>>>>>>> version. >>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. >>>>>>>>> Please find the >>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> Thanks and regards >>>>>>>>> > > > >>> Srinivas >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>>> balay at mcs.anl.gov> >>>>>>>>> > > wrote: >>>>>>>>> > > > >>> >>>>>>>>> > > > >>>> Perhaps you can try the following to get additional >>>>>>>>> info - and debug >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> Satish >>>>>>>>> > > > >>>> ---------- >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>> > > -Wall >>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > -fstack-protector >>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>> > > > >>>> >>>>>>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>>> -lpthread -lm -leng >>>>>>>>> > > -lmex >>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>>> -ldl -lmpifort >>>>>>>>> > > -lmpi >>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>> -lstdc++ -ldl -o >>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>> ./matlab_ls_test >>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>>> number of >>>>>>>>> > > processors >>>>>>>>> > > > >>>> = 1 >>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is >>>>>>>>> NIS >>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: >>>>>>>>> compute-386-07 >>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>> 1140850689 >>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>>> with command >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>>> string: >>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>>>>> string: >>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>> > > > >>>> 5 >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>>> works for you >>>>>>>>> > > - on >>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>>> MathWorks, Inc. >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>>>>> (glnxa64) >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>>> [reverting >>>>>>>>> > > thread >>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>> > > corresponding >>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>>>> Ubuntu-20.04, >>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>>> > > > >>>> > main >>>>>>>>> > > > >>>> > release >>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module >>>>>>>>> load >>>>>>>>> > > matlab/R2021a >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>>> matlab >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>> ./configure >>>>>>>>> > > > >>>> >>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > Compilers: >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>> > > -Wall >>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > -fstack-protector >>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > -fstack-protector >>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>> > > -Wall >>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>>> > Linkers: >>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>> > > -shared -fPIC >>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>> > > -shared -fPIC >>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>> > > > >>>> > make: >>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>> > > > >>>> > Library: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>> -omp_num_threads >>>>>>>>> > >

>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>> > > > >>>> > MPI: >>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>> > > > >>>> > Includes: >>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>> > > > >>>> > pthread: >>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>> > > > >>>> > cmake: >>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>> > > > >>>> > regex: >>>>>>>>> > > > >>>> > Matlab: >>>>>>>>> > > > >>>> > Includes: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>> > > > >>>> > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>> > > > >>>> > Library: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>> > > > >>>> > sowing: >>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>> > > > >>>> > valgrind: >>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>> > > > >>>> > PETSc: >>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>> > > > >>>> > Precision: double >>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>>>> with: >>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>> function >>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>> to >>>>>>>>> > > socket\n"); >>>>>>>>> > > > >>>> > | ^ >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>> function >>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>> to >>>>>>>>> > > socket\n"); >>>>>>>>> > > > >>>> > | ^ >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > ========================================= >>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>> > > > >>>> > ========================================= >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>> > > query=requires >>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed >>>>>>>>> so no diff >>>>>>>>> > > > >>>> > CC >>>>>>>>> > > > >>>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>> > > > >>>> > CLINKER >>>>>>>>> > > > >>>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>>> > not ok >>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>> > > code: >>>>>>>>> > > > >>>> 1 >>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> # SKIP >>>>>>>>> > > Command >>>>>>>>> > > > >>>> failed so no diff >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>>>> test >>>>>>>>> > > query=requires >>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>>> > ok >>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > # ------------- >>>>>>>>> > > > >>>> > # Summary >>>>>>>>> > > > >>>> > # ------------- >>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>> > > > >>>> > # >>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>>> 15.190000000000001 >>>>>>>>> > > sec >>>>>>>>> > > > >>>> > # >>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>> 6.47 sec / >>>>>>>>> > > 7.54 >>>>>>>>> > > > >>>> sec >>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>>> tried to >>>>>>>>> > > > >>>> configure petsc >>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>>> successful. After >>>>>>>>> > > > >>>> running make >>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>>> message. >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > not ok >>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>> > > > >>>> code: 124 >>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error >>>>>>>>> Message >>>>>>>>> > > > >>>> > > >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>>> 01, 2020 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>>> named >>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> COPTFLAGS=-O3 >>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>> > > > >>>> > > --with-x=0 >>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>>>>>>> 67 in >>>>>>>>> > > > >>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > > > >>>> > >>>>>>>> >>>>>>>> -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail2amneet at gmail.com Wed Sep 6 14:25:29 2023 From: mail2amneet at gmail.com (Amneet Bhalla) Date: Wed, 6 Sep 2023 12:25:29 -0700 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: Can you also logout and log back in and see if it still works? It is best to put LD_LIBRARY_PATH in your .bashrc file *export LD_LIBRARY_PATH=* */usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$* *LD_LIBRARY_PATH:* On Wed, Sep 6, 2023 at 12:02?PM INTURU SRINIVAS 20PHD0548 < inturu.srinivas2020 at vitstudent.ac.in> wrote: > I will try and let you know. > > Thanks and regards > Srinivas > > On Wed, Sep 6, 2023, 23:47 Barry Smith wrote: > >> >> Ok, so the C++ binding for Matlab engine is working on your machine. >> PETSc uses the C binding which links against different libraries but, one >> would think the C binding would work for sure if the C++ binding works. Can >> you try a Matlab Engine C example provided by Matlab? >> >> >> >> >> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >> Hi Amneet, >> >> I repeated the same procedure again and this time it is working. >> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp >> -lMatlabDataArray -lMatlabEngine* >> >> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >> *$export LD_LIBRARY_PATH* >> *$./a.out* >> Square root of -2 is 0 + 1.41421i >> Square root of 2 is 1.41421 + 0i >> Square root of 6 is 2.44949 + 0i >> Square root of 8 is 2.82843 + 0i >> I don't know how it is working this time? >> >> Thanks and regards >> Srinivas >> >> >> On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >>> Hi Amneet, >>> I tried the following example to run a matlab engine. >>> >>> #include "MatlabDataArray.hpp" >>> #include "MatlabEngine.hpp" >>> #include >>> void callSQRT() { >>> >>> using namespace matlab::engine; >>> >>> // Start MATLAB engine synchronously >>> std::unique_ptr matlabPtr = startMATLAB(); >>> >>> //Create MATLAB data array factory >>> matlab::data::ArrayFactory factory; >>> >>> // Define a four-element typed array >>> matlab::data::TypedArray const argArray = >>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >>> >>> // Call MATLAB sqrt function on the data array >>> matlab::data::Array const results = matlabPtr->feval(u"sqrt", >>> argArray); >>> >>> // Display results >>> for (int i = 0; i < results.getNumberOfElements(); i++) { >>> double a = argArray[i]; >>> std::complex v = results[i]; >>> double realPart = v.real(); >>> double imgPart = v.imag(); >>> std::cout << "Square root of " << a << " is " << >>> realPart << " + " << imgPart << "i" << std::endl; >>> } >>> } >>> >>> int main() { >>> callSQRT(); >>> return 0; >>> } >>> >>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp >>> -lMatlabDataArray -lMatlabEngine* >>> >>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >>> *$export LD_LIBRARY_PATH* >>> *$./a.out* >>> Starting >>> Error: The import statement 'import matlab.internal.engine.input' cannot >>> be found or cannot be imported. Imported names must end with '.*' or be >>> fully qualified. >>> >>> terminate called after throwing an instance of >>> 'matlab::engine::EngineException' >>> what(): MATLAB process cannot be created. >>> Aborted (core dumped) >>> >>> I got the above error for Matlab R2020b. Please help me to sort out this. >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla >>> wrote: >>> >>>> BTW, what Barry is suggesting is the following: >>>> >>>> Compile a sample code with a command line this: >>>> >>>> >>>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>> >>>> >>>> This command is provided here: >>>> >>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>>> >>>> >>>> A sample MATLAB code is here: >>>> >>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>>> >>>> >>>> (You can just pick a few lines of code from here to create a barebone example) >>>> >>>> >>>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >>>> wrote: >>>> >>>>> Srinivas --- Do you have a different version of MATLAB that you can >>>>> install? If your organization has a MATLAB license, you can install recent >>>>> versions of MATLAB from mathworks.com >>>>> >>>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>>>> >>>>>> >>>>>> Ok, I have no suggestions. It seems to be more an issue with the >>>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>>>> (in the Matlab documentation) and try it to see if it works. >>>>>> >>>>>> Barry >>>>>> >>>>>> >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>> >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>> I got the same errors for petsc 3.17.5 >>>>>> >>>>>> >>>>>> *make all* >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> ========================================= >>>>>> ========================================= >>>>>> Now to check if the libraries are working do: >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>> >>>>>> *make test query=requires queryval=matlab >>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>> queryval=matlab query=requires >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> -------------------------------------------------------------- >>>>>> # [0]PETSC ERROR: Error in external library >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>> shooting. >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Tue Sep 5 21:39:22 2023 >>>>>> # [0]PETSC ERROR: Configure options >>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> --known-64-bit-blas-indices=1 >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>> # [0]PETSC ERROR: #9 main() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> # with errorcode 85. >>>>>> # >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> # You may or may not see output from other processes, depending on >>>>>> # exactly when Open MPI kills them. >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> >>>>>> >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> # >>>>>> # To rerun failed tests: >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>>>> >>>>>>> >>>>>>> The error is occuring during >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>>>> stdout and stdin from the Matlab session that is launched to the >>>>>>> executable. >>>>>>> >>>>>>> You can try the following. In 3.17.5 edit the >>>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> replace it with >>>>>>> >>>>>>> e->ep = engOpen(""); >>>>>>> >>>>>>> Now in the PETSc directory do make all (it should recompile one >>>>>>> file) and then run the >>>>>>> >>>>>>> make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>>>> >>>>>>> again >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via >>>>>>> petsc-users wrote: >>>>>>> >>>>>>> Hi Amneeth, >>>>>>> >>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>> >>>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>> >>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>> The version of PETSc you are using is out-of-date, we recommend >>>>>>> updating to the new release >>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>> https://petsc.org/release/download/ >>>>>>> >>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>> >>>>>>> ============================================================================================= >>>>>>> Configuring PETSc to compile on your system >>>>>>> >>>>>>> >>>>>>> ============================================================================================= >>>>>>> Compilers: >>>>>>> >>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>>>> -fvisibility=hidden -O3 >>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> Linkers: >>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>> BlasLapack: >>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>

to control the number of threads >>>>>>> uses 8 byte integers >>>>>>> MPI: >>>>>>> Version: 3 >>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>> Implementation: openmpi >>>>>>> OMPI_VERSION: 4.0.3 >>>>>>> pthread: >>>>>>> cmake: >>>>>>> Version: 3.16.3 >>>>>>> /usr/bin/cmake >>>>>>> regex: >>>>>>> Matlab: >>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> /usr/local/MATLAB/R2020b >>>>>>> MatlabEngine: >>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>> Language used to compile PETSc: C >>>>>>> PETSc: >>>>>>> PETSC_ARCH: linux-opt >>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>> Prefix: >>>>>>> Scalar type: real >>>>>>> Precision: double >>>>>>> Support for __float128 >>>>>>> Integer size: 4 bytes >>>>>>> Single library: yes >>>>>>> Shared libraries: yes >>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>> Using GNU make: /usr/bin/make >>>>>>> >>>>>>> xxx=========================================================================xxx >>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 >>>>>>> PETSC_ARCH=linux-opt all >>>>>>> >>>>>>> xxx=========================================================================xxx >>>>>>> >>>>>>> *$make* >>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> ========================================= >>>>>>> ========================================= >>>>>>> Now to check if the libraries are working do: >>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>>>> check >>>>>>> >>>>>>> *$make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>>> /usr/bin/python3 >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>>>> --testdir=./linux-opt/tests >>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>> queryval=matlab query=requires >>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> -------------------------------------------------------------- >>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>>> shooting. >>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Tue Sep 5 10:15:57 2023 >>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>> # [0]PETSC ERROR: #9 main() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>> # with errorcode 85. >>>>>>> # >>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>> # You may or may not see output from other processes, depending on >>>>>>> # exactly when Open MPI kills them. >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>> >>>>>>> >>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> # >>>>>>> # To rerun failed tests: >>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> >>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>> >>>>>>> How to check error info and proceed further? >>>>>>> >>>>>>> Thanks and regards >>>>>>> Srinivas >>>>>>> >>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>>>> wrote: >>>>>>> >>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>>>>> options that Satish mentioned? >>>>>>>> >>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>>>> petsc-users wrote: >>>>>>>> >>>>>>>>> Sorry for missing that. >>>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>> -nosplash* >>>>>>>>> >>>>>>>>> < M A T L A B (R) > >>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>> November 23, 2020 >>>>>>>>> >>>>>>>>> >>>>>>>>> To get started, type doc. >>>>>>>>> For product information, visit www.mathworks.com. >>>>>>>>> >>>>>>>>> Thanks and regards >>>>>>>>> Srinivas >>>>>>>>> >>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> You are missing one more step: >>>>>>>>>> >>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>> >>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>> >>>>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>> >>>>>>>>>> Satish >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> > Hi Sathish, >>>>>>>>>> > >>>>>>>>>> > I tried the following procedure >>>>>>>>>> > >>>>>>>>>> > *$make * >>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>> socket\n"); >>>>>>>>>> > | ^ >>>>>>>>>> > >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>> socket\n"); >>>>>>>>>> > | ^ >>>>>>>>>> > >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > ========================================= >>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>>>> check >>>>>>>>>> > >>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>> queryval=matlab >>>>>>>>>> > query=requires >>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> > TEST >>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>> vit Mon Sep >>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>> vit Mon Sep >>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>> > >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>>>> Violation, >>>>>>>>>> > probably memory access out of range >>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>>>> -on_error_attach_debugger >>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>>>> Apple Mac OS >>>>>>>>>> > X to find memory corruption errors >>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>>>> recompile, link, >>>>>>>>>> > and run >>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>> vit Mon Sep >>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in >>>>>>>>>> unknown file >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>> > # >>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>> processes. >>>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>>> on >>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>> > CC >>>>>>>>>> > >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>> > CLINKER >>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > TEST >>>>>>>>>> > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>> code: 124 >>>>>>>>>> > # Running problem 5 >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>> MB108SMEC028 by >>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send entire >>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>> > # with errorcode 126076. >>>>>>>>>> > # >>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>> processes. >>>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>>> on >>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>> Command failed >>>>>>>>>> > so no diff >>>>>>>>>> > >>>>>>>>>> > # ------------- >>>>>>>>>> > # Summary >>>>>>>>>> > # ------------- >>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>> > # >>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>> > # >>>>>>>>>> > # To rerun failed tests: >>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>> > # >>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec >>>>>>>>>> / 0.01 sec >>>>>>>>>> > >>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>> -Wwrite-strings >>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>> -Wno-strict-aliasing >>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>> matlab_ls_test.c >>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>>>>>> -lmex -lmx >>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>> -lmpi_mpifh >>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>> -lpthread -lquadmath >>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>> > >>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>> ./matlab_ls_test >>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>> processors = 1 >>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>> > Running problem 5 >>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>> 140155238476992 >>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>> command >>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>>> -nosplash >>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send entire >>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>> > with errorcode 126076. >>>>>>>>>> > >>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>> processes. >>>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>> > >>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>> > >>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>>>> wrote: >>>>>>>>>> > >>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>> > > >>>>>>>>>> > > cd $HOME >>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>> > > >>>>>>>>> DATAFILESPATH - or set >>>>>>>>>> > > manually with make> >>>>>>>>>> > > >>>>>>>>>> > > make test query=requires queryval=matlab >>>>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>>>> > > >>>>>>>>>> > > Satish >>>>>>>>>> > > >>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>> > > >>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>>>> > > > >>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>> > > > > >>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I >>>>>>>>>> do not have >>>>>>>>>> > > any >>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>>>> help me how to >>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>> > > > > >>>>>>>>>> > > > >>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, >>>>>>>>>> we point to >>>>>>>>>> > > this >>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>>>> don't have those >>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>> > > > is why I suggested just using a different matrix, or >>>>>>>>>> running a problem >>>>>>>>>> > > you >>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>> > > > >>>>>>>>>> > > > Thanks, >>>>>>>>>> > > > >>>>>>>>>> > > > Matt >>>>>>>>>> > > > >>>>>>>>>> > > > >>>>>>>>>> > > > > Thanks and regards >>>>>>>>>> > > > > Srinivas. >>>>>>>>>> > > > > >>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>>>> knepley at gmail.com> >>>>>>>>>> > > wrote: >>>>>>>>>> > > > > >>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 >>>>>>>>>> via >>>>>>>>>> > > petsc-users < >>>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>>>> > > > >> >>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>>>> are giving me >>>>>>>>>> > > to >>>>>>>>>> > > > >>> sort this out. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed >>>>>>>>>> to build >>>>>>>>>> > > Petsc >>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$./configure >>>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> It appears you >>>>>>>>>> do not have >>>>>>>>>> > > valgrind >>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>>>> www.valgrind.org >>>>>>>>>> > > > >>> Or install >>>>>>>>>> > > valgrind-devel or >>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> Compilers: >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> C Compiler: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > -fPIC >>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> > > > >>> C++ Compiler: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>> > > > >>> Fortran Compiler: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu >>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> > > > >>> Linkers: >>>>>>>>>> > > > >>> Shared linker: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > -shared >>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> Dynamic linker: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > -shared >>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>> > > > >>> make: >>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>>>> -lpthread >>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>> -omp_num_threads >>>>>>>>>> > >

to >>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>> > > > >>> MPI: >>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>> > > --oversubscribe >>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>> > > > >>> pthread: >>>>>>>>>> > > > >>> cmake: >>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>> > > > >>> regex: >>>>>>>>>> > > > >>> Matlab: >>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>> > > > >>> Library: >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>>>>>>>> -lmex -lmx -lmat >>>>>>>>>> > > -lut >>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>> > > > >>> PETSc: >>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>> > > > >>> Precision: double >>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries >>>>>>>>>> with: >>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>>>> -licui18n -licuuc as >>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$make* >>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>> to socket\n"); >>>>>>>>>> > > > >>> | ^ >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>> to socket\n"); >>>>>>>>>> > > > >>> | ^ >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> ========================================= >>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>> > > > >>> =============================================== >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> > > > >>> TEST >>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > > > >>> >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>>>> defined, so it >>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>>>>> yours. >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> Thanks, >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> Matt >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> >>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> for trouble >>>>>>>>>> > > > >>> shooting. >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>>> 2020 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>> > > Sun >>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>>>>> line 1444 in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line >>>>>>>>>> 1511 in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send >>>>>>>>>> > > > >>> entire error message to >>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>> MPI_COMM_SELF >>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>> MPI processes. >>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>> depending on >>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>>>> no diff >>>>>>>>>> > > > >>> CC >>>>>>>>>> > > > >>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>> > > > >>> CLINKER >>>>>>>>>> > > > >>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > > > >>> TEST >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> # Error >>>>>>>>>> > > code: 124 >>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > > > >>> >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> for trouble >>>>>>>>>> > > > >>> shooting. >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>>> 2020 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>>>>>>> in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send >>>>>>>>>> > > > >>> entire error message to >>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>> MPI_COMM_SELF >>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>> MPI processes. >>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>> depending on >>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>> SKIP Command >>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> # ------------- >>>>>>>>>> > > > >>> # Summary >>>>>>>>>> > > > >>> # ------------- >>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>>> 0.02 sec / >>>>>>>>>> > > 0.02 sec >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>> > > -Wwrite-strings >>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>> -fstack-protector >>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>> matlab_ls_test.c >>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>>>> -leng -lmex >>>>>>>>>> > > -lmx >>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>> -lpthread >>>>>>>>>> > > -lquadmath >>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b >>>>>>>>>> version. >>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. >>>>>>>>>> Please find the >>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>> > > > >>> Srinivas >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>>>> balay at mcs.anl.gov> >>>>>>>>>> > > wrote: >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional >>>>>>>>>> info - and debug >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> Satish >>>>>>>>>> > > > >>>> ---------- >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>> > > -Wall >>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > -fstack-protector >>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>> > > > >>>> >>>>>>>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>>>> -lpthread -lm -leng >>>>>>>>>> > > -lmex >>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>>>> -ldl -lmpifort >>>>>>>>>> > > -lmpi >>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>> -lstdc++ -ldl -o >>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>> ./matlab_ls_test >>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>>>> number of >>>>>>>>>> > > processors >>>>>>>>>> > > > >>>> = 1 >>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely >>>>>>>>>> is NIS >>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: >>>>>>>>>> compute-386-07 >>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>> 1140850689 >>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>>>> with command >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>>>> string: >>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating >>>>>>>>>> Matlab string: >>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>> > > > >>>> 5 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>>>> works for you >>>>>>>>>> > > - on >>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>>>> MathWorks, Inc. >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) >>>>>>>>>> 64-bit (glnxa64) >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>>>> [reverting >>>>>>>>>> > > thread >>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>>> > > corresponding >>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>>>>> Ubuntu-20.04, >>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git >>>>>>>>>> branch >>>>>>>>>> > > > >>>> > main >>>>>>>>>> > > > >>>> > release >>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module >>>>>>>>>> load >>>>>>>>>> > > matlab/R2021a >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>>>> matlab >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>> ./configure >>>>>>>>>> > > > >>>> >>>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>> > > -Wall >>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > -fstack-protector >>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>> 9.4.0 >>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > -fstack-protector >>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>> 9.4.0 >>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>> > > -Wall >>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>> > > -shared -fPIC >>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>> > > -shared -fPIC >>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ >>>>>>>>>> -ldl >>>>>>>>>> > > > >>>> > make: >>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>> > > > >>>> > Library: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>> -omp_num_threads >>>>>>>>>> > >

>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>> > > > >>>> > regex: >>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>> > > > >>>> > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>> > > > >>>> > Library: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>>>>> with: >>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>> writing to >>>>>>>>>> > > socket\n"); >>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>> writing to >>>>>>>>>> > > socket\n"); >>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>>> > > query=requires >>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed >>>>>>>>>> so no diff >>>>>>>>>> > > > >>>> > CC >>>>>>>>>> > > > >>>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>> > > > >>>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>>> > not ok >>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>> > > code: >>>>>>>>>> > > > >>>> 1 >>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> # SKIP >>>>>>>>>> > > Command >>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>>>>> test >>>>>>>>>> > > query=requires >>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>>> > ok >>>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>> > > > >>>> > # >>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>>>> 15.190000000000001 >>>>>>>>>> > > sec >>>>>>>>>> > > > >>>> > # >>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>> > > > >>>> > # >>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>> > > 7.54 >>>>>>>>>> > > > >>>> sec >>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>>>> tried to >>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>>>> successful. After >>>>>>>>>> > > > >>>> running make >>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>>>> message. >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > not ok >>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error >>>>>>>>>> Message >>>>>>>>>> > > > >>>> > > >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>> Aug 01, 2020 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>>>> named >>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>> > > > >>>> > > --with-x=0 >>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>> line 67 in >>>>>>>>>> > > > >>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > > > >>>> > >>>>>>>>> >>>>>>>>> > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > -- --Amneet -------------- next part -------------- An HTML attachment was scrubbed... URL: From mail2amneet at gmail.com Wed Sep 6 14:30:14 2023 From: mail2amneet at gmail.com (Amneet Bhalla) Date: Wed, 6 Sep 2023 12:30:14 -0700 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: Sorry there was an extra : towards the end. It should be export LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH On Wed, Sep 6, 2023 at 12:25?PM Amneet Bhalla wrote: > Can you also logout and log back in and see if it still works? It is best > to put LD_LIBRARY_PATH in your .bashrc file > > *export LD_LIBRARY_PATH=* > */usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$* > *LD_LIBRARY_PATH:* > > > On Wed, Sep 6, 2023 at 12:02?PM INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > >> I will try and let you know. >> >> Thanks and regards >> Srinivas >> >> On Wed, Sep 6, 2023, 23:47 Barry Smith wrote: >> >>> >>> Ok, so the C++ binding for Matlab engine is working on your machine. >>> PETSc uses the C binding which links against different libraries but, one >>> would think the C binding would work for sure if the C++ binding works. Can >>> you try a Matlab Engine C example provided by Matlab? >>> >>> >>> >>> >>> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < >>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> >>> Hi Amneet, >>> >>> I repeated the same procedure again and this time it is working. >>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp >>> -lMatlabDataArray -lMatlabEngine* >>> >>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >>> *$export LD_LIBRARY_PATH* >>> *$./a.out* >>> Square root of -2 is 0 + 1.41421i >>> Square root of 2 is 1.41421 + 0i >>> Square root of 6 is 2.44949 + 0i >>> Square root of 8 is 2.82843 + 0i >>> I don't know how it is working this time? >>> >>> Thanks and regards >>> Srinivas >>> >>> >>> On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < >>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> >>>> Hi Amneet, >>>> I tried the following example to run a matlab engine. >>>> >>>> #include "MatlabDataArray.hpp" >>>> #include "MatlabEngine.hpp" >>>> #include >>>> void callSQRT() { >>>> >>>> using namespace matlab::engine; >>>> >>>> // Start MATLAB engine synchronously >>>> std::unique_ptr matlabPtr = startMATLAB(); >>>> >>>> //Create MATLAB data array factory >>>> matlab::data::ArrayFactory factory; >>>> >>>> // Define a four-element typed array >>>> matlab::data::TypedArray const argArray = >>>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >>>> >>>> // Call MATLAB sqrt function on the data array >>>> matlab::data::Array const results = matlabPtr->feval(u"sqrt", >>>> argArray); >>>> >>>> // Display results >>>> for (int i = 0; i < results.getNumberOfElements(); i++) { >>>> double a = argArray[i]; >>>> std::complex v = results[i]; >>>> double realPart = v.real(); >>>> double imgPart = v.imag(); >>>> std::cout << "Square root of " << a << " is " << >>>> realPart << " + " << imgPart << "i" << std::endl; >>>> } >>>> } >>>> >>>> int main() { >>>> callSQRT(); >>>> return 0; >>>> } >>>> >>>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >>>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp >>>> -lMatlabDataArray -lMatlabEngine* >>>> >>>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >>>> *$export LD_LIBRARY_PATH* >>>> *$./a.out* >>>> Starting >>>> Error: The import statement 'import matlab.internal.engine.input' >>>> cannot be found or cannot be imported. Imported names must end with '.*' or >>>> be fully qualified. >>>> >>>> terminate called after throwing an instance of >>>> 'matlab::engine::EngineException' >>>> what(): MATLAB process cannot be created. >>>> Aborted (core dumped) >>>> >>>> I got the above error for Matlab R2020b. Please help me to sort out >>>> this. >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla >>>> wrote: >>>> >>>>> BTW, what Barry is suggesting is the following: >>>>> >>>>> Compile a sample code with a command line this: >>>>> >>>>> >>>>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >>>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>>> >>>>> >>>>> This command is provided here: >>>>> >>>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>>>> >>>>> >>>>> A sample MATLAB code is here: >>>>> >>>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>>>> >>>>> >>>>> (You can just pick a few lines of code from here to create a barebone example) >>>>> >>>>> >>>>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >>>>> wrote: >>>>> >>>>>> Srinivas --- Do you have a different version of MATLAB that you can >>>>>> install? If your organization has a MATLAB license, you can install recent >>>>>> versions of MATLAB from mathworks.com >>>>>> >>>>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>>>>> >>>>>>> >>>>>>> Ok, I have no suggestions. It seems to be more an issue with the >>>>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>>>>> (in the Matlab documentation) and try it to see if it works. >>>>>>> >>>>>>> Barry >>>>>>> >>>>>>> >>>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>> >>>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>>> I got the same errors for petsc 3.17.5 >>>>>>> >>>>>>> >>>>>>> *make all* >>>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> ========================================= >>>>>>> ========================================= >>>>>>> Now to check if the libraries are working do: >>>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>> >>>>>>> *make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>> queryval=matlab query=requires >>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> -------------------------------------------------------------- >>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>>> shooting. >>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Tue Sep 5 21:39:22 2023 >>>>>>> # [0]PETSC ERROR: Configure options >>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> --known-64-bit-blas-indices=1 >>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>> # [0]PETSC ERROR: #9 main() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>> # with errorcode 85. >>>>>>> # >>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>> # You may or may not see output from other processes, depending on >>>>>>> # exactly when Open MPI kills them. >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>> >>>>>>> >>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> # >>>>>>> # To rerun failed tests: >>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> >>>>>>> Thanks and regards >>>>>>> Srinivas >>>>>>> >>>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>>>>> >>>>>>>> >>>>>>>> The error is occuring during >>>>>>>> >>>>>>>> e->ep = engOpen(buffer); >>>>>>>> >>>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>>>>> stdout and stdin from the Matlab session that is launched to the >>>>>>>> executable. >>>>>>>> >>>>>>>> You can try the following. In 3.17.5 edit the >>>>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>>> >>>>>>>> e->ep = engOpen(buffer); >>>>>>>> >>>>>>>> replace it with >>>>>>>> >>>>>>>> e->ep = engOpen(""); >>>>>>>> >>>>>>>> Now in the PETSc directory do make all (it should recompile one >>>>>>>> file) and then run the >>>>>>>> >>>>>>>> make test query=requires queryval=matlab >>>>>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> >>>>>>>> again >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via >>>>>>>> petsc-users wrote: >>>>>>>> >>>>>>>> Hi Amneeth, >>>>>>>> >>>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>>> >>>>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>> >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> The version of PETSc you are using is out-of-date, we recommend >>>>>>>> updating to the new release >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>>> https://petsc.org/release/download/ >>>>>>>> >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> >>>>>>>> ============================================================================================= >>>>>>>> Configuring PETSc to compile on your >>>>>>>> system >>>>>>>> >>>>>>>> ============================================================================================= >>>>>>>> Compilers: >>>>>>>> >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>>>>> -fvisibility=hidden -O3 >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> Linkers: >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>> BlasLapack: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>

to control the number of threads >>>>>>>> uses 8 byte integers >>>>>>>> MPI: >>>>>>>> Version: 3 >>>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>>> Implementation: openmpi >>>>>>>> OMPI_VERSION: 4.0.3 >>>>>>>> pthread: >>>>>>>> cmake: >>>>>>>> Version: 3.16.3 >>>>>>>> /usr/bin/cmake >>>>>>>> regex: >>>>>>>> Matlab: >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> /usr/local/MATLAB/R2020b >>>>>>>> MatlabEngine: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>>> Language used to compile PETSc: C >>>>>>>> PETSc: >>>>>>>> PETSC_ARCH: linux-opt >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>> Prefix: >>>>>>>> Scalar type: real >>>>>>>> Precision: double >>>>>>>> Support for __float128 >>>>>>>> Integer size: 4 bytes >>>>>>>> Single library: yes >>>>>>>> Shared libraries: yes >>>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>>> Using GNU make: /usr/bin/make >>>>>>>> >>>>>>>> xxx=========================================================================xxx >>>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>> >>>>>>>> xxx=========================================================================xxx >>>>>>>> >>>>>>>> *$make* >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>>> [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>>> [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> ========================================= >>>>>>>> ========================================= >>>>>>>> Now to check if the libraries are working do: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>>>>> check >>>>>>>> >>>>>>>> *$make test query=requires queryval=matlab >>>>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>>>> /usr/bin/python3 >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>>>>> --testdir=./linux-opt/tests >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> queryval=matlab query=requires >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> -------------------------------------------------------------- >>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>>>> shooting. >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>>> Tue Sep 5 10:15:57 2023 >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>> # [0]PETSC ERROR: #9 main() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>> # with errorcode 85. >>>>>>>> # >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>> processes. >>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>> # exactly when Open MPI kills them. >>>>>>>> # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>> >>>>>>>> >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> # >>>>>>>> # To rerun failed tests: >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> >>>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>>> >>>>>>>> How to check error info and proceed further? >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new >>>>>>>>> configure options that Satish mentioned? >>>>>>>>> >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>>>>> petsc-users wrote: >>>>>>>>> >>>>>>>>>> Sorry for missing that. >>>>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>>> -nosplash* >>>>>>>>>> >>>>>>>>>> < M A T L A B (R) > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>>> November 23, 2020 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> To get started, type doc. >>>>>>>>>> For product information, visit www.mathworks.com. >>>>>>>>>> >>>>>>>>>> Thanks and regards >>>>>>>>>> Srinivas >>>>>>>>>> >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> You are missing one more step: >>>>>>>>>>> >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>> >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>>> >>>>>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>>> >>>>>>>>>>> Satish >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> > Hi Sathish, >>>>>>>>>>> > >>>>>>>>>>> > I tried the following procedure >>>>>>>>>>> > >>>>>>>>>>> > *$make * >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > ========================================= >>>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>>>>> check >>>>>>>>>>> > >>>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>>> queryval=matlab >>>>>>>>>>> > query=requires >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > TEST >>>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>>> vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>>> vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > >>>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>>>>> Violation, >>>>>>>>>>> > probably memory access out of range >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>>>>> -on_error_attach_debugger >>>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>>>>> Apple Mac OS >>>>>>>>>>> > X to find memory corruption errors >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>>>>> recompile, link, >>>>>>>>>>> > and run >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>>> vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in >>>>>>>>>>> unknown file >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_WORLD >>>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> processes. >>>>>>>>>>> > # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > CC >>>>>>>>>>> > >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > CLINKER >>>>>>>>>>> > >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > TEST >>>>>>>>>>> > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> Error code: 124 >>>>>>>>>>> > # Running problem 5 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>> MB108SMEC028 by >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > # with errorcode 126076. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> processes. >>>>>>>>>>> > # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>> Command failed >>>>>>>>>>> > so no diff >>>>>>>>>>> > >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # Summary >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>>> > # >>>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>>> > # >>>>>>>>>>> > # To rerun failed tests: >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > # >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec >>>>>>>>>>> / 0.01 sec >>>>>>>>>>> > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>> -Wwrite-strings >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> -Wno-strict-aliasing >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> matlab_ls_test.c >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>>>>>>> -lmex -lmx >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>>> -lmpi_mpifh >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>>> -lpthread -lquadmath >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>>> ./matlab_ls_test >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>>> processors = 1 >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > Running problem 5 >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>>> 140155238476992 >>>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>>> command >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>>>> -nosplash >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > with errorcode 126076. >>>>>>>>>>> > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> processes. >>>>>>>>>>> > You may or may not see output from other processes, depending >>>>>>>>>>> on >>>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>>> > >>>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>>> > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>>>>> wrote: >>>>>>>>>>> > >>>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>>> > > >>>>>>>>>>> > > cd $HOME >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>>> > > >>>>>>>>>> DATAFILESPATH - or set >>>>>>>>>>> > > manually with make> >>>>>>>>>>> > > >>>>>>>>>>> > > make test query=requires queryval=matlab >>>>>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>>>>> > > >>>>>>>>>>> > > Satish >>>>>>>>>>> > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>>> > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I >>>>>>>>>>> do not have >>>>>>>>>>> > > any >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>>>>> help me how to >>>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, >>>>>>>>>>> we point to >>>>>>>>>>> > > this >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>>>>> don't have those >>>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>>> > > > is why I suggested just using a different matrix, or >>>>>>>>>>> running a problem >>>>>>>>>>> > > you >>>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>>> > > > >>>>>>>>>>> > > > Thanks, >>>>>>>>>>> > > > >>>>>>>>>>> > > > Matt >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Thanks and regards >>>>>>>>>>> > > > > Srinivas. >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>>>>> knepley at gmail.com> >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS >>>>>>>>>>> 20PHD0548 via >>>>>>>>>>> > > petsc-users < >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>>>>> are giving me >>>>>>>>>>> > > to >>>>>>>>>>> > > > >>> sort this out. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you >>>>>>>>>>> followed to build >>>>>>>>>>> > > Petsc >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$./configure >>>>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your >>>>>>>>>>> system >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> It appears you >>>>>>>>>>> do not have >>>>>>>>>>> > > valgrind >>>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>>>>> www.valgrind.org >>>>>>>>>>> > > > >>> Or install >>>>>>>>>>> > > valgrind-devel or >>>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> Compilers: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> C Compiler: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -fPIC >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> C++ Compiler: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>> > > > >>> Fortran Compiler: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu >>>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> Linkers: >>>>>>>>>>> > > > >>> Shared linker: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Dynamic linker: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>> > > > >>> make: >>>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>>>>> -lpthread >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>>> -omp_num_threads >>>>>>>>>>> > >

to >>>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>>> > > > >>> MPI: >>>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> > > > >>> Mpiexec: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>>> > > --oversubscribe >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>>> > > > >>> pthread: >>>>>>>>>>> > > > >>> cmake: >>>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>>> > > > >>> regex: >>>>>>>>>>> > > > >>> Matlab: >>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>> Library: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>>>>>>>>> -lmex -lmx -lmat >>>>>>>>>>> > > -lut >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>>> > > > >>> PETSc: >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>>> > > > >>> Precision: double >>>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries >>>>>>>>>>> with: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>>>>> -licui18n -licuuc as >>>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make* >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>>> to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>>> to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> ========================================= >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>> =============================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>> TEST >>>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>>>>> defined, so it >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test >>>>>>>>>>> of yours. >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Thanks, >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Matt >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>>>>> 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>>> > > Sun >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 >>>>>>>>>>> PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line >>>>>>>>>>> 1511 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send >>>>>>>>>>> > > > >>> entire error message to >>>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>>> MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>>>>> no diff >>>>>>>>>>> > > > >>> CC >>>>>>>>>>> > > > >>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>> CLINKER >>>>>>>>>>> > > > >>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>> TEST >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>> not ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: 124 >>>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>>>>> 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>>>>> named >>>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>>>>>>>> in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send >>>>>>>>>>> > > > >>> entire error message to >>>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>>> MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> SKIP Command >>>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # Summary >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>>>> 0.02 sec / >>>>>>>>>>> > > 0.02 sec >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>> > > -Wwrite-strings >>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> -fstack-protector >>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> matlab_ls_test.c >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>>>>> -leng -lmex >>>>>>>>>>> > > -lmx >>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>>> -lpthread >>>>>>>>>>> > > -lquadmath >>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b >>>>>>>>>>> version. >>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. >>>>>>>>>>> Please find the >>>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>>> > > > >>> Srinivas >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>>>>> balay at mcs.anl.gov> >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional >>>>>>>>>>> info - and debug >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Satish >>>>>>>>>>> > > > >>>> ---------- >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> >>>>>>>>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>>>>> -lpthread -lm -leng >>>>>>>>>>> > > -lmex >>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>>>>> -ldl -lmpifort >>>>>>>>>>> > > -lmpi >>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>>> -lstdc++ -ldl -o >>>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>>> ./matlab_ls_test >>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>>>>> number of >>>>>>>>>>> > > processors >>>>>>>>>>> > > > >>>> = 1 >>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely >>>>>>>>>>> is NIS >>>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: >>>>>>>>>>> compute-386-07 >>>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>>> 1140850689 >>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>>>>> with command >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>>>>> string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating >>>>>>>>>>> Matlab string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> 5 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>>>>> works for you >>>>>>>>>>> > > - on >>>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>>>>> MathWorks, Inc. >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) >>>>>>>>>>> 64-bit (glnxa64) >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users >>>>>>>>>>> wrote: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>>>>> [reverting >>>>>>>>>>> > > thread >>>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send >>>>>>>>>>> the >>>>>>>>>>> > > corresponding >>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) >>>>>>>>>>> on Ubuntu-20.04, >>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git >>>>>>>>>>> branch >>>>>>>>>>> > > > >>>> > main >>>>>>>>>>> > > > >>>> > release >>>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module >>>>>>>>>>> load >>>>>>>>>>> > > matlab/R2021a >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>>>>> matlab >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> ./configure >>>>>>>>>>> > > > >>>> >>>>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>>> 9.4.0 >>>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>>> 9.4.0 >>>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ >>>>>>>>>>> -ldl >>>>>>>>>>> > > > >>>> > make: >>>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>>> -omp_num_threads >>>>>>>>>>> > >

>>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>>> > > > >>>> > regex: >>>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n >>>>>>>>>>> -licuuc >>>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc >>>>>>>>>>> libraries with: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>>> writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>>> writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>> test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>> linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed >>>>>>>>>>> so no diff >>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>> > > > >>>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>>> > > > >>>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > not ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: >>>>>>>>>>> > > > >>>> 1 >>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>> > > Command >>>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>>> make test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > ok >>>>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>>>>> 15.190000000000001 >>>>>>>>>>> > > sec >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU >>>>>>>>>>> time): >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>>> > > 7.54 >>>>>>>>>>> > > > >>>> sec >>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>>>>> tried to >>>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>>>>> successful. After >>>>>>>>>>> > > > >>>> running make >>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>>>>> message. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > not ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>> Message >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>> Aug 01, 2020 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>> linux-opt named >>>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>>> > > > >>>> > > --with-x=0 >>>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>> line 67 in >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > >>>>>>>>>> >>>>>>>>>> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> > > > -- > --Amneet > > > > -- --Amneet -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Wed Sep 6 15:34:40 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Wed, 6 Sep 2023 15:34:40 -0500 (CDT) Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: <3aa83331-d640-1a0f-9d36-d9c01c948f83@mcs.anl.gov> BTW: Stepping back and looking that the error message: > > > >> Error: The import statement 'import matlab.internal.engine.input' > > cannot be found or cannot be imported. Imported names must end with '.*' or > > be fully qualified. Google suggests: https://www.mathworks.com/matlabcentral/answers/494387-python-engineerror-import-argument-matlab-internal-engine-input-cannot-be-found-or-cannot-be-impo i.e a wrong "input.m" file is loaded - that's causing grief? But its not clear to me how one would track this file. MATLABPATH? some default matlab config files? And is this conflicting file coming from matlab install or $HOME? Or the conflict is due to a different ".m" file - then input.m? Assuming this is indeed the issue (a- I would suggest trying this out in a fresh user account - and see if things work [both basic matlab only test - and the petsc+matlab] Satish On Thu, 7 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > I tried with different examples and all are working later. > As you said there may be a license issue. > I will try with latest matlab version. > > Thanks and regards > Srinivas > > On Thu, Sep 7, 2023, 00:24 Satish Balay wrote: > > > I'm still curios why the first [c++] attempt failed but the second one > > succeeded. > > > > The only difference I can spot is myEngineApp.cpp vs myEngineApp2.cpp. > > What is the difference here between these 2 source files? > > > > Or is it some random error [the same source code worked failed before - > > but works now - and might fail again later?] > > > > Maybe there is some issue with matlab license here - that prevents some > > usages (or usage patterns) to fail? > > > > Satish > > > > On Wed, 6 Sep 2023, Barry Smith wrote: > > > > > > > > Ok, so the C++ binding for Matlab engine is working on your machine. > > PETSc uses the C binding which links against different libraries but, one > > would think the C binding would work for sure if the C++ binding works. Can > > you try a Matlab Engine C example provided by Matlab? > > > > > > > > > > > > > > > > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < > > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > > > > > > > Hi Amneet, > > > > > > > > I repeated the same procedure again and this time it is working. > > > > $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp > > -lMatlabDataArray -lMatlabEngine > > > > > > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > > $export LD_LIBRARY_PATH > > > > $./a.out > > > > Square root of -2 is 0 + 1.41421i > > > > Square root of 2 is 1.41421 + 0i > > > > Square root of 6 is 2.44949 + 0i > > > > Square root of 8 is 2.82843 + 0i > > > > I don't know how it is working this time? > > > > > > > > Thanks and regards > > > > Srinivas > > > > > > > > > > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < > > inturu.srinivas2020 at vitstudent.ac.in > inturu.srinivas2020 at vitstudent.ac.in>> wrote: > > > >> Hi Amneet, > > > >> I tried the following example to run a matlab engine. > > > >> > > > >> #include "MatlabDataArray.hpp" > > > >> #include "MatlabEngine.hpp" > > > >> #include > > > >> void callSQRT() { > > > >> > > > >> using namespace matlab::engine; > > > >> > > > >> // Start MATLAB engine synchronously > > > >> std::unique_ptr matlabPtr = startMATLAB(); > > > >> > > > >> //Create MATLAB data array factory > > > >> matlab::data::ArrayFactory factory; > > > >> > > > >> // Define a four-element typed array > > > >> matlab::data::TypedArray const argArray = > > > >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); > > > >> > > > >> // Call MATLAB sqrt function on the data array > > > >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", > > argArray); > > > >> > > > >> // Display results > > > >> for (int i = 0; i < results.getNumberOfElements(); i++) { > > > >> double a = argArray[i]; > > > >> std::complex v = results[i]; > > > >> double realPart = v.real(); > > > >> double imgPart = v.imag(); > > > >> std::cout << "Square root of " << a << " is " << > > > >> realPart << " + " << imgPart << "i" << std::endl; > > > >> } > > > >> } > > > >> > > > >> int main() { > > > >> callSQRT(); > > > >> return 0; > > > >> } > > > >> > > > >> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp > > -lMatlabDataArray -lMatlabEngine > > > >> > > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >> $export LD_LIBRARY_PATH > > > >> $./a.out > > > >> Starting > > > >> Error: The import statement 'import matlab.internal.engine.input' > > cannot be found or cannot be imported. Imported names must end with '.*' or > > be fully qualified. > > > >> > > > >> terminate called after throwing an instance of > > 'matlab::engine::EngineException' > > > >> what(): MATLAB process cannot be created. > > > >> Aborted (core dumped) > > > >> > > > >> I got the above error for Matlab R2020b. Please help me to sort out > > this. > > > >> > > > >> Thanks and regards > > > >> Srinivas > > > >> > > > >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > > wrote: > > > >>> BTW, what Barry is suggesting is the following: > > > >>> > > > >>> Compile a sample code with a command line this: > > > >>> > > > >>> g++ -std=c++11 -I matlabroot/extern/include/ -L > > matlabroot/extern/bin/glnxa64/ > > > >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine > > > >>> > > > >>> This command is provided here: > > > >>> > > https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html > > > >>> > > > >>> A sample MATLAB code is here: > > > >>> > > https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html > > > >>> > > > >>> (You can just pick a few lines of code from here to create a > > barebone example) > > > >>> > > > >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > > wrote: > > > >>>> Srinivas --- Do you have a different version of MATLAB that you can > > install? If your organization has a MATLAB license, you can install recent > > versions of MATLAB from mathworks.com > > > >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > > wrote: > > > >>>>> > > > >>>>> Ok, I have no suggestions. It seems to be more an issue with > > the Matlab than PETSc. You could find a pure Matlab example of using the > > engine (in the Matlab documentation) and try it to see if it works. > > > >>>>> > > > >>>>> Barry > > > >>>>> > > > >>>>> > > > >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < > > inturu.srinivas2020 at vitstudent.ac.in > inturu.srinivas2020 at vitstudent.ac.in>> wrote: > > > >>>>>> > > > >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); > > > >>>>>> I got the same errors for petsc 3.17.5 > > > >>>>>> > > > >>>>>> make all > > > >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o > > > >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 > > > >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE > > > >>>>>> Building with 'gcc'. > > > >>>>>> > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > >>>>>> > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > > >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>>>> | ^ > > > >>>>>> > > > >>>>>> MEX completed successfully. > > > >>>>>> Building with 'gcc'. > > > >>>>>> MEX completed successfully. > > > >>>>>> Building with 'gcc'. > > > >>>>>> MEX completed successfully. > > > >>>>>> Building with 'gcc'. > > > >>>>>> > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > >>>>>> > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > > >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>>>> | ^ > > > >>>>>> > > > >>>>>> MEX completed successfully. > > > >>>>>> ========================================= > > > >>>>>> ========================================= > > > >>>>>> Now to check if the libraries are working do: > > > >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt > > check > > > >>>>>> > > > >>>>>> make test query=requires queryval=matlab > > DATAFILESPATH=/home/vit/datafiles/ > > > >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ > > queryval=matlab query=requires > > > >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > >>>>>> TEST > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > > > >>>>>> # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > > >>>>>> # [0]PETSC ERROR: Error in external library > > > >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with > > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > > >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble > > shooting. > > > >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > > > >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by > > vit Tue Sep 5 21:39:22 2023 > > > >>>>>> # [0]PETSC ERROR: Configure options > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 > > > >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 > > > >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 > > > >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at > > /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 > > > >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at > > /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > > > >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at > > /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > > > >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at > > /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > > > >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at > > /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > > > >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at > > /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > > > >>>>>> # [0]PETSC ERROR: #9 main() at > > /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > > > >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 > > > >>>>>> # [0]PETSC ERROR: -error_output_stdout > > > >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > > > >>>>>> # [0]PETSC ERROR: -malloc_dump > > > >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > > >>>>>> # [0]PETSC ERROR: -pc_type lu > > > >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > > > >>>>>> # [0]PETSC ERROR: ----------------End of Error Message > > -------send entire error message to petsc-maint at mcs.anl.gov---------- > > > >>>>>> # > > -------------------------------------------------------------------------- > > > >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > > >>>>>> # with errorcode 85. > > > >>>>>> # > > > >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > >>>>>> # You may or may not see output from other processes, depending on > > > >>>>>> # exactly when Open MPI kills them. > > > >>>>>> # > > -------------------------------------------------------------------------- > > > >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > >>>>>> > > > >>>>>> > > > >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 > > > >>>>>> # > > > >>>>>> # To rerun failed tests: > > > >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 > > > >>>>>> > > > >>>>>> Thanks and regards > > > >>>>>> Srinivas > > > >>>>>> > > > >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > > wrote: > > > >>>>>>> > > > >>>>>>> The error is occuring during > > > >>>>>>> > > > >>>>>>> e->ep = engOpen(buffer); > > > >>>>>>> > > > >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab > > -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to > > assume the problem is occuring when engOpen() is attempting to connect the > > stdout and stdin from the Matlab session that is launched to the > > executable. > > > >>>>>>> > > > >>>>>>> You can try the following. In 3.17.5 edit the file > > src/sys/classes/matlabengine/matlab.c and locate the line > > > >>>>>>> > > > >>>>>>> e->ep = engOpen(buffer); > > > >>>>>>> > > > >>>>>>> replace it with > > > >>>>>>> > > > >>>>>>> e->ep = engOpen(""); > > > >>>>>>> > > > >>>>>>> Now in the PETSc directory do make all (it should recompile one > > file) and then run the > > > >>>>>>> > > > >>>>>>> make test query=requires queryval=matlab > > DATAFILESPATH=/home/vit/datafiles/ > > > >>>>>>> > > > >>>>>>> again > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > >>>>>>> > > > >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via > > petsc-users > > > wrote: > > > >>>>>>>> > > > >>>>>>>> Hi Amneeth, > > > >>>>>>>> > > > >>>>>>>> I think the errors are different with petsc 3.17.5 > > > >>>>>>>> > > > >>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx > > --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > > PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>> > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > >>>>>>>> The version of PETSc you are using is out-of-date, we recommend > > updating to the new release > > > >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 > > > >>>>>>>> https://petsc.org/release/download/ > > > >>>>>>>> > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > >>>>>>>> > > ============================================================================================= > > > >>>>>>>> Configuring PETSc to compile on your > > system > > > >>>>>>>> > > ============================================================================================= > > > >>>>>>>> Compilers: > > > > > >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall > > -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch > > -fstack-protector -fvisibility=hidden -O3 > > > >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings > > -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch > > -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC > > > >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 > > > >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall > > -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 > > > >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>>>>>>> Linkers: > > > >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall > > -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch > > -fstack-protector -fvisibility=hidden -O3 > > > >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall > > -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch > > -fstack-protector -fvisibility=hidden -O3 > > > >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl > > > >>>>>>>> BlasLapack: > > > >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread > > > >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or > > -omp_num_threads

to control the number of threads > > > >>>>>>>> uses 8 byte integers > > > >>>>>>>> MPI: > > > >>>>>>>> Version: 3 > > > >>>>>>>> mpiexec: /usr/bin/mpiexec > > > >>>>>>>> Implementation: openmpi > > > >>>>>>>> OMPI_VERSION: 4.0.3 > > > >>>>>>>> pthread: > > > >>>>>>>> cmake: > > > >>>>>>>> Version: 3.16.3 > > > >>>>>>>> /usr/bin/cmake > > > >>>>>>>> regex: > > > >>>>>>>> Matlab: > > > >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include > > > >>>>>>>> /usr/local/MATLAB/R2020b > > > >>>>>>>> MatlabEngine: > > > >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 > > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat > > -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher > > -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c > > > >>>>>>>> Language used to compile PETSc: C > > > >>>>>>>> PETSc: > > > >>>>>>>> PETSC_ARCH: linux-opt > > > >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 > > > >>>>>>>> Prefix: > > > >>>>>>>> Scalar type: real > > > >>>>>>>> Precision: double > > > >>>>>>>> Support for __float128 > > > >>>>>>>> Integer size: 4 bytes > > > >>>>>>>> Single library: yes > > > >>>>>>>> Shared libraries: yes > > > >>>>>>>> Memory alignment from malloc(): 16 bytes > > > >>>>>>>> Using GNU make: /usr/bin/make > > > >>>>>>>> > > xxx=========================================================================xxx > > > >>>>>>>> Configure stage complete. Now build PETSc libraries with: > > > >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 > > PETSC_ARCH=linux-opt all > > > >>>>>>>> > > xxx=========================================================================xxx > > > >>>>>>>> > > > >>>>>>>> $make > > > >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 > > > >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE > > > >>>>>>>> Building with 'gcc'. > > > >>>>>>>> > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > >>>>>>>> > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > > >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>>>>>> | ^ > > > >>>>>>>> > > > >>>>>>>> MEX completed successfully. > > > >>>>>>>> Building with 'gcc'. > > > >>>>>>>> MEX completed successfully. > > > >>>>>>>> Building with 'gcc'. > > > >>>>>>>> MEX completed successfully. > > > >>>>>>>> Building with 'gcc'. > > > >>>>>>>> > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > In function ?PetscBinaryWrite?: > > > >>>>>>>> > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: > > warning: ?err? may be used uninitialized in this function > > [-Wmaybe-uninitialized] > > > >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>>>>>> | ^ > > > >>>>>>>> > > > >>>>>>>> MEX completed successfully. > > > >>>>>>>> ========================================= > > > >>>>>>>> ========================================= > > > >>>>>>>> Now to check if the libraries are working do: > > > >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 > > PETSC_ARCH=linux-opt check > > > >>>>>>>> > > > >>>>>>>> $make test query=requires queryval=matlab > > DATAFILESPATH=/home/vit/datafiles/ > > > >>>>>>>> /usr/bin/python3 > > /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py > > --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt > > --testdir=./linux-opt/tests > > > >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ > > queryval=matlab query=requires > > > >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > >>>>>>>> TEST > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 > > > >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message > > -------------------------------------------------------------- > > > >>>>>>>> # [0]PETSC ERROR: Error in external library > > > >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with > > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > > >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for > > trouble shooting. > > > >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 > > > >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by > > vit Tue Sep 5 10:15:57 2023 > > > >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc > > --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 > > FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 > > > >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 > > > >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 > > > >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 > > > >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 > > > >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 > > > >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 > > > >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 > > > >>>>>>>> # [0]PETSC ERROR: #9 main() at > > /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 > > > >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 > > > >>>>>>>> # [0]PETSC ERROR: -error_output_stdout > > > >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 > > > >>>>>>>> # [0]PETSC ERROR: -malloc_dump > > > >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > > >>>>>>>> # [0]PETSC ERROR: -pc_type lu > > > >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 > > > >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message > > -------send entire error message to petsc-maint at mcs.anl.gov---------- > > > >>>>>>>> # > > -------------------------------------------------------------------------- > > > >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > > > >>>>>>>> # with errorcode 85. > > > >>>>>>>> # > > > >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > >>>>>>>> # You may or may not see output from other processes, depending > > on > > > >>>>>>>> # exactly when Open MPI kills them. > > > >>>>>>>> # > > -------------------------------------------------------------------------- > > > >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > > > >>>>>>>> > > > >>>>>>>> > > > >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 > > > >>>>>>>> # > > > >>>>>>>> # To rerun failed tests: > > > >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 > > > >>>>>>>> > > > >>>>>>>> To get the info of the error there is no specific probe id > > reported. > > > >>>>>>>> > > > >>>>>>>> How to check error info and proceed further? > > > >>>>>>>> > > > >>>>>>>> Thanks and regards > > > >>>>>>>> Srinivas > > > >>>>>>>> > > > >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla < > > mail2amneet at gmail.com > wrote: > > > >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new > > configure options that Satish mentioned? > > > >>>>>>>>> > > > >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via > > petsc-users > > > wrote: > > > >>>>>>>>>> Sorry for missing that. > > > >>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay > > -nosplash > > > >>>>>>>>>> > > > >>>>>>>>>> < M A T L A B (R) > > > > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. > > > >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) > > > >>>>>>>>>> November 23, 2020 > > > >>>>>>>>>> > > > >>>>>>>>>> > > > >>>>>>>>>> To get started, type doc. > > > >>>>>>>>>> For product information, visit www.mathworks.com < > > http://www.mathworks.com/>. > > > >>>>>>>>>> > > > >>>>>>>>>> Thanks and regards > > > >>>>>>>>>> Srinivas > > > >>>>>>>>>> > > > >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay < > > balay at mcs.anl.gov > wrote: > > > >>>>>>>>>>> You are missing one more step: > > > >>>>>>>>>>> > > > >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 > > > >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with > > command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > > > >>>>>>>>>>> > > > >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command > > "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" > > > >>>>>>>>>>> > > > >>>>>>>>>>> Does this work for you? As the message indicates this > > command is invoked by "matlab_ls_test" - and that is failing. > > > >>>>>>>>>>> > > > >>>>>>>>>>> Satish > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via > > petsc-users wrote: > > > >>>>>>>>>>> > > > >>>>>>>>>>> > Hi Sathish, > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > I tried the following procedure > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > *$make * > > > >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > > >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE > > > >>>>>>>>>>> > Building with 'gcc'. > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > >>>>>>>>>>> > In function ?PetscBinaryWrite?: > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function > > > >>>>>>>>>>> > [-Wmaybe-uninitialized] > > > >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>>>>>>>>> > | ^ > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > MEX completed successfully. > > > >>>>>>>>>>> > Building with 'gcc'. > > > >>>>>>>>>>> > MEX completed successfully. > > > >>>>>>>>>>> > Building with 'gcc'. > > > >>>>>>>>>>> > MEX completed successfully. > > > >>>>>>>>>>> > Building with 'gcc'. > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > >>>>>>>>>>> > In function ?PetscBinaryWrite?: > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function > > > >>>>>>>>>>> > [-Wmaybe-uninitialized] > > > >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to > > socket\n"); > > > >>>>>>>>>>> > | ^ > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > MEX completed successfully. > > > >>>>>>>>>>> > ========================================= > > > >>>>>>>>>>> > Now to check if the libraries are working do: > > > >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > > PETSC_ARCH=linux-opt check > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > *$make test query=requires queryval=matlab > > > >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* > > > >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ > > queryval=matlab > > > >>>>>>>>>>> > query=requires > > > >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > >>>>>>>>>>> > TEST > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 > > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > > >>>>>>>>>>> > > > -------------------------------------------------------------- > > > >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library > > > >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>>>>>>>>>> > # [0]PETSC ERROR: See > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>>>>>>>>> > for trouble shooting. > > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > > 2020 > > > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named > > MB108SMEC028 by vit Mon Sep > > > >>>>>>>>>>> > 4 10:02:32 2023 > > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > COPTFLAGS=-O3 > > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 > > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > > >>>>>>>>>>> > > > -------------------------------------------------------------- > > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data > > > >>>>>>>>>>> > # [0]PETSC ERROR: > > > >>>>>>>>>>> > # [0]PETSC ERROR: See > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>>>>>>>>> > for trouble shooting. > > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > > 2020 > > > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named > > MB108SMEC028 by vit Mon Sep > > > >>>>>>>>>>> > 4 10:02:32 2023 > > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > COPTFLAGS=-O3 > > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 > > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>>>>>>>>> > # [0]PETSC ERROR: > > > >>>>>>>>>>> > > > ------------------------------------------------------------------------ > > > >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: > > Segmentation Violation, > > > >>>>>>>>>>> > probably memory access out of range > > > >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or > > -on_error_attach_debugger > > > >>>>>>>>>>> > # [0]PETSC ERROR: or see > > > >>>>>>>>>>> > > > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > > > >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org < > > http://valgrind.org/> on GNU/linux and Apple Mac OS > > > >>>>>>>>>>> > X to find memory corruption errors > > > >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, > > recompile, link, > > > >>>>>>>>>>> > and run > > > >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. > > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > > >>>>>>>>>>> > > > -------------------------------------------------------------- > > > >>>>>>>>>>> > # [0]PETSC ERROR: Signal received > > > >>>>>>>>>>> > # [0]PETSC ERROR: See > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>>>>>>>>> > for trouble shooting. > > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > > 2020 > > > >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named > > MB108SMEC028 by vit Mon Sep > > > >>>>>>>>>>> > 4 10:02:32 2023 > > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > COPTFLAGS=-O3 > > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 > > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in > > unknown file > > > >>>>>>>>>>> > # > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator > > MPI_COMM_WORLD > > > >>>>>>>>>>> > # with errorcode 50162059. > > > >>>>>>>>>>> > # > > > >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > >>>>>>>>>>> > # You may or may not see output from other processes, > > depending on > > > >>>>>>>>>>> > # exactly when Open MPI kills them. > > > >>>>>>>>>>> > # > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no > > diff > > > >>>>>>>>>>> > CC > > > >>>>>>>>>>> > > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > >>>>>>>>>>> > CLINKER > > > >>>>>>>>>>> > > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>>>>>>>>>> > TEST > > > >>>>>>>>>>> > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > > Error code: 124 > > > >>>>>>>>>>> > # Running problem 5 > > > >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message > > > >>>>>>>>>>> > > > -------------------------------------------------------------- > > > >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library > > > >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>>>>>>>>>> > # [0]PETSC ERROR: See > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>>>>>>>>> > for trouble shooting. > > > >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, > > 2020 > > > >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named > > MB108SMEC028 by > > > >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 > > > >>>>>>>>>>> > # [0]PETSC ERROR: Configure options > > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > COPTFLAGS=-O3 > > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 > > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > > > >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 > > > >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor > > > >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message > > -------send entire > > > >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- > > > >>>>>>>>>>> > # > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator > > MPI_COMM_SELF > > > >>>>>>>>>>> > # with errorcode 126076. > > > >>>>>>>>>>> > # > > > >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > >>>>>>>>>>> > # You may or may not see output from other processes, > > depending on > > > >>>>>>>>>>> > # exactly when Open MPI kills them. > > > >>>>>>>>>>> > # > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # > > SKIP Command failed > > > >>>>>>>>>>> > so no diff > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > # ------------- > > > >>>>>>>>>>> > # Summary > > > >>>>>>>>>>> > # ------------- > > > >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 > > > >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test > > > >>>>>>>>>>> > # success 0/2 tests (0.0%) > > > >>>>>>>>>>> > # failed 2/2 tests (100.0%) > > > >>>>>>>>>>> > # todo 0/2 tests (0.0%) > > > >>>>>>>>>>> > # skip 0/2 tests (0.0%) > > > >>>>>>>>>>> > # > > > >>>>>>>>>>> > # Wall clock time for tests: 4 sec > > > >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec > > > >>>>>>>>>>> > # > > > >>>>>>>>>>> > # To rerun failed tests: > > > >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 > > > >>>>>>>>>>> > # > > > >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): > > > >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec > > > >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 > > sec / 0.01 sec > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* > > > >>>>>>>>>>> > *$make matlab_ls_test* > > > >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall > > -Wwrite-strings > > > >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > > > >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings > > -Wno-strict-aliasing > > > >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden > > -O3 > > > >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include > > > >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > > > >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include > > > >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include > > matlab_ls_test.c > > > >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > > >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > > > >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > > >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >>>>>>>>>>> > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > > > >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > > > >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > > > >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu > > > >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu > > -Wl,-rpath,/lib/x86_64-linux-gnu > > > >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm > > -leng -lmex -lmx > > > >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 > > -lmpi_usempi_ignore_tkr -lmpi_mpifh > > > >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath > > -lpthread -lquadmath > > > >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 > > ./matlab_ls_test > > > >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* > > > >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number > > of processors = 1 > > > >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > > > >>>>>>>>>>> > MB108SMEC028.(none) > > > >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 > > > >>>>>>>>>>> > Running problem 5 > > > >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator > > 140155238476992 > > > >>>>>>>>>>> > 94202473157392 max tags = 2147483647 > > > >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with > > command > > > >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay > > -nosplash > > > >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message > > > >>>>>>>>>>> > > > -------------------------------------------------------------- > > > >>>>>>>>>>> > [0]PETSC ERROR: Error in external library > > > >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on > > > >>>>>>>>>>> > [0]PETSC ERROR: See > > https://www.mcs.anl.gov/petsc/documentation/faq.html > > > >>>>>>>>>>> > for trouble shooting. > > > >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > > > >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named > > MB108SMEC028 by vit > > > >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 > > > >>>>>>>>>>> > [0]PETSC ERROR: Configure options > > > >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > COPTFLAGS=-O3 > > > >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 > > > >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > > > >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > > > >>>>>>>>>>> > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > > > >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c > > > >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: > > > >>>>>>>>>>> > [0]PETSC ERROR: -info > > > >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 > > > >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor > > > >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message > > -------send entire > > > >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- > > > >>>>>>>>>>> > > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator > > MPI_COMM_SELF > > > >>>>>>>>>>> > with errorcode 126076. > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI > > processes. > > > >>>>>>>>>>> > You may or may not see output from other processes, > > depending on > > > >>>>>>>>>>> > exactly when Open MPI kills them. > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > Please find the attachment for configure.log and make.log > > files > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay < > > balay at mcs.anl.gov > wrote: > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > To use datafiles in the test suite: > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > cd $HOME > > > >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles > > > >>>>>>>>>>> > > > DATAFILESPATH - or set > > > >>>>>>>>>>> > > manually with make> > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > make test query=requires queryval=matlab > > DATAFILESPATH=$HOME/datafiles > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > Satish > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: > > > >>>>>>>>>>> > > > > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS > > 20PHD0548 < > > > >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > inturu.srinivas2020 at vitstudent.ac.in>> wrote: > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > > Hi Matthew, > > > >>>>>>>>>>> > > > > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using > > IBAMR. I do not have > > > >>>>>>>>>>> > > any > > > >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you > > please help me how to > > > >>>>>>>>>>> > > > > define this DATAFILESPATH? > > > >>>>>>>>>>> > > > > > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our > > machine, we point to > > > >>>>>>>>>>> > > this > > > >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. > > You don't have those > > > >>>>>>>>>>> > > > matrices, since they are just for testing here. That > > > >>>>>>>>>>> > > > is why I suggested just using a different matrix, or > > running a problem > > > >>>>>>>>>>> > > you > > > >>>>>>>>>>> > > > care about in IBAMR. > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > Thanks, > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > Matt > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > > > > >>>>>>>>>>> > > > > Thanks and regards > > > >>>>>>>>>>> > > > > Srinivas. > > > >>>>>>>>>>> > > > > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < > > knepley at gmail.com > > > > >>>>>>>>>>> > > wrote: > > > >>>>>>>>>>> > > > > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS > > 20PHD0548 via > > > >>>>>>>>>>> > > petsc-users < > > > >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov > petsc-users at mcs.anl.gov>> wrote: > > > >>>>>>>>>>> > > > >> > > > >>>>>>>>>>> > > > >>> Hi Sathish, > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support > > you are giving me > > > >>>>>>>>>>> > > to > > > >>>>>>>>>>> > > > >>> sort this out. > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you > > followed to build > > > >>>>>>>>>>> > > Petsc > > > >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> *$./configure > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > > >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > > PETSC_ARCH=linux-opt > > > >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 > > > >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 > > --with-matlab-engine=1* > > > >>>>>>>>>>> > > > >>> Using python3 for Python > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > =============================================================================== > > > >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your > > system > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > =============================================================================== > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > =============================================================================== > > > >>>>>>>>>>> > > > >>> It appears > > you do not have > > > >>>>>>>>>>> > > valgrind > > > >>>>>>>>>>> > > > >>> installed on your system. > > > >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from > > www.valgrind.org > > > >>>>>>>>>>> > > > >>> Or > > install > > > >>>>>>>>>>> > > valgrind-devel or > > > >>>>>>>>>>> > > > >>> equivalent using your package manager. > > > >>>>>>>>>>> > > > >>> Then rerun ./configure > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > =============================================================================== > > > >>>>>>>>>>> > > > >>> Compilers: > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> C Compiler: > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>>>>>>>>>> > > -fPIC > > > >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas > > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) > > 9.4.0 > > > >>>>>>>>>>> > > > >>> C++ Compiler: > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx > > > >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing > > -Wno-unknown-pragmas > > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC > > > >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) > > 11.4.0 > > > >>>>>>>>>>> > > > >>> Fortran Compiler: > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 > > > >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 > > -Wno-unused-dummy-argument -O3 > > > >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu > > 9.4.0-1ubuntu1~20.04.2) 9.4.0 > > > >>>>>>>>>>> > > > >>> Linkers: > > > >>>>>>>>>>> > > > >>> Shared linker: > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>>>>>>>>>> > > -shared > > > >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > > >>>>>>>>>>> > > -Wno-unknown-pragmas > > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > >>>>>>>>>>> > > > >>> Dynamic linker: > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc > > > >>>>>>>>>>> > > -shared > > > >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > > > >>>>>>>>>>> > > -Wno-unknown-pragmas > > > >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 > > > >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ > > -ldl > > > >>>>>>>>>>> > > > >>> make: > > > >>>>>>>>>>> > > > >>> Version: 4.2 > > > >>>>>>>>>>> > > > >>> /usr/bin/make > > > >>>>>>>>>>> > > > >>> BlasLapack: > > > >>>>>>>>>>> > > > >>> Library: > > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > > > >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 > > -lpthread > > > >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or > > -omp_num_threads > > > >>>>>>>>>>> > >

to > > > >>>>>>>>>>> > > > >>> control the number of threads > > > >>>>>>>>>>> > > > >>> uses 8 byte integers > > > >>>>>>>>>>> > > > >>> MPI: > > > >>>>>>>>>>> > > > >>> Version: 3 > > > >>>>>>>>>>> > > > >>> Includes: > > -I/home/vit/sfw/linux/openmpi/4.1.4/include > > > >>>>>>>>>>> > > > >>> Mpiexec: > > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec > > > >>>>>>>>>>> > > --oversubscribe > > > >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 > > > >>>>>>>>>>> > > > >>> pthread: > > > >>>>>>>>>>> > > > >>> cmake: > > > >>>>>>>>>>> > > > >>> Version: 3.16.3 > > > >>>>>>>>>>> > > > >>> /usr/bin/cmake > > > >>>>>>>>>>> > > > >>> regex: > > > >>>>>>>>>>> > > > >>> Matlab: > > > >>>>>>>>>>> > > > >>> Includes: > > -I/usr/local/MATLAB/R2020b/extern/include > > > >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > > > >>> MatlabEngine: > > > >>>>>>>>>>> > > > >>> Library: > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 > > > >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > > -leng -lmex -lmx -lmat > > > >>>>>>>>>>> > > -lut > > > >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc > > > >>>>>>>>>>> > > > >>> Language used to compile PETSc: C > > > >>>>>>>>>>> > > > >>> PETSc: > > > >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt > > > >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 > > > >>>>>>>>>>> > > > >>> Scalar type: real > > > >>>>>>>>>>> > > > >>> Precision: double > > > >>>>>>>>>>> > > > >>> Support for __float128 > > > >>>>>>>>>>> > > > >>> Integer size: 4 bytes > > > >>>>>>>>>>> > > > >>> shared libraries: enabled > > > >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > xxx=========================================================================xxx > > > >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc > > libraries with: > > > >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > > PETSC_ARCH=linux-opt all > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > xxx=========================================================================xxx > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata > > -licui18n -licuuc as > > > >>>>>>>>>>> > > > >>> you suggested earlier. > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> *$make* > > > >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o > > > >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 > > > >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE > > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this > > function > > > >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] > > > >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error > > writing to socket\n"); > > > >>>>>>>>>>> > > > >>> | ^ > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > > >>>>>>>>>>> > > > >>> Building with 'gcc'. > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > > > >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > > > >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this > > function > > > >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] > > > >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error > > writing to socket\n"); > > > >>>>>>>>>>> > > > >>> | ^ > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> MEX completed successfully. > > > >>>>>>>>>>> > > > >>> ========================================= > > > >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: > > > >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 > > PETSC_ARCH=linux-opt check > > > >>>>>>>>>>> > > > >>> =============================================== > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* > > > >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires > > > >>>>>>>>>>> > > > >>> CC > > linux-opt/tests/ksp/ksp/tutorials/ex72.o > > > >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > > > >>>>>>>>>>> > > > >>> TEST > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > > > >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error > > Message > > > >>>>>>>>>>> > > > >>> > > -------------------------------------------------------------- > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: > > /matrices/arco1 > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > >> > > > >>>>>>>>>>> > > > >> No, the problem is that you do not have > > DATAFILESPATH defined, so it > > > >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some > > test of yours. > > > >>>>>>>>>>> > > > >> > > > >>>>>>>>>>> > > > >> Thanks, > > > >>>>>>>>>>> > > > >> > > > >>>>>>>>>>> > > > >> Matt > > > >>>>>>>>>>> > > > >> > > > >>>>>>>>>>> > > > >> > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See > > > >>>>>>>>>>> > > > >>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble > > > >>>>>>>>>>> > > > >>> shooting. > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, > > Aug 01, 2020 > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named > > MB108SMEC028 by vit > > > >>>>>>>>>>> > > Sun > > > >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options > > > >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 > > COPTFLAGS=-O3 > > > >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt > > --with-debugging=0 > > > >>>>>>>>>>> > > > >>> --with-x=0 > > --with-matlab-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b > > > >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 > > --with-matlab-engine=1 > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 > > PetscViewerFileSetUp_BinarySTDIO() line 1444 in > > > >>>>>>>>>>> > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() > > line 1511 in > > > >>>>>>>>>>> > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in > > > >>>>>>>>>>> > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in > > > >>>>>>>>>>> > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in > > > >>>>>>>>>>> > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in > > > >>>>>>>>>>> > > > >>> > > /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error > > Message -------send > > > >>>>>>>>>>> > > > >>> entire error message to > > petsc-maint at mcs.anl.gov---------- > > > >>>>>>>>>>> > > > >>> # > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator > > MPI_COMM_SELF > > > >>>>>>>>>>> > > > >>> # with errorcode 113065. > > > >>>>>>>>>>> > > > >>> # > > > >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill > > all MPI processes. > > > >>>>>>>>>>> > > > >>> # You may or may not see output from other > > processes, depending on > > > >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. > > > >>>>>>>>>>> > > > >>> # > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command > > failed so no diff > > > >>>>>>>>>>> > > > >>> CC > > > >>>>>>>>>>> > > > >>> > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > > > >>>>>>>>>>> > > > >>> CLINKER > > > >>>>>>>>>>> > > > >>> > > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > > > >>>>>>>>>>> > > > >>> TEST > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > > > >>>>>>>>>>> > > > >>> not ok > > tao_leastsquares_tutorials_matlab-matlab_ls_test # Error > > > >>>>>>>>>>> > > code: 124 > > > >>>>>>>>>>> > > > >>> # Running problem 5 > > > >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error > > Message > > > >>>>>>>>>>> > > > >>> > > -------------------------------------------------------------- > > > >>>>>>> > > From karthikeyan.chockalingam at stfc.ac.uk Thu Sep 7 05:07:48 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Thu, 7 Sep 2023 10:07:48 +0000 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH Message-ID: Hello, The non-linear solution diverged. The final solution seems right and I believe the Jacobian is correct (not 100% certain). I am not sure if I doing something wrong in the solver setting. 0 SNES Function norm 3.890991210938e-03 0 KSP Residual norm 9.037762538598e+00 1 KSP Residual norm 2.120375403775e-01 2 KSP Residual norm 5.155439334511e-03 3 KSP Residual norm 1.394364169369e-04 4 KSP Residual norm 9.233543407204e-06 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: Using full step: fnorm 3.890991210938e-03 gnorm 7.701511565083e-06 1 SNES Function norm 7.701511565083e-06 0 KSP Residual norm 5.630229687829e-03 1 KSP Residual norm 1.030475601271e-04 2 KSP Residual norm 2.576454714319e-06 3 KSP Residual norm 6.669316846898e-08 4 KSP Residual norm 3.215810984829e-09 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: gnorm after quadratic fit 1.805500533481e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 2.563759884284e-05 lambda=3.0804668685096816e-02 Line search: Cubic step no good, shrinking lambda, current gnorm 3.332721829751e-05 lambda=3.0804668685096817e-03 Line search: Cubic step no good, shrinking lambda, current gnorm 4.102754045833e-05 lambda=3.0804668685096822e-04 Line search: Cubic step no good, shrinking lambda, current gnorm 4.872893294880e-05 lambda=3.0804668685096822e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 5.643043250787e-05 lambda=3.0804668685096822e-06 Line search: Cubic step no good, shrinking lambda, current gnorm 6.413194279696e-05 lambda=3.0804668685096827e-07 Line search: Cubic step no good, shrinking lambda, current gnorm 7.183345417492e-05 lambda=3.0804668685096828e-08 Line search: Cubic step no good, shrinking lambda, current gnorm 7.953496567312e-05 lambda=3.0804668685096829e-09 Line search: Cubic step no good, shrinking lambda, current gnorm 8.723647719173e-05 lambda=3.0804668685096831e-10 Line search: Cubic step no good, shrinking lambda, current gnorm 9.493798871875e-05 lambda=3.0804668685096832e-11 Line search: Cubic step no good, shrinking lambda, current gnorm 1.026395002516e-04 lambda=3.0804668685096835e-12 Line search: Cubic step no good, shrinking lambda, current gnorm 1.103410117889e-04 lambda=3.0804668685096835e-13 Line search: unable to find good step length! After 12 tries Line search: fnorm=7.7015115650831560e-06, gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial slope=-5.9313318983096354e-11 Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 Thank you for your help. Kind regards, Karthik. -- Dr. Karthik Chockalingam Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk [signature_3970890138] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 18270 bytes Desc: image001.png URL: From stefano.zampini at gmail.com Thu Sep 7 05:49:22 2023 From: stefano.zampini at gmail.com (Stefano Zampini) Date: Thu, 7 Sep 2023 13:49:22 +0300 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: The solver did not diverge. It was the line search that was not able to make further progress in minimizing the 2-norm of the residual. This is common in nonlinear solvers. It would help if you tell us what you are trying to solve. Note that at the first step, your residual norm is already 1.e-6. What kind of accuracy do you want? Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC UKRI via petsc-users ha scritto: > Hello, > > > > The non-linear solution diverged. The final solution seems right and I > believe the Jacobian is correct (not 100% certain). > > > > I am not sure if I doing something wrong in the solver setting. > > > > > > 0 SNES Function norm 3.890991210938e-03 > > 0 KSP Residual norm 9.037762538598e+00 > > 1 KSP Residual norm 2.120375403775e-01 > > 2 KSP Residual norm 5.155439334511e-03 > > 3 KSP Residual norm 1.394364169369e-04 > > 4 KSP Residual norm 9.233543407204e-06 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: Using full step: fnorm 3.890991210938e-03 gnorm > 7.701511565083e-06 > > 1 SNES Function norm 7.701511565083e-06 > > 0 KSP Residual norm 5.630229687829e-03 > > 1 KSP Residual norm 1.030475601271e-04 > > 2 KSP Residual norm 2.576454714319e-06 > > 3 KSP Residual norm 6.669316846898e-08 > > 4 KSP Residual norm 3.215810984829e-09 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: gnorm after quadratic fit 1.805500533481e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 2.563759884284e-05 lambda=3.0804668685096816e-02 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 3.332721829751e-05 lambda=3.0804668685096817e-03 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.102754045833e-05 lambda=3.0804668685096822e-04 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.872893294880e-05 lambda=3.0804668685096822e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 5.643043250787e-05 lambda=3.0804668685096822e-06 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 6.413194279696e-05 lambda=3.0804668685096827e-07 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.183345417492e-05 lambda=3.0804668685096828e-08 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.953496567312e-05 lambda=3.0804668685096829e-09 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 8.723647719173e-05 lambda=3.0804668685096831e-10 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 9.493798871875e-05 lambda=3.0804668685096832e-11 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.026395002516e-04 lambda=3.0804668685096835e-12 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.103410117889e-04 lambda=3.0804668685096835e-13 > > Line search: unable to find good step length! After 12 tries > > Line search: fnorm=7.7015115650831560e-06, > gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, > minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial > slope=-5.9313318983096354e-11 > > Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 > > > > > > Thank you for your help. > > > > Kind regards, > > Karthik. > > > > -- > > *Dr. Karthik Chockalingam* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > [image: signature_3970890138] > > > -- Stefano -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 18270 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 18270 bytes Desc: not available URL: From karthikeyan.chockalingam at stfc.ac.uk Thu Sep 7 06:19:40 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Thu, 7 Sep 2023 11:19:40 +0000 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: I am trying to solve the non-linear scalar problem -\nabla \cdot \big( (1+u^2)\nabla u\big)=f Using finite element formulation. The linear iteration converged ? does that mean my Jacobian is correct?? I am hoping the non-linear residual goes down to 1-e11. Kind regards, Karthik. From: Stefano Zampini Date: Thursday, 7 September 2023 at 11:49 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH The solver did not diverge. It was the line search that was not able to make further progress in minimizing the 2-norm of the residual. This is common in nonlinear solvers. It would help if you tell us what you are trying to solve. Note that at the first step, your residual norm is already 1.e-6. What kind of accuracy do you want? Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC UKRI via petsc-users > ha scritto: Hello, The non-linear solution diverged. The final solution seems right and I believe the Jacobian is correct (not 100% certain). I am not sure if I doing something wrong in the solver setting. 0 SNES Function norm 3.890991210938e-03 0 KSP Residual norm 9.037762538598e+00 1 KSP Residual norm 2.120375403775e-01 2 KSP Residual norm 5.155439334511e-03 3 KSP Residual norm 1.394364169369e-04 4 KSP Residual norm 9.233543407204e-06 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: Using full step: fnorm 3.890991210938e-03 gnorm 7.701511565083e-06 1 SNES Function norm 7.701511565083e-06 0 KSP Residual norm 5.630229687829e-03 1 KSP Residual norm 1.030475601271e-04 2 KSP Residual norm 2.576454714319e-06 3 KSP Residual norm 6.669316846898e-08 4 KSP Residual norm 3.215810984829e-09 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: gnorm after quadratic fit 1.805500533481e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 2.563759884284e-05 lambda=3.0804668685096816e-02 Line search: Cubic step no good, shrinking lambda, current gnorm 3.332721829751e-05 lambda=3.0804668685096817e-03 Line search: Cubic step no good, shrinking lambda, current gnorm 4.102754045833e-05 lambda=3.0804668685096822e-04 Line search: Cubic step no good, shrinking lambda, current gnorm 4.872893294880e-05 lambda=3.0804668685096822e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 5.643043250787e-05 lambda=3.0804668685096822e-06 Line search: Cubic step no good, shrinking lambda, current gnorm 6.413194279696e-05 lambda=3.0804668685096827e-07 Line search: Cubic step no good, shrinking lambda, current gnorm 7.183345417492e-05 lambda=3.0804668685096828e-08 Line search: Cubic step no good, shrinking lambda, current gnorm 7.953496567312e-05 lambda=3.0804668685096829e-09 Line search: Cubic step no good, shrinking lambda, current gnorm 8.723647719173e-05 lambda=3.0804668685096831e-10 Line search: Cubic step no good, shrinking lambda, current gnorm 9.493798871875e-05 lambda=3.0804668685096832e-11 Line search: Cubic step no good, shrinking lambda, current gnorm 1.026395002516e-04 lambda=3.0804668685096835e-12 Line search: Cubic step no good, shrinking lambda, current gnorm 1.103410117889e-04 lambda=3.0804668685096835e-13 Line search: unable to find good step length! After 12 tries Line search: fnorm=7.7015115650831560e-06, gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial slope=-5.9313318983096354e-11 Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 Thank you for your help. Kind regards, Karthik. -- Dr. Karthik Chockalingam Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk [signature_3970890138] -- Stefano -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Thu Sep 7 07:42:04 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Thu, 7 Sep 2023 12:42:04 +0000 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: I just noticed that the line search diverges even for the linear Poisson equation (where the Jacobian is a constant). I am not sure, what I am doing wrong. Best, Karthik. From: Chockalingam, Karthikeyan (STFC,DL,HC) Date: Thursday, 7 September 2023 at 12:19 To: Stefano Zampini Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH I am trying to solve the non-linear scalar problem -\nabla \cdot \big( (1+u^2)\nabla u\big)=f Using finite element formulation. The linear iteration converged ? does that mean my Jacobian is correct?? I am hoping the non-linear residual goes down to 1-e11. Kind regards, Karthik. From: Stefano Zampini Date: Thursday, 7 September 2023 at 11:49 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH The solver did not diverge. It was the line search that was not able to make further progress in minimizing the 2-norm of the residual. This is common in nonlinear solvers. It would help if you tell us what you are trying to solve. Note that at the first step, your residual norm is already 1.e-6. What kind of accuracy do you want? Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC UKRI via petsc-users > ha scritto: Hello, The non-linear solution diverged. The final solution seems right and I believe the Jacobian is correct (not 100% certain). I am not sure if I doing something wrong in the solver setting. 0 SNES Function norm 3.890991210938e-03 0 KSP Residual norm 9.037762538598e+00 1 KSP Residual norm 2.120375403775e-01 2 KSP Residual norm 5.155439334511e-03 3 KSP Residual norm 1.394364169369e-04 4 KSP Residual norm 9.233543407204e-06 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: Using full step: fnorm 3.890991210938e-03 gnorm 7.701511565083e-06 1 SNES Function norm 7.701511565083e-06 0 KSP Residual norm 5.630229687829e-03 1 KSP Residual norm 1.030475601271e-04 2 KSP Residual norm 2.576454714319e-06 3 KSP Residual norm 6.669316846898e-08 4 KSP Residual norm 3.215810984829e-09 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: gnorm after quadratic fit 1.805500533481e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 2.563759884284e-05 lambda=3.0804668685096816e-02 Line search: Cubic step no good, shrinking lambda, current gnorm 3.332721829751e-05 lambda=3.0804668685096817e-03 Line search: Cubic step no good, shrinking lambda, current gnorm 4.102754045833e-05 lambda=3.0804668685096822e-04 Line search: Cubic step no good, shrinking lambda, current gnorm 4.872893294880e-05 lambda=3.0804668685096822e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 5.643043250787e-05 lambda=3.0804668685096822e-06 Line search: Cubic step no good, shrinking lambda, current gnorm 6.413194279696e-05 lambda=3.0804668685096827e-07 Line search: Cubic step no good, shrinking lambda, current gnorm 7.183345417492e-05 lambda=3.0804668685096828e-08 Line search: Cubic step no good, shrinking lambda, current gnorm 7.953496567312e-05 lambda=3.0804668685096829e-09 Line search: Cubic step no good, shrinking lambda, current gnorm 8.723647719173e-05 lambda=3.0804668685096831e-10 Line search: Cubic step no good, shrinking lambda, current gnorm 9.493798871875e-05 lambda=3.0804668685096832e-11 Line search: Cubic step no good, shrinking lambda, current gnorm 1.026395002516e-04 lambda=3.0804668685096835e-12 Line search: Cubic step no good, shrinking lambda, current gnorm 1.103410117889e-04 lambda=3.0804668685096835e-13 Line search: unable to find good step length! After 12 tries Line search: fnorm=7.7015115650831560e-06, gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial slope=-5.9313318983096354e-11 Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 Thank you for your help. Kind regards, Karthik. -- Dr. Karthik Chockalingam Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk [signature_3970890138] -- Stefano -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Sep 7 08:19:15 2023 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 7 Sep 2023 09:19:15 -0400 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: On Thu, Sep 7, 2023 at 8:49?AM Karthikeyan Chockalingam - STFC UKRI via petsc-users wrote: > I just noticed that the line search diverges even for the linear Poisson > equation (where the Jacobian is a constant). I am not sure, what I am doing > wrong. > You need to test the Jacobian. We have facilities for this. Run using --snes_test_jacobian This will tell you at each step whether the Jacobian matches the finite difference approximant. It looks like your Jacobian at the second step is wrong. Is it possible that you are not zeroing out the matrix before adding in updates? That would make the second step wrong. Thanks, Matt > > > Best, > > Karthik. > > > > *From: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Date: *Thursday, 7 September 2023 at 12:19 > *To: *Stefano Zampini > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > I am trying to solve the non-linear scalar problem > > -\nabla \cdot \big( (1+u^2)\nabla u\big)=f > > Using finite element formulation. > > > > The linear iteration converged ? does that mean my Jacobian is correct?? > > > > I am hoping the non-linear residual goes down to 1-e11. > > > > Kind regards, > > Karthik. > > > > > > *From: *Stefano Zampini > *Date: *Thursday, 7 September 2023 at 11:49 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > The solver did not diverge. > > It was the line search that was not able to make further progress in > minimizing the 2-norm of the residual. > > This is common in nonlinear solvers. It would help if you tell us what you > are trying to solve. > > Note that at the first step, your residual norm is already 1.e-6. What > kind of accuracy do you want? > > > > > > Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC > UKRI via petsc-users ha scritto: > > Hello, > > > > The non-linear solution diverged. The final solution seems right and I > believe the Jacobian is correct (not 100% certain). > > > > I am not sure if I doing something wrong in the solver setting. > > > > > > 0 SNES Function norm 3.890991210938e-03 > > 0 KSP Residual norm 9.037762538598e+00 > > 1 KSP Residual norm 2.120375403775e-01 > > 2 KSP Residual norm 5.155439334511e-03 > > 3 KSP Residual norm 1.394364169369e-04 > > 4 KSP Residual norm 9.233543407204e-06 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: Using full step: fnorm 3.890991210938e-03 gnorm > 7.701511565083e-06 > > 1 SNES Function norm 7.701511565083e-06 > > 0 KSP Residual norm 5.630229687829e-03 > > 1 KSP Residual norm 1.030475601271e-04 > > 2 KSP Residual norm 2.576454714319e-06 > > 3 KSP Residual norm 6.669316846898e-08 > > 4 KSP Residual norm 3.215810984829e-09 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: gnorm after quadratic fit 1.805500533481e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 2.563759884284e-05 lambda=3.0804668685096816e-02 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 3.332721829751e-05 lambda=3.0804668685096817e-03 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.102754045833e-05 lambda=3.0804668685096822e-04 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.872893294880e-05 lambda=3.0804668685096822e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 5.643043250787e-05 lambda=3.0804668685096822e-06 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 6.413194279696e-05 lambda=3.0804668685096827e-07 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.183345417492e-05 lambda=3.0804668685096828e-08 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.953496567312e-05 lambda=3.0804668685096829e-09 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 8.723647719173e-05 lambda=3.0804668685096831e-10 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 9.493798871875e-05 lambda=3.0804668685096832e-11 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.026395002516e-04 lambda=3.0804668685096835e-12 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.103410117889e-04 lambda=3.0804668685096835e-13 > > Line search: unable to find good step length! After 12 tries > > Line search: fnorm=7.7015115650831560e-06, > gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, > minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial > slope=-5.9313318983096354e-11 > > Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 > > > > > > Thank you for your help. > > > > Kind regards, > > Karthik. > > > > -- > > *Dr. Karthik Chockalingam* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > [image: signature_3970890138] > > > > > > -- > > Stefano > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Thu Sep 7 08:27:53 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Thu, 7 Sep 2023 13:27:53 +0000 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: Thank you for your response. I will test the Jacobian. The linear solve in the second step convergences. Is it possible that Jacobian had been zeroed out? Best, Karthik. From: Matthew Knepley Date: Thursday, 7 September 2 ot023 at 14:19 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: Stefano Zampini , petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH On Thu, Sep 7, 2023 at 8:49?AM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: I just noticed that the line search diverges even for the linear Poisson equation (where the Jacobian is a constant). I am not sure, what I am doing wrong. You need to test the Jacobian. We have facilities for this. Run using --snes_test_jacobian This will tell you at each step whether the Jacobian matches the finite difference approximant. It looks like your Jacobian at the second step is wrong. Is it possible that you are not zeroing out the matrix before adding in updates? That would make the second step wrong. Thanks, Matt Best, Karthik. From: Chockalingam, Karthikeyan (STFC,DL,HC) > Date: Thursday, 7 September 2023 at 12:19 To: Stefano Zampini > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH I am trying to solve the non-linear scalar problem -\nabla \cdot \big( (1+u^2)\nabla u\big)=f Using finite element formulation. The linear iteration converged ? does that mean my Jacobian is correct?? I am hoping the non-linear residual goes down to 1-e11. Kind regards, Karthik. From: Stefano Zampini > Date: Thursday, 7 September 2023 at 11:49 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH The solver did not diverge. It was the line search that was not able to make further progress in minimizing the 2-norm of the residual. This is common in nonlinear solvers. It would help if you tell us what you are trying to solve. Note that at the first step, your residual norm is already 1.e-6. What kind of accuracy do you want? Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC UKRI via petsc-users > ha scritto: Hello, The non-linear solution diverged. The final solution seems right and I believe the Jacobian is correct (not 100% certain). I am not sure if I doing something wrong in the solver setting. 0 SNES Function norm 3.890991210938e-03 0 KSP Residual norm 9.037762538598e+00 1 KSP Residual norm 2.120375403775e-01 2 KSP Residual norm 5.155439334511e-03 3 KSP Residual norm 1.394364169369e-04 4 KSP Residual norm 9.233543407204e-06 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: Using full step: fnorm 3.890991210938e-03 gnorm 7.701511565083e-06 1 SNES Function norm 7.701511565083e-06 0 KSP Residual norm 5.630229687829e-03 1 KSP Residual norm 1.030475601271e-04 2 KSP Residual norm 2.576454714319e-06 3 KSP Residual norm 6.669316846898e-08 4 KSP Residual norm 3.215810984829e-09 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: gnorm after quadratic fit 1.805500533481e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 2.563759884284e-05 lambda=3.0804668685096816e-02 Line search: Cubic step no good, shrinking lambda, current gnorm 3.332721829751e-05 lambda=3.0804668685096817e-03 Line search: Cubic step no good, shrinking lambda, current gnorm 4.102754045833e-05 lambda=3.0804668685096822e-04 Line search: Cubic step no good, shrinking lambda, current gnorm 4.872893294880e-05 lambda=3.0804668685096822e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 5.643043250787e-05 lambda=3.0804668685096822e-06 Line search: Cubic step no good, shrinking lambda, current gnorm 6.413194279696e-05 lambda=3.0804668685096827e-07 Line search: Cubic step no good, shrinking lambda, current gnorm 7.183345417492e-05 lambda=3.0804668685096828e-08 Line search: Cubic step no good, shrinking lambda, current gnorm 7.953496567312e-05 lambda=3.0804668685096829e-09 Line search: Cubic step no good, shrinking lambda, current gnorm 8.723647719173e-05 lambda=3.0804668685096831e-10 Line search: Cubic step no good, shrinking lambda, current gnorm 9.493798871875e-05 lambda=3.0804668685096832e-11 Line search: Cubic step no good, shrinking lambda, current gnorm 1.026395002516e-04 lambda=3.0804668685096835e-12 Line search: Cubic step no good, shrinking lambda, current gnorm 1.103410117889e-04 lambda=3.0804668685096835e-13 Line search: unable to find good step length! After 12 tries Line search: fnorm=7.7015115650831560e-06, gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial slope=-5.9313318983096354e-11 Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 Thank you for your help. Kind regards, Karthik. -- Dr. Karthik Chockalingam Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- Stefano -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Sep 7 08:32:04 2023 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 7 Sep 2023 09:32:04 -0400 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: On Thu, Sep 7, 2023 at 9:28?AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > Thank you for your response. > > > > I will test the Jacobian. > > > > The linear solve in the second step convergences. Is it possible that > Jacobian had been zeroed out? > I think you miss my point. Suppose you did not zero out the Jacobian when you started adding entries. Then you will get something close to twice the value. The linear system will solve fine, but the sep would be wrong. Thanks, Matt > > > Best, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Thursday, 7 September 2 ot023 at 14:19 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *Stefano Zampini , petsc-users at mcs.anl.gov > > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > On Thu, Sep 7, 2023 at 8:49?AM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > I just noticed that the line search diverges even for the linear Poisson > equation (where the Jacobian is a constant). I am not sure, what I am doing > wrong. > > > > You need to test the Jacobian. We have facilities for this. Run using > > > > --snes_test_jacobian > > > > This will tell you at each step whether the Jacobian matches the finite > difference approximant. It looks like your Jacobian at the second step is > wrong. Is it possible that you are not zeroing out the matrix before adding > in updates? That would make the second step wrong. > > > > Thanks, > > > > Matt > > > > > > Best, > > Karthik. > > > > *From: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Date: *Thursday, 7 September 2023 at 12:19 > *To: *Stefano Zampini > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > I am trying to solve the non-linear scalar problem > > -\nabla \cdot \big( (1+u^2)\nabla u\big)=f > > Using finite element formulation. > > > > The linear iteration converged ? does that mean my Jacobian is correct?? > > > > I am hoping the non-linear residual goes down to 1-e11. > > > > Kind regards, > > Karthik. > > > > > > *From: *Stefano Zampini > *Date: *Thursday, 7 September 2023 at 11:49 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > The solver did not diverge. > > It was the line search that was not able to make further progress in > minimizing the 2-norm of the residual. > > This is common in nonlinear solvers. It would help if you tell us what you > are trying to solve. > > Note that at the first step, your residual norm is already 1.e-6. What > kind of accuracy do you want? > > > > > > Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC > UKRI via petsc-users ha scritto: > > Hello, > > > > The non-linear solution diverged. The final solution seems right and I > believe the Jacobian is correct (not 100% certain). > > > > I am not sure if I doing something wrong in the solver setting. > > > > > > 0 SNES Function norm 3.890991210938e-03 > > 0 KSP Residual norm 9.037762538598e+00 > > 1 KSP Residual norm 2.120375403775e-01 > > 2 KSP Residual norm 5.155439334511e-03 > > 3 KSP Residual norm 1.394364169369e-04 > > 4 KSP Residual norm 9.233543407204e-06 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: Using full step: fnorm 3.890991210938e-03 gnorm > 7.701511565083e-06 > > 1 SNES Function norm 7.701511565083e-06 > > 0 KSP Residual norm 5.630229687829e-03 > > 1 KSP Residual norm 1.030475601271e-04 > > 2 KSP Residual norm 2.576454714319e-06 > > 3 KSP Residual norm 6.669316846898e-08 > > 4 KSP Residual norm 3.215810984829e-09 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: gnorm after quadratic fit 1.805500533481e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 2.563759884284e-05 lambda=3.0804668685096816e-02 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 3.332721829751e-05 lambda=3.0804668685096817e-03 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.102754045833e-05 lambda=3.0804668685096822e-04 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.872893294880e-05 lambda=3.0804668685096822e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 5.643043250787e-05 lambda=3.0804668685096822e-06 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 6.413194279696e-05 lambda=3.0804668685096827e-07 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.183345417492e-05 lambda=3.0804668685096828e-08 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.953496567312e-05 lambda=3.0804668685096829e-09 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 8.723647719173e-05 lambda=3.0804668685096831e-10 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 9.493798871875e-05 lambda=3.0804668685096832e-11 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.026395002516e-04 lambda=3.0804668685096835e-12 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.103410117889e-04 lambda=3.0804668685096835e-13 > > Line search: unable to find good step length! After 12 tries > > Line search: fnorm=7.7015115650831560e-06, > gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, > minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial > slope=-5.9313318983096354e-11 > > Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 > > > > > > Thank you for your help. > > > > Kind regards, > > Karthik. > > > > -- > > *Dr. Karthik Chockalingam* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > -- > > Stefano > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Thu Sep 7 09:17:46 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Thu, 7 Sep 2023 14:17:46 +0000 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: Yes, I had to zero both the Jacobian and Residual which fixed the SNES convergence problem! This is my first time solving using SNES. From the tutorial https://petsc4py.readthedocs.io/en/stable/manual/snes/ I didn?t notice the Jacobian and Residual had to be zeroed. Thank you. Best, Karthik. From: Matthew Knepley Date: Thursday, 7 September 2023 at 14:32 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: Stefano Zampini , petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH On Thu, Sep 7, 2023 at 9:28?AM Karthikeyan Chockalingam - STFC UKRI > wrote: Thank you for your response. I will test the Jacobian. The linear solve in the second step convergences. Is it possible that Jacobian had been zeroed out? I think you miss my point. Suppose you did not zero out the Jacobian when you started adding entries. Then you will get something close to twice the value. The linear system will solve fine, but the sep would be wrong. Thanks, Matt Best, Karthik. From: Matthew Knepley > Date: Thursday, 7 September 2 ot023 at 14:19 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: Stefano Zampini >, petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH On Thu, Sep 7, 2023 at 8:49?AM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: I just noticed that the line search diverges even for the linear Poisson equation (where the Jacobian is a constant). I am not sure, what I am doing wrong. You need to test the Jacobian. We have facilities for this. Run using --snes_test_jacobian This will tell you at each step whether the Jacobian matches the finite difference approximant. It looks like your Jacobian at the second step is wrong. Is it possible that you are not zeroing out the matrix before adding in updates? That would make the second step wrong. Thanks, Matt Best, Karthik. From: Chockalingam, Karthikeyan (STFC,DL,HC) > Date: Thursday, 7 September 2023 at 12:19 To: Stefano Zampini > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH I am trying to solve the non-linear scalar problem -\nabla \cdot \big( (1+u^2)\nabla u\big)=f Using finite element formulation. The linear iteration converged ? does that mean my Jacobian is correct?? I am hoping the non-linear residual goes down to 1-e11. Kind regards, Karthik. From: Stefano Zampini > Date: Thursday, 7 September 2023 at 11:49 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH The solver did not diverge. It was the line search that was not able to make further progress in minimizing the 2-norm of the residual. This is common in nonlinear solvers. It would help if you tell us what you are trying to solve. Note that at the first step, your residual norm is already 1.e-6. What kind of accuracy do you want? Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC UKRI via petsc-users > ha scritto: Hello, The non-linear solution diverged. The final solution seems right and I believe the Jacobian is correct (not 100% certain). I am not sure if I doing something wrong in the solver setting. 0 SNES Function norm 3.890991210938e-03 0 KSP Residual norm 9.037762538598e+00 1 KSP Residual norm 2.120375403775e-01 2 KSP Residual norm 5.155439334511e-03 3 KSP Residual norm 1.394364169369e-04 4 KSP Residual norm 9.233543407204e-06 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: Using full step: fnorm 3.890991210938e-03 gnorm 7.701511565083e-06 1 SNES Function norm 7.701511565083e-06 0 KSP Residual norm 5.630229687829e-03 1 KSP Residual norm 1.030475601271e-04 2 KSP Residual norm 2.576454714319e-06 3 KSP Residual norm 6.669316846898e-08 4 KSP Residual norm 3.215810984829e-09 Linear solve converged due to CONVERGED_RTOL iterations 4 Line search: gnorm after quadratic fit 1.805500533481e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 2.563759884284e-05 lambda=3.0804668685096816e-02 Line search: Cubic step no good, shrinking lambda, current gnorm 3.332721829751e-05 lambda=3.0804668685096817e-03 Line search: Cubic step no good, shrinking lambda, current gnorm 4.102754045833e-05 lambda=3.0804668685096822e-04 Line search: Cubic step no good, shrinking lambda, current gnorm 4.872893294880e-05 lambda=3.0804668685096822e-05 Line search: Cubic step no good, shrinking lambda, current gnorm 5.643043250787e-05 lambda=3.0804668685096822e-06 Line search: Cubic step no good, shrinking lambda, current gnorm 6.413194279696e-05 lambda=3.0804668685096827e-07 Line search: Cubic step no good, shrinking lambda, current gnorm 7.183345417492e-05 lambda=3.0804668685096828e-08 Line search: Cubic step no good, shrinking lambda, current gnorm 7.953496567312e-05 lambda=3.0804668685096829e-09 Line search: Cubic step no good, shrinking lambda, current gnorm 8.723647719173e-05 lambda=3.0804668685096831e-10 Line search: Cubic step no good, shrinking lambda, current gnorm 9.493798871875e-05 lambda=3.0804668685096832e-11 Line search: Cubic step no good, shrinking lambda, current gnorm 1.026395002516e-04 lambda=3.0804668685096835e-12 Line search: Cubic step no good, shrinking lambda, current gnorm 1.103410117889e-04 lambda=3.0804668685096835e-13 Line search: unable to find good step length! After 12 tries Line search: fnorm=7.7015115650831560e-06, gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial slope=-5.9313318983096354e-11 Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 Thank you for your help. Kind regards, Karthik. -- Dr. Karthik Chockalingam Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- Stefano -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Sep 7 13:27:46 2023 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 7 Sep 2023 14:27:46 -0400 Subject: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH In-Reply-To: References: Message-ID: On Thu, Sep 7, 2023 at 10:18?AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > Yes, I had to zero both the Jacobian and Residual which fixed the SNES > convergence problem! > > > > This is my first time solving using SNES. From the tutorial > > https://petsc4py.readthedocs.io/en/stable/manual/snes/ > > I didn?t notice the Jacobian and Residual had to be zeroed. > Yes, these examples are all FD so the entries are not added to, but set directly. The FEM examples do this zeroing out in the wrapper functions like DMComputeResidualLocal, so it is hard to see. Thanks, Matt > Thank you. > > > > Best, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Thursday, 7 September 2023 at 14:32 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *Stefano Zampini , petsc-users at mcs.anl.gov > > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > On Thu, Sep 7, 2023 at 9:28?AM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > Thank you for your response. > > > > I will test the Jacobian. > > > > The linear solve in the second step convergences. Is it possible that > Jacobian had been zeroed out? > > > > I think you miss my point. Suppose you did not zero out the Jacobian when > you started adding entries. Then you will get something close to twice the > value. The linear system will solve fine, but the sep would be wrong. > > > > Thanks, > > > > Matt > > > > > > Best, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Thursday, 7 September 2 ot023 at 14:19 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *Stefano Zampini , petsc-users at mcs.anl.gov > > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > On Thu, Sep 7, 2023 at 8:49?AM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > I just noticed that the line search diverges even for the linear Poisson > equation (where the Jacobian is a constant). I am not sure, what I am doing > wrong. > > > > You need to test the Jacobian. We have facilities for this. Run using > > > > --snes_test_jacobian > > > > This will tell you at each step whether the Jacobian matches the finite > difference approximant. It looks like your Jacobian at the second step is > wrong. Is it possible that you are not zeroing out the matrix before adding > in updates? That would make the second step wrong. > > > > Thanks, > > > > Matt > > > > > > Best, > > Karthik. > > > > *From: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Date: *Thursday, 7 September 2023 at 12:19 > *To: *Stefano Zampini > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > I am trying to solve the non-linear scalar problem > > -\nabla \cdot \big( (1+u^2)\nabla u\big)=f > > Using finite element formulation. > > > > The linear iteration converged ? does that mean my Jacobian is correct?? > > > > I am hoping the non-linear residual goes down to 1-e11. > > > > Kind regards, > > Karthik. > > > > > > *From: *Stefano Zampini > *Date: *Thursday, 7 September 2023 at 11:49 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Non-linear solve: DIVERGED_LINE_SEARCH > > The solver did not diverge. > > It was the line search that was not able to make further progress in > minimizing the 2-norm of the residual. > > This is common in nonlinear solvers. It would help if you tell us what you > are trying to solve. > > Note that at the first step, your residual norm is already 1.e-6. What > kind of accuracy do you want? > > > > > > Il giorno gio 7 set 2023 alle ore 13:08 Karthikeyan Chockalingam - STFC > UKRI via petsc-users ha scritto: > > Hello, > > > > The non-linear solution diverged. The final solution seems right and I > believe the Jacobian is correct (not 100% certain). > > > > I am not sure if I doing something wrong in the solver setting. > > > > > > 0 SNES Function norm 3.890991210938e-03 > > 0 KSP Residual norm 9.037762538598e+00 > > 1 KSP Residual norm 2.120375403775e-01 > > 2 KSP Residual norm 5.155439334511e-03 > > 3 KSP Residual norm 1.394364169369e-04 > > 4 KSP Residual norm 9.233543407204e-06 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: Using full step: fnorm 3.890991210938e-03 gnorm > 7.701511565083e-06 > > 1 SNES Function norm 7.701511565083e-06 > > 0 KSP Residual norm 5.630229687829e-03 > > 1 KSP Residual norm 1.030475601271e-04 > > 2 KSP Residual norm 2.576454714319e-06 > > 3 KSP Residual norm 6.669316846898e-08 > > 4 KSP Residual norm 3.215810984829e-09 > > Linear solve converged due to CONVERGED_RTOL iterations 4 > > > > Line search: gnorm after quadratic fit 1.805500533481e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 2.563759884284e-05 lambda=3.0804668685096816e-02 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 3.332721829751e-05 lambda=3.0804668685096817e-03 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.102754045833e-05 lambda=3.0804668685096822e-04 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 4.872893294880e-05 lambda=3.0804668685096822e-05 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 5.643043250787e-05 lambda=3.0804668685096822e-06 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 6.413194279696e-05 lambda=3.0804668685096827e-07 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.183345417492e-05 lambda=3.0804668685096828e-08 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 7.953496567312e-05 lambda=3.0804668685096829e-09 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 8.723647719173e-05 lambda=3.0804668685096831e-10 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 9.493798871875e-05 lambda=3.0804668685096832e-11 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.026395002516e-04 lambda=3.0804668685096835e-12 > > Line search: Cubic step no good, shrinking lambda, current gnorm > 1.103410117889e-04 lambda=3.0804668685096835e-13 > > Line search: unable to find good step length! After 12 tries > > Line search: fnorm=7.7015115650831560e-06, > gnorm=1.1034101178892401e-04, ynorm=6.2052357872955976e-03, > minlambda=9.9999999999999998e-13, lambda=3.0804668685096835e-13, initial > slope=-5.9313318983096354e-11 > > Nonlinear solve did not converge due to DIVERGED_LINE_SEARCH iterations 1 > > > > > > Thank you for your help. > > > > Kind regards, > > Karthik. > > > > -- > > *Dr. Karthik Chockalingam* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > -- > > Stefano > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Fri Sep 8 09:33:18 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Fri, 8 Sep 2023 20:03:18 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: Hi Barry, I tried to run Matlab Engine C example provided in the link " https://in.mathworks.com/help/matlab/matlab_external/build-unix-engine-example.html " *in Matlab:* copyfile(fullfile(matlabroot,'extern','examples','eng_mat','engdemo.c'),'.','f') mex -v -client engine engdemo.c *in linux terminal :* LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 export LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH *./engdemo* ./engdemo: error while loading shared libraries: libmx.so: cannot open shared object file: No such file or directory how to sort out this error? Is this the right way to check MatlabEngine with C? Thanks and regards Srinivas On Wed, Sep 6, 2023 at 11:47?PM Barry Smith wrote: > > Ok, so the C++ binding for Matlab engine is working on your machine. > PETSc uses the C binding which links against different libraries but, one > would think the C binding would work for sure if the C++ binding works. Can > you try a Matlab Engine C example provided by Matlab? > > > > > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > Hi Amneet, > > I repeated the same procedure again and this time it is working. > *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp > -lMatlabDataArray -lMatlabEngine* > > *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* > *$export LD_LIBRARY_PATH* > *$./a.out* > Square root of -2 is 0 + 1.41421i > Square root of 2 is 1.41421 + 0i > Square root of 6 is 2.44949 + 0i > Square root of 8 is 2.82843 + 0i > I don't know how it is working this time? > > Thanks and regards > Srinivas > > > On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > >> Hi Amneet, >> I tried the following example to run a matlab engine. >> >> #include "MatlabDataArray.hpp" >> #include "MatlabEngine.hpp" >> #include >> void callSQRT() { >> >> using namespace matlab::engine; >> >> // Start MATLAB engine synchronously >> std::unique_ptr matlabPtr = startMATLAB(); >> >> //Create MATLAB data array factory >> matlab::data::ArrayFactory factory; >> >> // Define a four-element typed array >> matlab::data::TypedArray const argArray = >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >> >> // Call MATLAB sqrt function on the data array >> matlab::data::Array const results = matlabPtr->feval(u"sqrt", >> argArray); >> >> // Display results >> for (int i = 0; i < results.getNumberOfElements(); i++) { >> double a = argArray[i]; >> std::complex v = results[i]; >> double realPart = v.real(); >> double imgPart = v.imag(); >> std::cout << "Square root of " << a << " is " << >> realPart << " + " << imgPart << "i" << std::endl; >> } >> } >> >> int main() { >> callSQRT(); >> return 0; >> } >> >> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp >> -lMatlabDataArray -lMatlabEngine* >> >> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >> *$export LD_LIBRARY_PATH* >> *$./a.out* >> Starting >> Error: The import statement 'import matlab.internal.engine.input' cannot >> be found or cannot be imported. Imported names must end with '.*' or be >> fully qualified. >> >> terminate called after throwing an instance of >> 'matlab::engine::EngineException' >> what(): MATLAB process cannot be created. >> Aborted (core dumped) >> >> I got the above error for Matlab R2020b. Please help me to sort out this. >> >> Thanks and regards >> Srinivas >> >> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla >> wrote: >> >>> BTW, what Barry is suggesting is the following: >>> >>> Compile a sample code with a command line this: >>> >>> >>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>> >>> >>> This command is provided here: >>> >>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>> >>> >>> A sample MATLAB code is here: >>> >>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>> >>> >>> (You can just pick a few lines of code from here to create a barebone example) >>> >>> >>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >>> wrote: >>> >>>> Srinivas --- Do you have a different version of MATLAB that you can >>>> install? If your organization has a MATLAB license, you can install recent >>>> versions of MATLAB from mathworks.com >>>> >>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>>> >>>>> >>>>> Ok, I have no suggestions. It seems to be more an issue with the >>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>>> (in the Matlab documentation) and try it to see if it works. >>>>> >>>>> Barry >>>>> >>>>> >>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>> >>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>> I got the same errors for petsc 3.17.5 >>>>> >>>>> >>>>> *make all* >>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>> Building with 'gcc'. >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> In function ?PetscBinaryWrite?: >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>> warning: ?err? may be used uninitialized in this function >>>>> [-Wmaybe-uninitialized] >>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> | ^ >>>>> >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> MEX completed successfully. >>>>> Building with 'gcc'. >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>> In function ?PetscBinaryWrite?: >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>> warning: ?err? may be used uninitialized in this function >>>>> [-Wmaybe-uninitialized] >>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>> | ^ >>>>> >>>>> MEX completed successfully. >>>>> ========================================= >>>>> ========================================= >>>>> Now to check if the libraries are working do: >>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>> >>>>> *make test query=requires queryval=matlab >>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>> query=requires >>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> # [0]PETSC ERROR: Error in external library >>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>> shooting. >>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue >>>>> Sep 5 21:39:22 2023 >>>>> # [0]PETSC ERROR: Configure options >>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>> --known-64-bit-blas-indices=1 >>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>> # [0]PETSC ERROR: #9 main() at >>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>> # [0]PETSC ERROR: -error_output_stdout >>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>> # [0]PETSC ERROR: -malloc_dump >>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>> # [0]PETSC ERROR: -pc_type lu >>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>> # >>>>> -------------------------------------------------------------------------- >>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>> # with errorcode 85. >>>>> # >>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>> # You may or may not see output from other processes, depending on >>>>> # exactly when Open MPI kills them. >>>>> # >>>>> -------------------------------------------------------------------------- >>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>> >>>>> >>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>> # >>>>> # To rerun failed tests: >>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>>> >>>>>> >>>>>> The error is occuring during >>>>>> >>>>>> e->ep = engOpen(buffer); >>>>>> >>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>>> stdout and stdin from the Matlab session that is launched to the >>>>>> executable. >>>>>> >>>>>> You can try the following. In 3.17.5 edit the >>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>> >>>>>> e->ep = engOpen(buffer); >>>>>> >>>>>> replace it with >>>>>> >>>>>> e->ep = engOpen(""); >>>>>> >>>>>> Now in the PETSc directory do make all (it should recompile one file) >>>>>> and then run the >>>>>> >>>>>> make test query=requires queryval=matlab >>>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>>> >>>>>> again >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>> wrote: >>>>>> >>>>>> Hi Amneeth, >>>>>> >>>>>> I think the errors are different with petsc 3.17.5 >>>>>> >>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>> >>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>> The version of PETSc you are using is out-of-date, we recommend >>>>>> updating to the new release >>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>> https://petsc.org/release/download/ >>>>>> >>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>> >>>>>> ============================================================================================= >>>>>> Configuring PETSc to compile on your system >>>>>> >>>>>> >>>>>> ============================================================================================= >>>>>> Compilers: >>>>>> >>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>>> -fvisibility=hidden -O3 >>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>> Linkers: >>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>> BlasLapack: >>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

>>>>>> to control the number of threads >>>>>> uses 8 byte integers >>>>>> MPI: >>>>>> Version: 3 >>>>>> mpiexec: /usr/bin/mpiexec >>>>>> Implementation: openmpi >>>>>> OMPI_VERSION: 4.0.3 >>>>>> pthread: >>>>>> cmake: >>>>>> Version: 3.16.3 >>>>>> /usr/bin/cmake >>>>>> regex: >>>>>> Matlab: >>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>> /usr/local/MATLAB/R2020b >>>>>> MatlabEngine: >>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>> Language used to compile PETSc: C >>>>>> PETSc: >>>>>> PETSC_ARCH: linux-opt >>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>> Prefix: >>>>>> Scalar type: real >>>>>> Precision: double >>>>>> Support for __float128 >>>>>> Integer size: 4 bytes >>>>>> Single library: yes >>>>>> Shared libraries: yes >>>>>> Memory alignment from malloc(): 16 bytes >>>>>> Using GNU make: /usr/bin/make >>>>>> >>>>>> xxx=========================================================================xxx >>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 >>>>>> PETSC_ARCH=linux-opt all >>>>>> >>>>>> xxx=========================================================================xxx >>>>>> >>>>>> *$make* >>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> Building with 'gcc'. >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> ========================================= >>>>>> ========================================= >>>>>> Now to check if the libraries are working do: >>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>>> check >>>>>> >>>>>> *$make test query=requires queryval=matlab >>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>> /usr/bin/python3 >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>>> --testdir=./linux-opt/tests >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>> queryval=matlab query=requires >>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> -------------------------------------------------------------- >>>>>> # [0]PETSC ERROR: Error in external library >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>> shooting. >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Tue Sep 5 10:15:57 2023 >>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>> # [0]PETSC ERROR: #9 main() at >>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> # with errorcode 85. >>>>>> # >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> # You may or may not see output from other processes, depending on >>>>>> # exactly when Open MPI kills them. >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> >>>>>> >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> # >>>>>> # To rerun failed tests: >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> >>>>>> To get the info of the error there is no specific probe id reported. >>>>>> >>>>>> How to check error info and proceed further? >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>>> wrote: >>>>>> >>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>>>> options that Satish mentioned? >>>>>>> >>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>>> petsc-users wrote: >>>>>>> >>>>>>>> Sorry for missing that. >>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash* >>>>>>>> >>>>>>>> < M A T L A B (R) > >>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>> November 23, 2020 >>>>>>>> >>>>>>>> >>>>>>>> To get started, type doc. >>>>>>>> For product information, visit www.mathworks.com. >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>>> wrote: >>>>>>>> >>>>>>>>> You are missing one more step: >>>>>>>>> >>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>> >>>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>> >>>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>>> >>>>>>>>> Satish >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>> > Hi Sathish, >>>>>>>>> > >>>>>>>>> > I tried the following procedure >>>>>>>>> > >>>>>>>>> > *$make * >>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > | ^ >>>>>>>>> > >>>>>>>>> > MEX completed successfully. >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > MEX completed successfully. >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > MEX completed successfully. >>>>>>>>> > Building with 'gcc'. >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > | ^ >>>>>>>>> > >>>>>>>>> > MEX completed successfully. >>>>>>>>> > ========================================= >>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>>> check >>>>>>>>> > >>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>> queryval=matlab >>>>>>>>> > query=requires >>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>> > TEST >>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>> vit Mon Sep >>>>>>>>> > 4 10:02:32 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>> vit Mon Sep >>>>>>>>> > 4 10:02:32 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>> > >>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>>> Violation, >>>>>>>>> > probably memory access out of range >>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>>> -on_error_attach_debugger >>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>>> Apple Mac OS >>>>>>>>> > X to find memory corruption errors >>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>>> recompile, link, >>>>>>>>> > and run >>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>> vit Mon Sep >>>>>>>>> > 4 10:02:32 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown >>>>>>>>> file >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>> > # with errorcode 50162059. >>>>>>>>> > # >>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>> processes. >>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>> on >>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>> > CC >>>>>>>>> > >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>> > CLINKER >>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > TEST >>>>>>>>> > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>> code: 124 >>>>>>>>> > # Running problem 5 >>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>> MB108SMEC028 by >>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>> > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>> -------send entire >>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>> > # with errorcode 126076. >>>>>>>>> > # >>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>> processes. >>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>> on >>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>> > # >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>> Command failed >>>>>>>>> > so no diff >>>>>>>>> > >>>>>>>>> > # ------------- >>>>>>>>> > # Summary >>>>>>>>> > # ------------- >>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>> > # >>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>> > # >>>>>>>>> > # To rerun failed tests: >>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>> > # >>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / >>>>>>>>> 0.01 sec >>>>>>>>> > >>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>> > *$make matlab_ls_test* >>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>> -Wwrite-strings >>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>> -Wno-strict-aliasing >>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>>>>> -lmex -lmx >>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>> -lmpi_mpifh >>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>>> -lquadmath >>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>> > >>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>> ./matlab_ls_test >>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>> processors = 1 >>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>> > MB108SMEC028.(none) >>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>> > Running problem 5 >>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>> 140155238476992 >>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>> command >>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>> -nosplash >>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > -------------------------------------------------------------- >>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > [0]PETSC ERROR: See >>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > for trouble shooting. >>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>>> MB108SMEC028 by vit >>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>> entire >>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>> > with errorcode 126076. >>>>>>>>> > >>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>> processes. >>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>> > >>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>> > >>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>>> wrote: >>>>>>>>> > >>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>> > > >>>>>>>>> > > cd $HOME >>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>> > > >>>>>>>> DATAFILESPATH - or set >>>>>>>>> > > manually with make> >>>>>>>>> > > >>>>>>>>> > > make test query=requires queryval=matlab >>>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>>> > > >>>>>>>>> > > Satish >>>>>>>>> > > >>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>> > > >>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>>> > > > >>>>>>>>> > > > > Hi Matthew, >>>>>>>>> > > > > >>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I >>>>>>>>> do not have >>>>>>>>> > > any >>>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>>> help me how to >>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>> > > > > >>>>>>>>> > > > >>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, >>>>>>>>> we point to >>>>>>>>> > > this >>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>>> don't have those >>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>> > > > is why I suggested just using a different matrix, or running >>>>>>>>> a problem >>>>>>>>> > > you >>>>>>>>> > > > care about in IBAMR. >>>>>>>>> > > > >>>>>>>>> > > > Thanks, >>>>>>>>> > > > >>>>>>>>> > > > Matt >>>>>>>>> > > > >>>>>>>>> > > > >>>>>>>>> > > > > Thanks and regards >>>>>>>>> > > > > Srinivas. >>>>>>>>> > > > > >>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>>> knepley at gmail.com> >>>>>>>>> > > wrote: >>>>>>>>> > > > > >>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 >>>>>>>>> via >>>>>>>>> > > petsc-users < >>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>>> > > > >> >>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>>> are giving me >>>>>>>>> > > to >>>>>>>>> > > > >>> sort this out. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> I tried to follow the same procedure which you followed >>>>>>>>> to build >>>>>>>>> > > Petsc >>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$./configure >>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> It appears you >>>>>>>>> do not have >>>>>>>>> > > valgrind >>>>>>>>> > > > >>> installed on your system. >>>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>>> www.valgrind.org >>>>>>>>> > > > >>> Or install >>>>>>>>> > > valgrind-devel or >>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> =============================================================================== >>>>>>>>> > > > >>> Compilers: >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> C Compiler: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > -fPIC >>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>> C++ Compiler: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>> > > > >>> Fortran Compiler: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>> 9.4.0 >>>>>>>>> > > > >>> Linkers: >>>>>>>>> > > > >>> Shared linker: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > -shared >>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>> Dynamic linker: >>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > -shared >>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>> > > > >>> make: >>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>> > > > >>> BlasLapack: >>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>>> -lpthread >>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>> -omp_num_threads >>>>>>>>> > >

to >>>>>>>>> > > > >>> control the number of threads >>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>> > > > >>> MPI: >>>>>>>>> > > > >>> Version: 3 >>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>> > > --oversubscribe >>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>> > > > >>> pthread: >>>>>>>>> > > > >>> cmake: >>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>> > > > >>> regex: >>>>>>>>> > > > >>> Matlab: >>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>> > > > >>> Library: >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>>>>>>> -lmex -lmx -lmat >>>>>>>>> > > -lut >>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>> > > > >>> PETSc: >>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>> > > > >>> Scalar type: real >>>>>>>>> > > > >>> Precision: double >>>>>>>>> > > > >>> Support for __float128 >>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries >>>>>>>>> with: >>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>>> -licui18n -licuuc as >>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$make* >>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > > > >>> | ^ >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>> socket\n"); >>>>>>>>> > > > >>> | ^ >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>> > > > >>> ========================================= >>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>> > > > >>> =============================================== >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>> > > > >>> TEST >>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > > > >>> >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>> > > > >>> >>>>>>>>> > > > >> >>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>>> defined, so it >>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>>>> yours. >>>>>>>>> > > > >> >>>>>>>>> > > > >> Thanks, >>>>>>>>> > > > >> >>>>>>>>> > > > >> Matt >>>>>>>>> > > > >> >>>>>>>>> > > > >> >>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> for trouble >>>>>>>>> > > > >>> shooting. >>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>> 2020 >>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>>> MB108SMEC028 by vit >>>>>>>>> > > Sun >>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> COPTFLAGS=-O3 >>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>>>> line 1444 in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 >>>>>>>>> in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>> -------send >>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>> MPI_COMM_SELF >>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>> MPI processes. >>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>> depending on >>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>>> no diff >>>>>>>>> > > > >>> CC >>>>>>>>> > > > >>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>> > > > >>> CLINKER >>>>>>>>> > > > >>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > > > >>> TEST >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> # Error >>>>>>>>> > > code: 124 >>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>> > > > >>> >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> for trouble >>>>>>>>> > > > >>> shooting. >>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>> 2020 >>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>> > > MB108SMEC028 by >>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> COPTFLAGS=-O3 >>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> --with-debugging=0 >>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>> > > > >>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>> -------send >>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>> MPI_COMM_SELF >>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>> MPI processes. >>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>> depending on >>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>> SKIP Command >>>>>>>>> > > > >>> failed so no diff >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> # ------------- >>>>>>>>> > > > >>> # Summary >>>>>>>>> > > > >>> # ------------- >>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>> > > > >>> # >>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>> 0.02 sec / >>>>>>>>> > > 0.02 sec >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>> > > -Wwrite-strings >>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>> -fstack-protector >>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>> matlab_ls_test.c >>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>> > > > >>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>>> -leng -lmex >>>>>>>>> > > -lmx >>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>>> > > -lmpi_mpifh >>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>> -lpthread >>>>>>>>> > > -lquadmath >>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b >>>>>>>>> version. >>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. >>>>>>>>> Please find the >>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> Thanks and regards >>>>>>>>> > > > >>> Srinivas >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> >>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>>> balay at mcs.anl.gov> >>>>>>>>> > > wrote: >>>>>>>>> > > > >>> >>>>>>>>> > > > >>>> Perhaps you can try the following to get additional >>>>>>>>> info - and debug >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> Satish >>>>>>>>> > > > >>>> ---------- >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>> > > -Wall >>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > -fstack-protector >>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>> > > > >>>> >>>>>>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>>> -lpthread -lm -leng >>>>>>>>> > > -lmex >>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>>> -ldl -lmpifort >>>>>>>>> > > -lmpi >>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>> -lstdc++ -ldl -o >>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>> ./matlab_ls_test >>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>>> number of >>>>>>>>> > > processors >>>>>>>>> > > > >>>> = 1 >>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is >>>>>>>>> NIS >>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: >>>>>>>>> compute-386-07 >>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>> 1140850689 >>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>>> with command >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>>> string: >>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab >>>>>>>>> string: >>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>> > > > >>>> 5 >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>>> works for you >>>>>>>>> > > - on >>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>>> MathWorks, Inc. >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit >>>>>>>>> (glnxa64) >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>>> [reverting >>>>>>>>> > > thread >>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>> > > corresponding >>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>>>> Ubuntu-20.04, >>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>>> > > > >>>> > main >>>>>>>>> > > > >>>> > release >>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module >>>>>>>>> load >>>>>>>>> > > matlab/R2021a >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>>> matlab >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>> ./configure >>>>>>>>> > > > >>>> >>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > Compilers: >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>> > > -Wall >>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > -fstack-protector >>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > -fstack-protector >>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>> > > -Wall >>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>> > > > >>>> > Linkers: >>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>> > > -shared -fPIC >>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>> > > > >>>> >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>> > > -shared -fPIC >>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>> -Wno-unknown-pragmas >>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>> > > > >>>> > make: >>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>> > > > >>>> > Library: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>> -omp_num_threads >>>>>>>>> > >

>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>> > > > >>>> > MPI: >>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>> > > > >>>> > Includes: >>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>> > > > >>>> > pthread: >>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>> > > > >>>> > cmake: >>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>> > > > >>>> > regex: >>>>>>>>> > > > >>>> > Matlab: >>>>>>>>> > > > >>>> > Includes: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>> > > > >>>> > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>> > > > >>>> > Library: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>> > > > >>>> > sowing: >>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>> > > > >>>> > valgrind: >>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>> > > > >>>> > PETSc: >>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>> > > > >>>> > Precision: double >>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>>>> with: >>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> xxx=========================================================================xxx >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>> function >>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>> to >>>>>>>>> > > socket\n"); >>>>>>>>> > > > >>>> > | ^ >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>> function >>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>> to >>>>>>>>> > > socket\n"); >>>>>>>>> > > > >>>> > | ^ >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>> > > > >>>> > ========================================= >>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>> > > > >>>> > ========================================= >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>> > > query=requires >>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed >>>>>>>>> so no diff >>>>>>>>> > > > >>>> > CC >>>>>>>>> > > > >>>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>> > > > >>>> > CLINKER >>>>>>>>> > > > >>>> >>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>>> > not ok >>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>> > > code: >>>>>>>>> > > > >>>> 1 >>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> # SKIP >>>>>>>>> > > Command >>>>>>>>> > > > >>>> failed so no diff >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>>>> test >>>>>>>>> > > query=requires >>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>> > > > >>>> > TEST >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>>> > ok >>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > # ------------- >>>>>>>>> > > > >>>> > # Summary >>>>>>>>> > > > >>>> > # ------------- >>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>> > > > >>>> > # >>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>>> 15.190000000000001 >>>>>>>>> > > sec >>>>>>>>> > > > >>>> > # >>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>> 6.47 sec / >>>>>>>>> > > 7.54 >>>>>>>>> > > > >>>> sec >>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>> > > > >>>> > >>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>>> tried to >>>>>>>>> > > > >>>> configure petsc >>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>>> successful. After >>>>>>>>> > > > >>>> running make >>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>>> message. >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > not ok >>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>> > > > >>>> code: 124 >>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error >>>>>>>>> Message >>>>>>>>> > > > >>>> > > >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>>> 01, 2020 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>>> named >>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> COPTFLAGS=-O3 >>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>> > > > >>>> > > --with-x=0 >>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line >>>>>>>>> 67 in >>>>>>>>> > > > >>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error >>>>>>>>> Message >>>>>>>>> > > -------send >>>>>>>>> > > > >>>> entire >>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>>> > > # >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>> MPI_COMM_SELF >>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>> > > > >>>> > > # >>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>>>>>>> all MPI >>>>>>>>> > > > >>>> processes. >>>>>>>>> > > > >>>> > > # You may or may not see output from other >>>>>>>>> processes, depending >>>>>>>>> > > on >>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>> > > > >>>> > > # >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > Thanks >>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>>>>> > > > >>>> > > >>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > > >>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>> > > > >>>> > > > >>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > > >>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>>>>> 20PHD0548 via >>>>>>>>> > > > >>>> petsc-users < >>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>>>>> > > > >>>> > > > >>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>> > > > >>>> > > >> >>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>>>>> balay at mcs.anl.gov> >>>>>>>>> > > > >>>> wrote: >>>>>>>>> > > > >>>> > > >> >>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if >>>>>>>>> hypre will work >>>>>>>>> > > > >>>> here]. >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> > > >>> ./configure >>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>> via >>>>>>>>> > > petsc-users >>>>>>>>> > > > >>>> wrote: >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>> > > > >>>> > > >>> > >>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>> > > > >>>> > > >>> > >>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>> > > > >>>> > > >>> > >>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>> > > balay at mcs.anl.gov> >>>>>>>>> > > > >>>> wrote: >>>>>>>>> > > > >>>> > > >>> > >>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work >>>>>>>>> in this mode. >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>>>>> dependency/conflicts >>>>>>>>> > > across >>>>>>>>> > > > >>>> packages] >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>>>>> petsc-users wrote: >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit >>>>>>>>> integers] conflict >>>>>>>>> > > with >>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>>>>> blas/lapack with >>>>>>>>> > > > >>>> matlab - to >>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>>>>> 20PHD0548 via >>>>>>>>> > > > >>>> petsc-users >>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>>>>> MATLAB is not >>>>>>>>> > > > >>>> working. It is >>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 >>>>>>>>> versions. >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>>>>> cluster with >>>>>>>>> > > > >>>> libmesh and >>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I >>>>>>>>> tried without >>>>>>>>> > > > >>>> linking >>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>>>>>>> configuring >>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>> > > > >>>> > > >>> that >>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>> > > > >>>> > > >>> > > > > was not found but >>>>>>>>> --enable-petsc-required is >>>>>>>>> > > specified. >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>>>>>>> libmesh with >>>>>>>>> > > > >>>> PETSc and >>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for >>>>>>>>> complicated >>>>>>>>> > > geometries >>>>>>>>> > > > >>>> it is >>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh >>>>>>>>> construct. >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>>>>>>> various >>>>>>>>> > > things >>>>>>>>> > > > >>>> and ended >>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed >>>>>>>>> further to do my >>>>>>>>> > > > >>>> research work. >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as >>>>>>>>> possible. >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet >>>>>>>>> Bhalla < >>>>>>>>> > > > >>>> mail2amneet at gmail.com> >>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>>>>>> libMesh for >>>>>>>>> > > the >>>>>>>>> > > > >>>> WEC >>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>>>>>>> builds with >>>>>>>>> > > > >>>> Matlab. >>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for >>>>>>>>> wanting to build >>>>>>>>> > > > >>>> libMesh? >>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM >>>>>>>>> INTURU SRINIVAS >>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>> > > > >>>> > > >>> > > > > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by >>>>>>>>> removing all >>>>>>>>> > > > >>>> occurrences >>>>>>>>> > > > >>>> > > >>> of >>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I >>>>>>>>> ran "make >>>>>>>>> > > test" >>>>>>>>> > > > >>>> got the >>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>> --------------------- Error >>>>>>>>> > > Message >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>>>> library >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>>> MATLAB engine >>>>>>>>> > > on >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > > > >>>> for >>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>>> Version 3.13.4, >>>>>>>>> > > Aug >>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test >>>>>>>>> on a >>>>>>>>> > > linux-debug >>>>>>>>> > > > >>>> named >>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>>>>>> --download-fblaslapack=1 >>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>>> PetscMatlabEngineCreate() >>>>>>>>> > > line >>>>>>>>> > > > >>>> 67 in >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 >>>>>>>>> in >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>>>>> entries: >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>> ----------------End of Error >>>>>>>>> > > > >>>> Message >>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>>>>> communicator >>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>>> Open MPI to >>>>>>>>> > > kill >>>>>>>>> > > > >>>> all MPI >>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>>>>> other >>>>>>>>> > > processes, >>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>>> # SKIP >>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>> --------------------- Error >>>>>>>>> > > Message >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> >>>>>>>>> -------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>>>> library >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>>> MATLAB engine >>>>>>>>> > > on >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>> > > > >>>> for >>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>>> Version 3.13.4, >>>>>>>>> > > Aug >>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test >>>>>>>>> on a >>>>>>>>> > > linux-opt >>>>>>>>> > > > >>>> named >>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>>> PetscMatlabEngineCreate() >>>>>>>>> > > line >>>>>>>>> > > > >>>> 67 in >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 >>>>>>>>> in >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table >>>>>>>>> entries: >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>> ----------------End of Error >>>>>>>>> > > > >>>> Message >>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in >>>>>>>>> communicator >>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>>> Open MPI to >>>>>>>>> > > kill >>>>>>>>> > > > >>>> all MPI >>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from >>>>>>>>> other >>>>>>>>> > > processes, >>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>> > > > >>>> # SKIP >>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc >>>>>>>>> 3.17.5 >>>>>>>>> > > version. I >>>>>>>>> > > > >>>> am >>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both >>>>>>>>> petsc 3.13.4 and >>>>>>>>> > > > >>>> petsc >>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM >>>>>>>>> Satish Balay < >>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>>>>>>> petsc's >>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>> > > -leng >>>>>>>>> > > > >>>> -lmex >>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) >>>>>>>>> - we are >>>>>>>>> > > seeing: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n >>>>>>>>> -licuuc" are not >>>>>>>>> > > > >>>> preset here. >>>>>>>>> > > > >>>> > > >>> This >>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab >>>>>>>>> versions. >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>>>>>> -licudata >>>>>>>>> > > -licui18n >>>>>>>>> > > > >>>> -licuuc" >>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU >>>>>>>>> SRINIVAS 20PHD0548 >>>>>>>>> > > via >>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>>>>>>> building >>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building >>>>>>>>> libmesh with >>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>>> > > successfully. >>>>>>>>> > > > >>>> But >>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>>>>>> Satish Balay < >>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log >>>>>>>>> from both >>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the >>>>>>>>> logs >>>>>>>>> > > friendly to >>>>>>>>> > > > >>>> mailing >>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with >>>>>>>>> 3.17? [or >>>>>>>>> > > 3.19?] >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU >>>>>>>>> SRINIVAS >>>>>>>>> > > 20PHD0548 >>>>>>>>> > > > >>>> via >>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log >>>>>>>>> file while >>>>>>>>> > > building >>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment >>>>>>>>> and do the >>>>>>>>> > > needful. >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at >>>>>>>>> 10:19?AM INTURU >>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>>>>>> > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. >>>>>>>>> During >>>>>>>>> > > building >>>>>>>>> > > > >>>> of >>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at >>>>>>>>> 9:43?PM Satish >>>>>>>>> > > > >>>> Balay < >>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> https://ibamr.github.io/linux says >>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>>>>>> petsc-3.17.5? >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, >>>>>>>>> INTURU SRINIVAS >>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc >>>>>>>>> with MATLAB for >>>>>>>>> > > > >>>> working on >>>>>>>>> > > > >>>> > > >>> the >>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>>>>>> building the >>>>>>>>> > > PETSc, >>>>>>>>> > > > >>>> using the >>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export >>>>>>>>> PETSC_ARCH=linux-debug >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> --download-fblaslapack=1 \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>>> `EvaluateResidual': >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>>> `EvaluateJacobian': >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> > > >>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld >>>>>>>>> returned 1 exit >>>>>>>>> > > > >>>> status >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>>>>>> [gmakefile.test:185: >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> >>>>>>>>> > > > >>>> >>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>>>>>> unfinished >>>>>>>>> > > jobs.... >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve >>>>>>>>> this issue >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent >>>>>>>>> from Vellore >>>>>>>>> > > > >>>> Institute of >>>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may >>>>>>>>> contain legally >>>>>>>>> > > > >>>> protected >>>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>>>>>> Institute of >>>>>>>>> > > > >>>> 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URL: From bsmith at petsc.dev Fri Sep 8 13:28:46 2023 From: bsmith at petsc.dev (Barry Smith) Date: Fri, 8 Sep 2023 14:28:46 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> Message-ID: <58283126-56CF-4741-B264-3C7E68AA3655@petsc.dev> I expect a libmx.so in the directory /usr/local/MATLAB/R2020b/extern/bin/glnxa64. Do an ls on that directory and send all the output > On Sep 8, 2023, at 10:33 AM, INTURU SRINIVAS 20PHD0548 wrote: > > Hi Barry, > > I tried to run Matlab Engine C example provided in the link "https://in.mathworks.com/help/matlab/matlab_external/build-unix-engine-example.html" > in Matlab: copyfile(fullfile(matlabroot,'extern','examples','eng_mat','engdemo.c'),'.','f') > mex -v -client engine engdemo.c > in linux terminal : LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > export LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH > > ./engdemo > ./engdemo: error while loading shared libraries: libmx.so: cannot open shared object file: No such file or directory > > how to sort out this error? Is this the right way to check MatlabEngine with C? > > Thanks and regards > Srinivas > > > On Wed, Sep 6, 2023 at 11:47?PM Barry Smith > wrote: >> >> Ok, so the C++ binding for Matlab engine is working on your machine. PETSc uses the C binding which links against different libraries but, one would think the C binding would work for sure if the C++ binding works. Can you try a Matlab Engine C example provided by Matlab? >> >> >> >> >>> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 > wrote: >>> >>> Hi Amneet, >>> >>> I repeated the same procedure again and this time it is working. >>> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp -lMatlabDataArray -lMatlabEngine >>> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> $export LD_LIBRARY_PATH >>> $./a.out >>> Square root of -2 is 0 + 1.41421i >>> Square root of 2 is 1.41421 + 0i >>> Square root of 6 is 2.44949 + 0i >>> Square root of 8 is 2.82843 + 0i >>> I don't know how it is working this time? >>> >>> Thanks and regards >>> Srinivas >>> >>> >>> On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 > wrote: >>>> Hi Amneet, >>>> I tried the following example to run a matlab engine. >>>> >>>> #include "MatlabDataArray.hpp" >>>> #include "MatlabEngine.hpp" >>>> #include >>>> void callSQRT() { >>>> >>>> using namespace matlab::engine; >>>> >>>> // Start MATLAB engine synchronously >>>> std::unique_ptr matlabPtr = startMATLAB(); >>>> >>>> //Create MATLAB data array factory >>>> matlab::data::ArrayFactory factory; >>>> >>>> // Define a four-element typed array >>>> matlab::data::TypedArray const argArray = >>>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >>>> >>>> // Call MATLAB sqrt function on the data array >>>> matlab::data::Array const results = matlabPtr->feval(u"sqrt", argArray); >>>> >>>> // Display results >>>> for (int i = 0; i < results.getNumberOfElements(); i++) { >>>> double a = argArray[i]; >>>> std::complex v = results[i]; >>>> double realPart = v.real(); >>>> double imgPart = v.imag(); >>>> std::cout << "Square root of " << a << " is " << >>>> realPart << " + " << imgPart << "i" << std::endl; >>>> } >>>> } >>>> >>>> int main() { >>>> callSQRT(); >>>> return 0; >>>> } >>>> >>>> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>> $export LD_LIBRARY_PATH >>>> $./a.out >>>> Starting >>>> Error: The import statement 'import matlab.internal.engine.input' cannot be found or cannot be imported. Imported names must end with '.*' or be fully qualified. >>>> >>>> terminate called after throwing an instance of 'matlab::engine::EngineException' >>>> what(): MATLAB process cannot be created. >>>> Aborted (core dumped) >>>> >>>> I got the above error for Matlab R2020b. Please help me to sort out this. >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: >>>>> BTW, what Barry is suggesting is the following: >>>>> >>>>> Compile a sample code with a command line this: >>>>> >>>>> g++ -std=c++11 -I matlabroot/extern/include/ -L matlabroot/extern/bin/glnxa64/ >>>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>>> >>>>> This command is provided here: >>>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>>>> >>>>> A sample MATLAB code is here: >>>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>>>> >>>>> (You can just pick a few lines of code from here to create a barebone example) >>>>> >>>>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: >>>>>> Srinivas --- Do you have a different version of MATLAB that you can install? If your organization has a MATLAB license, you can install recent versions of MATLAB from mathworks.com >>>>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > wrote: >>>>>>> >>>>>>> Ok, I have no suggestions. It seems to be more an issue with the Matlab than PETSc. You could find a pure Matlab example of using the engine (in the Matlab documentation) and try it to see if it works. >>>>>>> >>>>>>> Barry >>>>>>> >>>>>>> >>>>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 > wrote: >>>>>>>> >>>>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>>>> I got the same errors for petsc 3.17.5 >>>>>>>> >>>>>>>> make all >>>>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> ========================================= >>>>>>>> ========================================= >>>>>>>> Now to check if the libraries are working do: >>>>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>>> >>>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 >>>>>>>> # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> # -------------------------------------------------------------------------- >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>> # with errorcode 85. >>>>>>>> # >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>> # exactly when Open MPI kills them. >>>>>>>> # -------------------------------------------------------------------------- >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>> >>>>>>>> >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> # >>>>>>>> # To rerun failed tests: >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: >>>>>>>>> >>>>>>>>> The error is occuring during >>>>>>>>> >>>>>>>>> e->ep = engOpen(buffer); >>>>>>>>> >>>>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. >>>>>>>>> >>>>>>>>> You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>>>> >>>>>>>>> e->ep = engOpen(buffer); >>>>>>>>> >>>>>>>>> replace it with >>>>>>>>> >>>>>>>>> e->ep = engOpen(""); >>>>>>>>> >>>>>>>>> Now in the PETSc directory do make all (it should recompile one file) and then run the >>>>>>>>> >>>>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>> >>>>>>>>> again >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>>>> >>>>>>>>>> Hi Amneeth, >>>>>>>>>> >>>>>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>>>>> >>>>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>>>> The version of PETSc you are using is out-of-date, we recommend updating to the new release >>>>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>>>>> https://petsc.org/release/download/ >>>>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>>>> ============================================================================================= >>>>>>>>>> Configuring PETSc to compile on your system >>>>>>>>>> ============================================================================================= >>>>>>>>>> Compilers: >>>>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> Linkers: >>>>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>> BlasLapack: >>>>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads >>>>>>>>>> uses 8 byte integers >>>>>>>>>> MPI: >>>>>>>>>> Version: 3 >>>>>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>>>>> Implementation: openmpi >>>>>>>>>> OMPI_VERSION: 4.0.3 >>>>>>>>>> pthread: >>>>>>>>>> cmake: >>>>>>>>>> Version: 3.16.3 >>>>>>>>>> /usr/bin/cmake >>>>>>>>>> regex: >>>>>>>>>> Matlab: >>>>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> /usr/local/MATLAB/R2020b >>>>>>>>>> MatlabEngine: >>>>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>>>>> Language used to compile PETSc: C >>>>>>>>>> PETSc: >>>>>>>>>> PETSC_ARCH: linux-opt >>>>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>>>> Prefix: >>>>>>>>>> Scalar type: real >>>>>>>>>> Precision: double >>>>>>>>>> Support for __float128 >>>>>>>>>> Integer size: 4 bytes >>>>>>>>>> Single library: yes >>>>>>>>>> Shared libraries: yes >>>>>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>>>>> Using GNU make: /usr/bin/make >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> >>>>>>>>>> $make >>>>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>> | ^ >>>>>>>>>> >>>>>>>>>> MEX completed successfully. >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> MEX completed successfully. >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> MEX completed successfully. >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>> | ^ >>>>>>>>>> >>>>>>>>>> MEX completed successfully. >>>>>>>>>> ========================================= >>>>>>>>>> ========================================= >>>>>>>>>> Now to check if the libraries are working do: >>>>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>>>>> >>>>>>>>>> $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests >>>>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 >>>>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> # -------------------------------------------------------------------------- >>>>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>> # with errorcode 85. >>>>>>>>>> # >>>>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>>>> # exactly when Open MPI kills them. >>>>>>>>>> # -------------------------------------------------------------------------- >>>>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>> # >>>>>>>>>> # To rerun failed tests: >>>>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>> >>>>>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>>>>> >>>>>>>>>> How to check error info and proceed further? >>>>>>>>>> >>>>>>>>>> Thanks and regards >>>>>>>>>> Srinivas >>>>>>>>>> >>>>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: >>>>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? >>>>>>>>>>> >>>>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>>>>>> Sorry for missing that. >>>>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>> >>>>>>>>>>>> < M A T L A B (R) > >>>>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>>>>> November 23, 2020 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> To get started, type doc. >>>>>>>>>>>> For product information, visit www.mathworks.com . >>>>>>>>>>>> >>>>>>>>>>>> Thanks and regards >>>>>>>>>>>> Srinivas >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: >>>>>>>>>>>>> You are missing one more step: >>>>>>>>>>>>> >>>>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>> >>>>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>>>>> >>>>>>>>>>>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>>>>> >>>>>>>>>>>>> Satish >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> > Hi Sathish, >>>>>>>>>>>>> > >>>>>>>>>>>>> > I tried the following procedure >>>>>>>>>>>>> > >>>>>>>>>>>>> > *$make * >>>>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>> > | ^ >>>>>>>>>>>>> > >>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>> > | ^ >>>>>>>>>>>>> > >>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>> > ========================================= >>>>>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>>>> > >>>>>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>>>>>>>>>> > query=requires >>>>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>>>> > ------------------------------------------------------------------------ >>>>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>>>>>>>>>>> > probably memory access out of range >>>>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>>>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS >>>>>>>>>>>>> > X to find memory corruption errors >>>>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, >>>>>>>>>>>>> > and run >>>>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>>>>> > # >>>>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>>> > CC >>>>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>>>> > CLINKER >>>>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>> > TEST >>>>>>>>>>>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>>>>>>>>>>>> > # Running problem 5 >>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>>>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>> > # with errorcode 126076. >>>>>>>>>>>>> > # >>>>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed >>>>>>>>>>>>> > so no diff >>>>>>>>>>>>> > >>>>>>>>>>>>> > # ------------- >>>>>>>>>>>>> > # Summary >>>>>>>>>>>>> > # ------------- >>>>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>>>>> > # >>>>>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>>>>> > # >>>>>>>>>>>>> > # To rerun failed tests: >>>>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>>>> > # >>>>>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec >>>>>>>>>>>>> > >>>>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>>>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>>>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>>>> > >>>>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 >>>>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>>>> > Running problem 5 >>>>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > -------------------------------------------------------------------------- >>>>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>> > with errorcode 126076. >>>>>>>>>>>>> > >>>>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>>>>> > >>>>>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>>>>> > >>>>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: >>>>>>>>>>>>> > >>>>>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>>>>> > > >>>>>>>>>>>>> > > cd $HOME >>>>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>>>>> > > >>>>>>>>>>>> > > manually with make> >>>>>>>>>>>>> > > >>>>>>>>>>>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles >>>>>>>>>>>>> > > >>>>>>>>>>>>> > > Satish >>>>>>>>>>>>> > > >>>>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>>>>> > > >>>>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have >>>>>>>>>>>>> > > any >>>>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please help me how to >>>>>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we point to >>>>>>>>>>>>> > > this >>>>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those >>>>>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>>>>> > > > is why I suggested just using a different matrix, or running a problem >>>>>>>>>>>>> > > you >>>>>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > Thanks, >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > Matt >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > > Thanks and regards >>>>>>>>>>>>> > > > > Srinivas. >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > >>>>>>>>>>>>> > > wrote: >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>> > > petsc-users < >>>>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you are giving me >>>>>>>>>>>>> > > to >>>>>>>>>>>>> > > > >>> sort this out. >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed to build >>>>>>>>>>>>> > > Petsc >>>>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>> > > > >>> It appears you do not have >>>>>>>>>>>>> > > valgrind >>>>>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>>>>>>>>> > > > >>> Or install >>>>>>>>>>>>> > > valgrind-devel or >>>>>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>> > > > >>> Compilers: >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>> > > -fPIC >>>>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>> > > > >>> Linkers: >>>>>>>>>>>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>> > > -shared >>>>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>> > > -shared >>>>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>>>> > > > >>> make: >>>>>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>>>> > >

to >>>>>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>>>>> > > > >>> MPI: >>>>>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>>>>> > > --oversubscribe >>>>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>>>>> > > > >>> pthread: >>>>>>>>>>>>> > > > >>> cmake: >>>>>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>>>>> > > > >>> regex: >>>>>>>>>>>>> > > > >>> Matlab: >>>>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>>>>> > > > >>> Library: >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>>>>>>>> > > -lut >>>>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>>>>> > > > >>> PETSc: >>>>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>>>>> > > > >>> Precision: double >>>>>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>>>>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> *$make* >>>>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>> > > > >>> ========================================= >>>>>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>>>> > > > >>> =============================================== >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it >>>>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> Thanks, >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> Matt >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>>>> > > Sun >>>>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>>> > > > >>> CC >>>>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>>>> > > > >>> CLINKER >>>>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>> > > > >>> TEST >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>>>> > > code: 124 >>>>>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>>>> > > > >>> # Summary >>>>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / >>>>>>>>>>>>> > > 0.02 sec >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>>>> > > -Wwrite-strings >>>>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>>>>>>>> > > -lmx >>>>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>>>>>>> > > -lquadmath >>>>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please find the >>>>>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>>>>> > > > >>> Srinivas >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > >>>>>>>>>>>>> > > wrote: >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional info - and debug >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> Satish >>>>>>>>>>>>> > > > >>>> ---------- >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>>>> > > -Wall >>>>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > -fstack-protector >>>>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng >>>>>>>>>>>>> > > -lmex >>>>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort >>>>>>>>>>>>> > > -lmpi >>>>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>>>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>>>>> > > processors >>>>>>>>>>>>> > > > >>>> = 1 >>>>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>>>> > > > >>>> 5 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you >>>>>>>>>>>>> > > - on >>>>>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com . >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>>>>>>>>>>>> > > thread >>>>>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>>>>>> > > corresponding >>>>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>>>>>>> > > > >>>> > main >>>>>>>>>>>>> > > > >>>> > release >>>>>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>>>>>>>> > > matlab/R2021a >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>>>>>>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>>>> > > -Wall >>>>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > -fstack-protector >>>>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > -fstack-protector >>>>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>>>>> > > -Wall >>>>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>>>> > > > >>>> > make: >>>>>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>>>> > >

>>>>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>>>>> > > > >>>> > regex: >>>>>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>>>> > > socket\n"); >>>>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>>>> > > socket\n"); >>>>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>>>>>> > > query=requires >>>>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>>>> > > code: >>>>>>>>>>>>> > > > >>>> 1 >>>>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>>>> > > Command >>>>>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>>>>>>>>> > > query=requires >>>>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>>>>> > > > >>>> > # >>>>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 >>>>>>>>>>>>> > > sec >>>>>>>>>>>>> > > > >>>> > # >>>>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>>>>> > > 7.54 >>>>>>>>>>>>> > > > >>>> sec >>>>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>>>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>>>>>>>>>>> > > > >>>> running make >>>>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error message. >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>> > > > >>>> > > -------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>>>> > > -------send >>>>>>>>>>>>> > > > >>>> entire >>>>>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>>>> > > > >>>> processes. >>>>>>>>>>>>> > > > >>>> > > # You may or may not see output from other processes, depending >>>>>>>>>>>>> > > on >>>>>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > Thanks >>>>>>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > wrote: >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>> > > > >>>> petsc-users < >>>>>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>>>>>>>>>>> > > > >>>> here]. >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>> > > petsc-users >>>>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>>>>>> > > balay at mcs.anl.gov > >>>>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts >>>>>>>>>>>>> > > across >>>>>>>>>>>>> > > > >>>> packages] >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict >>>>>>>>>>>>> > > with >>>>>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>>>>>>>>>>> > > > >>>> matlab - to >>>>>>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>> > > > >>>> petsc-users >>>>>>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>>>>>>>>>>> > > > >>>> working. It is >>>>>>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>>>>>>>>>>> > > > >>>> libmesh and >>>>>>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>>>>>>>>>>> > > > >>>> linking >>>>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>>>>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>>>>>> > > > >>>> > > >>> that >>>>>>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>>>>>>>>>>> > > specified. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>>>>>>>>>>> > > > >>>> PETSc and >>>>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>>>>>>>>>>> > > geometries >>>>>>>>>>>>> > > > >>>> it is >>>>>>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>>>>>>>>>>>> > > things >>>>>>>>>>>>> > > > >>>> and ended >>>>>>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>>>>>>>>>>> > > > >>>> research work. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > >>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for >>>>>>>>>>>>> > > the >>>>>>>>>>>>> > > > >>>> WEC >>>>>>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>>>>>>>>>>> > > > >>>> Matlab. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>>>>>>>>>>> > > > >>>> libMesh? >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>>>>>>>>>>> > > > >>>> occurrences >>>>>>>>>>>>> > > > >>>> > > >>> of >>>>>>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make >>>>>>>>>>>>> > > test" >>>>>>>>>>>>> > > > >>>> got the >>>>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>>>> > > Message >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>>>> > > on >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > > > >>>> for >>>>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>>>> > > Aug >>>>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>>>> > > linux-debug >>>>>>>>>>>>> > > > >>>> named >>>>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>>>>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>>>> > > line >>>>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>>>> > > > >>>> Message >>>>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>>>> > > kill >>>>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>>>> > > processes, >>>>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>>>> > > Message >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>>>> > > on >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>> > > > >>>> for >>>>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>>>> > > Aug >>>>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>>>> > > linux-opt >>>>>>>>>>>>> > > > >>>> named >>>>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>>>> > > line >>>>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>>>> > > > >>>> Message >>>>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>>>> > > kill >>>>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>>>> > > processes, >>>>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>>>>>>>>>>> > > version. I >>>>>>>>>>>>> > > > >>>> am >>>>>>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>>>>>>>>>>> > > > >>>> petsc >>>>>>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>>>>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>> > > -leng >>>>>>>>>>>>> > > > >>>> -lmex >>>>>>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are >>>>>>>>>>>>> > > seeing: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>>>>>>>>>>> > > > >>>> preset here. >>>>>>>>>>>>> > > > >>>> > > >>> This >>>>>>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>>>>>>>>>>> > > -licui18n >>>>>>>>>>>>> > > > >>>> -licuuc" >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>>>>>> > > via >>>>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>>>>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>>>>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>>>>>>> > > successfully. >>>>>>>>>>>>> > > > >>>> But >>>>>>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>>>>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>>>>>>>>>> > > friendly to >>>>>>>>>>>>> > > > >>>> mailing >>>>>>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or >>>>>>>>>>>>> > > 3.19?] >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>>>>>>>>> > > 20PHD0548 >>>>>>>>>>>>> > > > >>>> via >>>>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>>>>>>>>>>>> > > building >>>>>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the >>>>>>>>>>>>> > > needful. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>>>>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > >>>>>>>>>>>>> > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>>>>>>>>>>> > > building >>>>>>>>>>>>> > > > >>>> of >>>>>>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>>>>>>>>>>> > > > >>>> Balay < >>>>>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>>>>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>>>>>>>>>>> > > > >>>> working on >>>>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the >>>>>>>>>>>>> > > PETSc, >>>>>>>>>>>>> > > > >>>> using the >>>>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>>>>>>>>>>> > > > >>>> status >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished >>>>>>>>>>>>> > > jobs.... >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore >>>>>>>>>>>>> > > > >>>> Institute of >>>>>>>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain legally >>>>>>>>>>>>> > > > >>>> protected >>>>>>>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore Institute of >>>>>>>>>>>>> > > > >>>> Technology?. >>>>>>>>>>>>> > > > >>>> > > >>> If >>>>>>>>>>>>> > > > >>>> > > >>> > > you are >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should not >>>>>>>>>>>>> > > > >>>> disseminate, >>>>>>>>>>>>> > > > >>>> > > >>> distribute >>>>>>>>>>>>> > > > >>>> > > >>> > > or copy >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately >>>>>>>>>>>>> > > > >>>> and destroy >>>>>>>>>>>>> > > > >>>> > > >>> all >>>>>>>>>>>>> > > > >>>> > > >>> > > copies of >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you have >>>>>>>>>>>>> > > > >>>> received this >>>>>>>>>>>>> > > > >>>> > > >>> email >>>>>>>>>>>>> > > > >>>> > > >>> > > in error, >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by reply email >>>>>>>>>>>>> > > and >>>>>>>>>>>>> > > > >>>> delete >>>>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>>>> > > > >>>> > > >>> > > original >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without reading >>>>>>>>>>>>> > > them.* >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>>>>> > > > >>>> Technology. >>>>>>>>>>>>> > > > >>>> > > >> The contents of this email may contain legally protected >>>>>>>>>>>>> > > > >>>> confidential or >>>>>>>>>>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>>>>>>>>>> > > Technology?. If >>>>>>>>>>>>> > > > >>>> you are >>>>>>>>>>>>> > > > >>>> > > >> not the intended recipient, you should not disseminate, >>>>>>>>>>>>> > > > >>>> distribute or copy >>>>>>>>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately and destroy >>>>>>>>>>>>> > > > >>>> all copies of >>>>>>>>>>>>> > > > >>>> > > >> this message and any attachments. If you have received this >>>>>>>>>>>>> > > > >>>> email in error, >>>>>>>>>>>>> > > > >>>> > > >> please promptly notify the sender by reply email and delete >>>>>>>>>>>>> > > the >>>>>>>>>>>>> > > > >>>> original >>>>>>>>>>>>> > > > >>>> > > >> email and any backup copies without reading them.* >>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > -- >>>>>>>>>>>>> > > > >>>> > > > --Amneet >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>>>>> > > Technology. >>>>>>>>>>>>> > > > >>> The contents of this email may contain legally protected >>>>>>>>>>>>> > > confidential or >>>>>>>>>>>>> > > > >>> privileged information of ?Vellore Institute of Technology?. If you >>>>>>>>>>>>> > > are >>>>>>>>>>>>> > > > >>> not the intended recipient, you should not disseminate, distribute >>>>>>>>>>>>> > > or copy >>>>>>>>>>>>> > > > >>> this e-mail. Please notify the sender immediately and destroy all >>>>>>>>>>>>> > > copies of >>>>>>>>>>>>> > > > >>> this message and any attachments. If you have received this email in >>>>>>>>>>>>> > > error, >>>>>>>>>>>>> > > > >>> please promptly notify the sender by reply email and delete the >>>>>>>>>>>>> > > original >>>>>>>>>>>>> > > > >>> email and any backup copies without reading them.* >>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> -- >>>>>>>>>>>>> > > > >> What most experimenters take for granted before they begin their >>>>>>>>>>>>> > > > >> experiments is infinitely more interesting than any results to which >>>>>>>>>>>>> > > their >>>>>>>>>>>>> > > > >> experiments lead. >>>>>>>>>>>>> > > > >> -- Norbert Wiener >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> https://www.cse.buffalo.edu/~knepley/ >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > >> >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > > *Disclaimer:This message was sent from Vellore Institute of Technology. >>>>>>>>>>>>> > > > > The contents of this email may contain legally protected confidential >>>>>>>>>>>>> > > or >>>>>>>>>>>>> > > > > privileged information of ?Vellore Institute of Technology?. If you >>>>>>>>>>>>> > > are >>>>>>>>>>>>> > > > > not the intended recipient, you should not disseminate, distribute or >>>>>>>>>>>>> > > copy >>>>>>>>>>>>> > > > > this e-mail. Please notify the sender immediately and destroy all >>>>>>>>>>>>> > > copies of >>>>>>>>>>>>> > > > > this message and any attachments. If you have received this email in >>>>>>>>>>>>> > > error, >>>>>>>>>>>>> > > > > please promptly notify the sender by reply email and delete the >>>>>>>>>>>>> > > original >>>>>>>>>>>>> > > > > email and any backup copies without reading them.* >>>>>>>>>>>>> > > > > >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > > >>>>>>>>>>>>> > > >>>>>>>>>>>>> > >>>>>>>>>>>>> > >>>>>>>>>>>> >>>>>>>>>>>> Disclaimer: >>>>>>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> --Amneet >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Disclaimer: >>>>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>>>>>> >>>>>>>> >>>>>>>> Disclaimer: >>>>>>>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> --Amneet >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> -- >>>>> --Amneet >>>>> >>>>> >>>>> >>> >>> Disclaimer: >>> This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >> > > Disclaimer: > This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris at resfrac.com Fri Sep 8 15:52:54 2023 From: chris at resfrac.com (Chris Hewson) Date: Fri, 8 Sep 2023 14:52:54 -0600 Subject: [petsc-users] Slower performance using more MPI processes Message-ID: Hi There, I am trying to solve a linear problem and am having an issue when I use more MPI processes with the KSPsolve slowing down considerably the more processes I add. The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I am using petsc version 3.19.5 and have tried with a couple different versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and v3.3.2 w/ ch3:sock). In testing, I've noticed the following trend for speed for the KSPSolve function call: 1 core: 4042 ms 2 core: 7085 ms 4 core: 26573 ms 8 core: 65745 ms 16 core: 149283 ms This was all done on a single node machine w/ 16 non-hyperthreaded cores. We solve quite a few different matrices with PETSc using MPI and haven't noticed an impact like this on performance before. I am very confused by this and am a little stumped at the moment as to why this was happening. I've been using the KSPBCGS solver to solve the problem. I have tried with multiple different solvers and pre-conditioners (we usually don't use a pre-conditioner for this part of our code). It did seem that using the piped BCGS solver did help improve the parallel speed slightly (maybe 15%), but it still doesn't come close to the single threaded speed. I'll attach a link to a folder that contains the specific A, x and b matrices for this problem, as well as a main.cpp file that I was using for testing. https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing I was testing this in our main code base, but don't include that here, and observe very similar speed results to the ones above. We do use Metis to graph partition in our own code and checked the vector and matrix partitioning and that all made sense. I could be doing the partitioning incorrectly in the example (not 100% sure how it works with the viewer/load functions). Any insight or thoughts on this would be greatly appreciated. Thanks, *Chris Hewson* Senior Reservoir Simulation Engineer ResFrac +1.587.575.9792 -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Fri Sep 8 15:59:31 2023 From: knepley at gmail.com (Matthew Knepley) Date: Fri, 8 Sep 2023 16:59:31 -0400 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: On Fri, Sep 8, 2023 at 4:53?PM Chris Hewson wrote: > Hi There, > > I am trying to solve a linear problem and am having an issue when I use > more MPI processes with the KSPsolve slowing down considerably the more > processes I add. > > The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I > am using petsc version 3.19.5 and have tried with a couple different > versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and > v3.3.2 w/ ch3:sock). > > In testing, I've noticed the following trend for speed for the KSPSolve > function call: > 1 core: 4042 ms > 2 core: 7085 ms > 4 core: 26573 ms > 8 core: 65745 ms > 16 core: 149283 ms > > This was all done on a single node machine w/ 16 non-hyperthreaded cores. > We solve quite a few different matrices with PETSc using MPI and haven't > noticed an impact like this on performance before. > > I am very confused by this and am a little stumped at the moment as to why > this was happening. I've been using the KSPBCGS solver to solve the > problem. I have tried with multiple different solvers and pre-conditioners > (we usually don't use a pre-conditioner for this part of our code). > > It did seem that using the piped BCGS solver did help improve the parallel > speed slightly (maybe 15%), but it still doesn't come close to the single > threaded speed. > > I'll attach a link to a folder that contains the specific A, x and b > matrices for this problem, as well as a main.cpp file that I was using for > testing. > > > https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing > > I was testing this in our main code base, but don't include that here, and > observe very similar speed results to the ones above. We do use Metis to > graph partition in our own code and checked the vector and matrix > partitioning and that all made sense. I could be doing the partitioning > incorrectly in the example (not 100% sure how it works with the viewer/load > functions). > > Any insight or thoughts on this would be greatly appreciated. > Send the output of -log_view for each case. These are all memory bandwidth-limited operations. When you exhaust the bandwidth you should see the performance stagnate, not steeply decay as you do here. Something definitely seems wrong. The first step is sending us the logs. Thanks, Matt > Thanks, > > *Chris Hewson* > Senior Reservoir Simulation Engineer > ResFrac > +1.587.575.9792 > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Fri Sep 8 16:00:07 2023 From: bsmith at petsc.dev (Barry Smith) Date: Fri, 8 Sep 2023 17:00:07 -0400 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: It would be very helpful if you could run on 1 and 2 ranks with -log_view and send all the output. > On Sep 8, 2023, at 4:52 PM, Chris Hewson wrote: > > Hi There, > > I am trying to solve a linear problem and am having an issue when I use more MPI processes with the KSPsolve slowing down considerably the more processes I add. > > The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I am using petsc version 3.19.5 and have tried with a couple different versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and v3.3.2 w/ ch3:sock). > > In testing, I've noticed the following trend for speed for the KSPSolve function call: > 1 core: 4042 ms > 2 core: 7085 ms > 4 core: 26573 ms > 8 core: 65745 ms > 16 core: 149283 ms > > This was all done on a single node machine w/ 16 non-hyperthreaded cores. We solve quite a few different matrices with PETSc using MPI and haven't noticed an impact like this on performance before. > > I am very confused by this and am a little stumped at the moment as to why this was happening. I've been using the KSPBCGS solver to solve the problem. I have tried with multiple different solvers and pre-conditioners (we usually don't use a pre-conditioner for this part of our code). > > It did seem that using the piped BCGS solver did help improve the parallel speed slightly (maybe 15%), but it still doesn't come close to the single threaded speed. > > I'll attach a link to a folder that contains the specific A, x and b matrices for this problem, as well as a main.cpp file that I was using for testing. > > https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing > > I was testing this in our main code base, but don't include that here, and observe very similar speed results to the ones above. We do use Metis to graph partition in our own code and checked the vector and matrix partitioning and that all made sense. I could be doing the partitioning incorrectly in the example (not 100% sure how it works with the viewer/load functions). > > Any insight or thoughts on this would be greatly appreciated. > > Thanks, > > Chris Hewson > Senior Reservoir Simulation Engineer > ResFrac > +1.587.575.9792 -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris at resfrac.com Fri Sep 8 16:22:29 2023 From: chris at resfrac.com (Chris Hewson) Date: Fri, 8 Sep 2023 15:22:29 -0600 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: Thanks for the quick response. The links to the log view files are below: 2 ranks: https://drive.google.com/file/d/1PGRsiHypWtN5h3uxdJBKy9WzEkE0mUgO/view?usp=drive_link 1 rank: https://drive.google.com/file/d/1hB2XyoNtLMHseZUT7jCuiixTQeBi_tjJ/view?usp=drive_link I'll also attach them to this email: **************************** 1 RANK ****************************** ------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------ ./petsc-testing on a named ubuntu-office with 1 processor, by chewson Fri Sep 8 15:16:51 2023 Using Petsc Release Version 3.19.5, unknown Max Max/Min Avg Total Time (sec): 2.746e+00 1.000 2.746e+00 Objects: 2.100e+01 1.000 2.100e+01 Flops: 4.117e+09 1.000 4.117e+09 4.117e+09 Flops/sec: 1.499e+09 1.000 1.499e+09 1.499e+09 MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00 MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00 MPI Reductions: 0.000e+00 0.000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total Count %Total Avg %Total Count %Total 0: Main Stage: 2.7458e+00 100.0% 4.1167e+09 100.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flop: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent AvgLen: average message length (bytes) Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %F - percent flop in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ Event Count Time (sec) Flop --- Global --- --- Stage ---- Total Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage MatMult 182 1.0 8.0351e-01 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 29 35 0 0 0 29 35 0 0 0 1775 MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 MatLUFactorNum 1 1.0 1.3892e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 934 MatILUFactorSym 1 1.0 2.1567e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 MatAssemblyBegin 1 1.0 1.0420e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyEnd 1 1.0 6.9049e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatGetRowIJ 1 1.0 3.8500e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatGetOrdering 1 1.0 1.7026e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatLoad 1 1.0 6.6749e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 VecCopy 2 1.0 6.8473e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 3 1.0 1.3256e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecAXPBYCZ 182 1.0 1.6542e-01 1.0 4.51e+08 1.0 0.0e+00 0.0e+00 0.0e+00 6 11 0 0 0 6 11 0 0 0 2729 VecWAXPY 182 1.0 1.4476e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 5 5 0 0 0 5 5 0 0 0 1559 VecLoad 2 1.0 1.0104e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSetUp 1 1.0 9.9204e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 1 1.0 2.6210e+00 1.0 4.10e+09 1.0 0.0e+00 0.0e+00 0.0e+00 95 100 0 0 0 95 100 0 0 0 1566 PCSetUp 1 1.0 3.7232e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 349 PCApply 183 1.0 1.0885e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 --- Event Stage 1: Unknown ------------------------------------------------------------------------------------------------------------------------ Object Type Creations Destructions. Reports information only for process 0. --- Event Stage 0: Main Stage Viewer 4 1 Matrix 3 1 Vector 9 1 Krylov Solver 1 0 Preconditioner 1 0 Index Set 3 0 --- Event Stage 1: Unknown ======================================================================================================================== Average time to get PetscTime(): 1.51e-08 #PETSc Option Table entries: -log_view # (source: command line) #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 --download-mumps --download-scalapack --with-mpi=1 --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 ----------------------------------------- Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 Using PETSc directory: /opt/anl/petsc-3.19.5 Using PETSc arch: ----------------------------------------- Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -O2 Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O2 ----------------------------------------- Using include paths: -I/opt/anl/petsc-3.19.5/include -I/opt/anl/mpich/include ----------------------------------------- Using C linker: /opt/anl/mpich/bin/mpicc Using Fortran linker: /opt/anl/mpich/bin/mpif90 Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath ----------------------------------------- ************************* 2 RANKS ************************************ ------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------ ./petsc-testing on a named ubuntu-office with 2 processors, by chewson Fri Sep 8 15:16:43 2023 Using Petsc Release Version 3.19.5, unknown Max Max/Min Avg Total Time (sec): 6.167e+00 1.001 6.164e+00 Objects: 3.200e+01 1.000 3.200e+01 Flops: 2.233e+09 1.000 2.233e+09 4.467e+09 Flops/sec: 3.625e+08 1.001 3.623e+08 7.247e+08 MPI Msg Count: 2.050e+02 1.000 2.050e+02 4.100e+02 MPI Msg Len (bytes): 3.437e+07 1.000 1.676e+05 6.874e+07 MPI Reductions: 4.580e+02 1.000 Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) e.g., VecAXPY() for real vectors of length N --> 2N flops and VecAXPY() for complex vectors of length N --> 8N flops Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions -- Avg %Total Avg %Total Count %Total Avg %Total Count %Total 0: Main Stage: 6.1642e+00 100.0% 4.4670e+09 100.0% 4.100e+02 100.0% 1.676e+05 100.0% 4.400e+02 96.1% ------------------------------------------------------------------------------------------------------------------------ See the 'Profiling' chapter of the users' manual for details on interpreting output. Phase summary info: Count: number of times phase was executed Time and Flop: Max - maximum over all processors Ratio - ratio of maximum to minimum over all processors Mess: number of messages sent AvgLen: average message length (bytes) Reduct: number of global reductions Global: entire computation Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). %T - percent time in this phase %F - percent flop in this phase %M - percent messages in this phase %L - percent message lengths in this phase %R - percent reductions in this phase Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors) ------------------------------------------------------------------------------------------------------------------------ Event Count Time (sec) Flop --- Global --- --- Stage ---- Total Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s ------------------------------------------------------------------------------------------------------------------------ --- Event Stage 0: Main Stage BuildTwoSided 1 1.0 3.1824e-05 1.0 0.00e+00 0.0 2.0e+00 4.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatMult 198 1.0 1.3480e+00 1.4 7.76e+08 1.0 4.0e+02 9.4e+04 0.0e+00 19 35 97 54 0 19 35 97 54 0 1151 MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 MatLUFactorNum 1 1.0 7.1852e-03 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1789 MatILUFactorSym 1 1.0 1.0472e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyBegin 1 1.0 9.8700e-07 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatAssemblyEnd 1 1.0 6.8341e-03 1.1 0.00e+00 0.0 4.0e+00 2.3e+04 5.0e+00 0 0 1 0 1 0 0 1 0 1 0 MatGetRowIJ 1 1.0 1.9930e-06 6.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatGetOrdering 1 1.0 7.4472e-04 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 MatLoad 1 1.0 9.8562e-02 1.0 0.00e+00 0.0 1.0e+01 2.7e+06 1.7e+01 2 0 2 39 4 2 0 2 39 4 0 VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 VecCopy 2 1.0 7.4971e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 VecSet 202 1.0 8.0035e-02 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 VecAXPBYCZ 198 1.0 1.2889e-01 1.5 2.46e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 11 0 0 0 2 11 0 0 0 3811 VecWAXPY 198 1.0 9.1526e-02 1.0 1.23e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 5 0 0 0 1 5 0 0 0 2683 VecLoad 2 1.0 9.8983e-03 1.0 0.00e+00 0.0 4.0e+00 1.2e+06 1.6e+01 0 0 1 7 3 0 0 1 7 4 0 VecScatterBegin 198 1.0 1.2941e-03 1.0 0.00e+00 0.0 4.0e+02 9.4e+04 0.0e+00 0 0 97 54 0 0 0 97 54 0 0 VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 SFSetGraph 1 1.0 7.6630e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFSetUp 1 1.0 1.2410e-04 1.0 0.00e+00 0.0 4.0e+00 2.3e+04 1.0e+00 0 0 1 0 0 0 0 1 0 0 0 SFPack 198 1.0 5.1814e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 SFUnpack 198 1.0 3.8273e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSetUp 2 1.0 4.7077e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 KSPSolve 1 1.0 6.0344e+00 1.0 2.23e+09 1.0 4.0e+02 9.4e+04 4.0e+02 98 100 97 54 87 98 100 97 54 90 738 PCSetUp 2 1.0 1.8496e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 695 PCSetUpOnBlocks 1 1.0 1.8435e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 697 PCApply 199 1.0 9.5103e-01 1.1 7.75e+08 1.0 0.0e+00 0.0e+00 0.0e+00 15 35 0 0 0 15 35 0 0 0 1630 --- Event Stage 1: Unknown ------------------------------------------------------------------------------------------------------------------------ Object Type Creations Destructions. Reports information only for process 0. --- Event Stage 0: Main Stage Viewer 4 1 Matrix 5 1 Vector 13 2 Index Set 5 2 Star Forest Graph 1 0 Krylov Solver 2 0 Preconditioner 2 0 --- Event Stage 1: Unknown ======================================================================================================================== Average time to get PetscTime(): 2.47e-08 Average time for MPI_Barrier(): 4.406e-07 Average time for zero size MPI_Send(): 4.769e-06 #PETSc Option Table entries: -log_view # (source: command line) #End of PETSc Option Table entries Compiled without FORTRAN kernels Compiled with full precision matrices (default) sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 --download-mumps --download-scalapack --with-mpi=1 --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 ----------------------------------------- Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 Using PETSc directory: /opt/anl/petsc-3.19.5 Using PETSc arch: ----------------------------------------- Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -O2 Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O2 ----------------------------------------- Using include paths: -I/opt/anl/petsc-3.19.5/include -I/opt/anl/mpich/include ----------------------------------------- Using C linker: /opt/anl/mpich/bin/mpicc Using Fortran linker: /opt/anl/mpich/bin/mpif90 Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath ----------------------------------------- Chris On Fri, Sep 8, 2023 at 3:00?PM Barry Smith wrote: > > It would be very helpful if you could run on 1 and 2 ranks with > -log_view and send all the output. > > > > On Sep 8, 2023, at 4:52 PM, Chris Hewson wrote: > > Hi There, > > I am trying to solve a linear problem and am having an issue when I use > more MPI processes with the KSPsolve slowing down considerably the more > processes I add. > > The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I > am using petsc version 3.19.5 and have tried with a couple different > versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and > v3.3.2 w/ ch3:sock). > > In testing, I've noticed the following trend for speed for the KSPSolve > function call: > 1 core: 4042 ms > 2 core: 7085 ms > 4 core: 26573 ms > 8 core: 65745 ms > 16 core: 149283 ms > > This was all done on a single node machine w/ 16 non-hyperthreaded cores. > We solve quite a few different matrices with PETSc using MPI and haven't > noticed an impact like this on performance before. > > I am very confused by this and am a little stumped at the moment as to why > this was happening. I've been using the KSPBCGS solver to solve the > problem. I have tried with multiple different solvers and pre-conditioners > (we usually don't use a pre-conditioner for this part of our code). > > It did seem that using the piped BCGS solver did help improve the parallel > speed slightly (maybe 15%), but it still doesn't come close to the single > threaded speed. > > I'll attach a link to a folder that contains the specific A, x and b > matrices for this problem, as well as a main.cpp file that I was using for > testing. > > > https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing > > I was testing this in our main code base, but don't include that here, and > observe very similar speed results to the ones above. We do use Metis to > graph partition in our own code and checked the vector and matrix > partitioning and that all made sense. I could be doing the partitioning > incorrectly in the example (not 100% sure how it works with the viewer/load > functions). > > Any insight or thoughts on this would be greatly appreciated. > > Thanks, > > *Chris Hewson* > Senior Reservoir Simulation Engineer > ResFrac > +1.587.575.9792 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Fri Sep 8 16:53:29 2023 From: bsmith at petsc.dev (Barry Smith) Date: Fri, 8 Sep 2023 17:53:29 -0400 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: For the size problem you are running this is very unexpected. The reductions should only start to dominate for thousands of MPI ranks, not 2. First thing I recommend is to run the streams benchmark. Then check the binding that MPI is doing for the two processes. You want to bind to cores in different NUMA regions. It could be that it is binding both processes to cores that share the same cache. The MatSolve should be embarressingly parallel but you are getting almost no speed up in it, so something very "wrong" is happening. Event Count Time (sec) Flop --- Global --- --- Stage ---- Total Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 > On Sep 8, 2023, at 5:22 PM, Chris Hewson wrote: > > Thanks for the quick response. > > The links to the log view files are below: > 2 ranks: > https://drive.google.com/file/d/1PGRsiHypWtN5h3uxdJBKy9WzEkE0mUgO/view?usp=drive_link > > 1 rank: > https://drive.google.com/file/d/1hB2XyoNtLMHseZUT7jCuiixTQeBi_tjJ/view?usp=drive_link > > I'll also attach them to this email: > **************************** 1 RANK ****************************** > ------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------ > > ./petsc-testing on a named ubuntu-office with 1 processor, by chewson Fri Sep 8 15:16:51 2023 > Using Petsc Release Version 3.19.5, unknown > > Max Max/Min Avg Total > Time (sec): 2.746e+00 1.000 2.746e+00 > Objects: 2.100e+01 1.000 2.100e+01 > Flops: 4.117e+09 1.000 4.117e+09 4.117e+09 > Flops/sec: 1.499e+09 1.000 1.499e+09 1.499e+09 > MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00 > MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00 > MPI Reductions: 0.000e+00 0.000 > > Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N --> 2N flops > and VecAXPY() for complex vectors of length N --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total Count %Total Avg %Total Count %Total > 0: Main Stage: 2.7458e+00 100.0% 4.1167e+09 100.0% 0.000e+00 0.0% 0.000e+00 0.0% 0.000e+00 0.0% > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flop: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > AvgLen: average message length (bytes) > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). > %T - percent time in this phase %F - percent flop in this phase > %M - percent messages in this phase %L - percent message lengths in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors) > ------------------------------------------------------------------------------------------------------------------------ > Event Count Time (sec) Flop --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > MatMult 182 1.0 8.0351e-01 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 29 35 0 0 0 29 35 0 0 0 1775 > MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > MatLUFactorNum 1 1.0 1.3892e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 934 > MatILUFactorSym 1 1.0 2.1567e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > MatAssemblyBegin 1 1.0 1.0420e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 1 1.0 6.9049e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetRowIJ 1 1.0 3.8500e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 1.0 1.7026e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLoad 1 1.0 6.6749e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 > VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 > VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 > VecCopy 2 1.0 6.8473e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 3 1.0 1.3256e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecAXPBYCZ 182 1.0 1.6542e-01 1.0 4.51e+08 1.0 0.0e+00 0.0e+00 0.0e+00 6 11 0 0 0 6 11 0 0 0 2729 > VecWAXPY 182 1.0 1.4476e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 0.0e+00 5 5 0 0 0 5 5 0 0 0 1559 > VecLoad 2 1.0 1.0104e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSetUp 1 1.0 9.9204e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 2.6210e+00 1.0 4.10e+09 1.0 0.0e+00 0.0e+00 0.0e+00 95 100 0 0 0 95 100 0 0 0 1566 > PCSetUp 1 1.0 3.7232e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 349 > PCApply 183 1.0 1.0885e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > > --- Event Stage 1: Unknown > > ------------------------------------------------------------------------------------------------------------------------ > > Object Type Creations Destructions. Reports information only for process 0. > > --- Event Stage 0: Main Stage > > Viewer 4 1 > Matrix 3 1 > Vector 9 1 > Krylov Solver 1 0 > Preconditioner 1 0 > Index Set 3 0 > > --- Event Stage 1: Unknown > > ======================================================================================================================== > Average time to get PetscTime(): 1.51e-08 > #PETSc Option Table entries: > -log_view # (source: command line) > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 --download-mumps --download-scalapack --with-mpi=1 --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 > ----------------------------------------- > Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office > Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 > Using PETSc directory: /opt/anl/petsc-3.19.5 > Using PETSc arch: > ----------------------------------------- > > Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -O2 > Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O2 > ----------------------------------------- > > Using include paths: -I/opt/anl/petsc-3.19.5/include -I/opt/anl/mpich/include > ----------------------------------------- > > Using C linker: /opt/anl/mpich/bin/mpicc > Using Fortran linker: /opt/anl/mpich/bin/mpif90 > Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath > ----------------------------------------- > > ************************* 2 RANKS ************************************ > ------------------------------------------------------------------ PETSc Performance Summary: ------------------------------------------------------------------ > > ./petsc-testing on a named ubuntu-office with 2 processors, by chewson Fri Sep 8 15:16:43 2023 > Using Petsc Release Version 3.19.5, unknown > > Max Max/Min Avg Total > Time (sec): 6.167e+00 1.001 6.164e+00 > Objects: 3.200e+01 1.000 3.200e+01 > Flops: 2.233e+09 1.000 2.233e+09 4.467e+09 > Flops/sec: 3.625e+08 1.001 3.623e+08 7.247e+08 > MPI Msg Count: 2.050e+02 1.000 2.050e+02 4.100e+02 > MPI Msg Len (bytes): 3.437e+07 1.000 1.676e+05 6.874e+07 > MPI Reductions: 4.580e+02 1.000 > > Flop counting convention: 1 flop = 1 real number operation of type (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N --> 2N flops > and VecAXPY() for complex vectors of length N --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total Count %Total Avg %Total Count %Total > 0: Main Stage: 6.1642e+00 100.0% 4.4670e+09 100.0% 4.100e+02 100.0% 1.676e+05 100.0% 4.400e+02 96.1% > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flop: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > AvgLen: average message length (bytes) > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and PetscLogStagePop(). > %T - percent time in this phase %F - percent flop in this phase > %M - percent messages in this phase %L - percent message lengths in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over all processors) > ------------------------------------------------------------------------------------------------------------------------ > Event Count Time (sec) Flop --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > BuildTwoSided 1 1.0 3.1824e-05 1.0 0.00e+00 0.0 2.0e+00 4.0e+00 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatMult 198 1.0 1.3480e+00 1.4 7.76e+08 1.0 4.0e+02 9.4e+04 0.0e+00 19 35 97 54 0 19 35 97 54 0 1151 > MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 > MatLUFactorNum 1 1.0 7.1852e-03 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 1789 > MatILUFactorSym 1 1.0 1.0472e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyBegin 1 1.0 9.8700e-07 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 1 1.0 6.8341e-03 1.1 0.00e+00 0.0 4.0e+00 2.3e+04 5.0e+00 0 0 1 0 1 0 0 1 0 1 0 > MatGetRowIJ 1 1.0 1.9930e-06 6.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 1.0 7.4472e-04 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLoad 1 1.0 9.8562e-02 1.0 0.00e+00 0.0 1.0e+01 2.7e+06 1.7e+01 2 0 2 39 4 2 0 2 39 4 0 > VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 > VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 > VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 > VecCopy 2 1.0 7.4971e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 202 1.0 8.0035e-02 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecAXPBYCZ 198 1.0 1.2889e-01 1.5 2.46e+08 1.0 0.0e+00 0.0e+00 0.0e+00 2 11 0 0 0 2 11 0 0 0 3811 > VecWAXPY 198 1.0 9.1526e-02 1.0 1.23e+08 1.0 0.0e+00 0.0e+00 0.0e+00 1 5 0 0 0 1 5 0 0 0 2683 > VecLoad 2 1.0 9.8983e-03 1.0 0.00e+00 0.0 4.0e+00 1.2e+06 1.6e+01 0 0 1 7 3 0 0 1 7 4 0 > VecScatterBegin 198 1.0 1.2941e-03 1.0 0.00e+00 0.0 4.0e+02 9.4e+04 0.0e+00 0 0 97 54 0 0 0 97 54 0 0 > VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 > SFSetGraph 1 1.0 7.6630e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SFSetUp 1 1.0 1.2410e-04 1.0 0.00e+00 0.0 4.0e+00 2.3e+04 1.0e+00 0 0 1 0 0 0 0 1 0 0 0 > SFPack 198 1.0 5.1814e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SFUnpack 198 1.0 3.8273e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSetUp 2 1.0 4.7077e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 6.0344e+00 1.0 2.23e+09 1.0 4.0e+02 9.4e+04 4.0e+02 98 100 97 54 87 98 100 97 54 90 738 > PCSetUp 2 1.0 1.8496e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 695 > PCSetUpOnBlocks 1 1.0 1.8435e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 697 > PCApply 199 1.0 9.5103e-01 1.1 7.75e+08 1.0 0.0e+00 0.0e+00 0.0e+00 15 35 0 0 0 15 35 0 0 0 1630 > > --- Event Stage 1: Unknown > > ------------------------------------------------------------------------------------------------------------------------ > > Object Type Creations Destructions. Reports information only for process 0. > > --- Event Stage 0: Main Stage > > Viewer 4 1 > Matrix 5 1 > Vector 13 2 > Index Set 5 2 > Star Forest Graph 1 0 > Krylov Solver 2 0 > Preconditioner 2 0 > > --- Event Stage 1: Unknown > > ======================================================================================================================== > Average time to get PetscTime(): 2.47e-08 > Average time for MPI_Barrier(): 4.406e-07 > Average time for zero size MPI_Send(): 4.769e-06 > #PETSc Option Table entries: > -log_view # (source: command line) > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 --download-mumps --download-scalapack --with-mpi=1 --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 > ----------------------------------------- > Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office > Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 > Using PETSc directory: /opt/anl/petsc-3.19.5 > Using PETSc arch: > ----------------------------------------- > > Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow -fstack-protector -fvisibility=hidden -O2 > Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O2 > ----------------------------------------- > > Using include paths: -I/opt/anl/petsc-3.19.5/include -I/opt/anl/mpich/include > ----------------------------------------- > > Using C linker: /opt/anl/mpich/bin/mpicc > Using Fortran linker: /opt/anl/mpich/bin/mpif90 > Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath > ----------------------------------------- > > Chris > > > On Fri, Sep 8, 2023 at 3:00?PM Barry Smith > wrote: >> >> It would be very helpful if you could run on 1 and 2 ranks with -log_view and send all the output. >> >> >> >>> On Sep 8, 2023, at 4:52 PM, Chris Hewson > wrote: >>> >>> Hi There, >>> >>> I am trying to solve a linear problem and am having an issue when I use more MPI processes with the KSPsolve slowing down considerably the more processes I add. >>> >>> The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I am using petsc version 3.19.5 and have tried with a couple different versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and v3.3.2 w/ ch3:sock). >>> >>> In testing, I've noticed the following trend for speed for the KSPSolve function call: >>> 1 core: 4042 ms >>> 2 core: 7085 ms >>> 4 core: 26573 ms >>> 8 core: 65745 ms >>> 16 core: 149283 ms >>> >>> This was all done on a single node machine w/ 16 non-hyperthreaded cores. We solve quite a few different matrices with PETSc using MPI and haven't noticed an impact like this on performance before. >>> >>> I am very confused by this and am a little stumped at the moment as to why this was happening. I've been using the KSPBCGS solver to solve the problem. I have tried with multiple different solvers and pre-conditioners (we usually don't use a pre-conditioner for this part of our code). >>> >>> It did seem that using the piped BCGS solver did help improve the parallel speed slightly (maybe 15%), but it still doesn't come close to the single threaded speed. >>> >>> I'll attach a link to a folder that contains the specific A, x and b matrices for this problem, as well as a main.cpp file that I was using for testing. >>> >>> https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing >>> >>> I was testing this in our main code base, but don't include that here, and observe very similar speed results to the ones above. We do use Metis to graph partition in our own code and checked the vector and matrix partitioning and that all made sense. I could be doing the partitioning incorrectly in the example (not 100% sure how it works with the viewer/load functions). >>> >>> Any insight or thoughts on this would be greatly appreciated. >>> >>> Thanks, >>> >>> Chris Hewson >>> Senior Reservoir Simulation Engineer >>> ResFrac >>> +1.587.575.9792 >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrsd at gmail.com Fri Sep 8 17:26:31 2023 From: andrsd at gmail.com (David Andrs) Date: Fri, 8 Sep 2023 16:26:31 -0600 Subject: [petsc-users] Compute integral using DMPlexComputeIntegralFEM Message-ID: Hi all! I am trying to use DMPlexComputeIntegralFEM to compute an integral $\int_\Omega u d\Omega$. My domain is a square (-1, 1)^2 (2x2 QUAD4 elements), I add first order Lagrange FE field on it, set the solution vector (computed by a previous simulation). The value I am seeing computed by PETSc is -4, but the hand-calculated value of this integral is -4.6. I also checked this in paraview using the ?Integrate Variables? filter and it also returns -4.6 (this was to double check that my hand-calculated value is correct). So, I must be missing something obvious in my code. Attached is the minimal PETSc code to show what I am doing. This is against PETSc 3.19.4. Thanks in advance for your help, David -- -------------- next part -------------- A non-text attachment was scrubbed... Name: main.cpp Type: application/octet-stream Size: 2104 bytes Desc: not available URL: From chris at resfrac.com Fri Sep 8 17:28:20 2023 From: chris at resfrac.com (Chris Hewson) Date: Fri, 8 Sep 2023 16:28:20 -0600 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: Hi Barry, Looking at the streams output, that definitely seems to be the culprit, I get an output log of: Running streams with '/opt/anl/mpich/bin/mpiexec ' using 'NPMAX=16' 1 33795.3914 Rate (MB/s) 2 37155.5788 Rate (MB/s) 1.09943 3 35549.7490 Rate (MB/s) 1.05191 4 35045.2962 Rate (MB/s) 1.03698 5 42029.1432 Rate (MB/s) 1.24364 6 38167.6186 Rate (MB/s) 1.12937 7 39850.2228 Rate (MB/s) 1.17916 8 36602.9043 Rate (MB/s) 1.08307 9 36740.0487 Rate (MB/s) 1.08713 10 34839.9674 Rate (MB/s) 1.03091 11 31107.6189 Rate (MB/s) 0.920469 12 35057.6326 Rate (MB/s) 1.03735 13 35030.9879 Rate (MB/s) 1.03656 14 33619.9223 Rate (MB/s) 0.994808 15 33503.3583 Rate (MB/s) 0.991359 16 27556.2016 Rate (MB/s) 0.815383 [image: MPIscaling.png] Chris On Fri, Sep 8, 2023 at 3:53?PM Barry Smith wrote: > > For the size problem you are running this is very unexpected. The > reductions should only start to dominate for thousands of MPI ranks, not 2. > > First thing I recommend is to run the streams benchmark. Then check the > binding that MPI is doing for the two processes. You want to bind to cores > in different NUMA regions. It could be that it is binding both processes to > cores that share the same cache. The MatSolve should be embarressingly > parallel but you are getting almost no speed up in it, so something very > "wrong" is happening. > > > > Event Count Time (sec) Flop > --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen > Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > > VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 > VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 > VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 > > VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 > 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 > VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 > 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 > VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 > 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 > VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 > > MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 > > > On Sep 8, 2023, at 5:22 PM, Chris Hewson wrote: > > Thanks for the quick response. > > The links to the log view files are below: > 2 ranks: > > https://drive.google.com/file/d/1PGRsiHypWtN5h3uxdJBKy9WzEkE0mUgO/view?usp=drive_link > > 1 rank: > > https://drive.google.com/file/d/1hB2XyoNtLMHseZUT7jCuiixTQeBi_tjJ/view?usp=drive_link > > I'll also attach them to this email: > **************************** 1 RANK ****************************** > ------------------------------------------------------------------ PETSc > Performance Summary: > ------------------------------------------------------------------ > > ./petsc-testing on a named ubuntu-office with 1 processor, by chewson Fri > Sep 8 15:16:51 2023 > Using Petsc Release Version 3.19.5, unknown > > Max Max/Min Avg Total > Time (sec): 2.746e+00 1.000 2.746e+00 > Objects: 2.100e+01 1.000 2.100e+01 > Flops: 4.117e+09 1.000 4.117e+09 4.117e+09 > Flops/sec: 1.499e+09 1.000 1.499e+09 1.499e+09 > MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00 > MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00 > MPI Reductions: 0.000e+00 0.000 > > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total Count > %Total Avg %Total Count %Total > 0: Main Stage: 2.7458e+00 100.0% 4.1167e+09 100.0% 0.000e+00 > 0.0% 0.000e+00 0.0% 0.000e+00 0.0% > > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flop: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > AvgLen: average message length (bytes) > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %F - percent flop in this > phase > %M - percent messages in this phase %L - percent message lengths > in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over > all processors) > > ------------------------------------------------------------------------------------------------------------------------ > Event Count Time (sec) Flop > --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen > Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > MatMult 182 1.0 8.0351e-01 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 29 35 0 0 0 29 35 0 0 0 1775 > MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > MatLUFactorNum 1 1.0 1.3892e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 934 > MatILUFactorSym 1 1.0 2.1567e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > MatAssemblyBegin 1 1.0 1.0420e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 1 1.0 6.9049e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetRowIJ 1 1.0 3.8500e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 1.0 1.7026e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLoad 1 1.0 6.6749e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 > VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 > VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 > VecCopy 2 1.0 6.8473e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 3 1.0 1.3256e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecAXPBYCZ 182 1.0 1.6542e-01 1.0 4.51e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 6 11 0 0 0 6 11 0 0 0 2729 > VecWAXPY 182 1.0 1.4476e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 5 5 0 0 0 5 5 0 0 0 1559 > VecLoad 2 1.0 1.0104e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSetUp 1 1.0 9.9204e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 2.6210e+00 1.0 4.10e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 95 100 0 0 0 95 100 0 0 0 1566 > PCSetUp 1 1.0 3.7232e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 349 > PCApply 183 1.0 1.0885e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > > --- Event Stage 1: Unknown > > > ------------------------------------------------------------------------------------------------------------------------ > > Object Type Creations Destructions. Reports information only > for process 0. > > --- Event Stage 0: Main Stage > > Viewer 4 1 > Matrix 3 1 > Vector 9 1 > Krylov Solver 1 0 > Preconditioner 1 0 > Index Set 3 0 > > --- Event Stage 1: Unknown > > > ======================================================================================================================== > Average time to get PetscTime(): 1.51e-08 > #PETSc Option Table entries: > -log_view # (source: command line) > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 > --download-mumps --download-scalapack --with-mpi=1 > --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 > ----------------------------------------- > Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office > Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 > Using PETSc directory: /opt/anl/petsc-3.19.5 > Using PETSc arch: > ----------------------------------------- > > Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow > -fstack-protector -fvisibility=hidden -O2 > Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall > -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch > -Wno-unused-dummy-argument -O2 > ----------------------------------------- > > Using include paths: -I/opt/anl/petsc-3.19.5/include > -I/opt/anl/mpich/include > ----------------------------------------- > > Using C linker: /opt/anl/mpich/bin/mpicc > Using Fortran linker: /opt/anl/mpich/bin/mpif90 > Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib > -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 > -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread > -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm > -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath > ----------------------------------------- > > ************************* 2 RANKS ************************************ > ------------------------------------------------------------------ PETSc > Performance Summary: > ------------------------------------------------------------------ > > ./petsc-testing on a named ubuntu-office with 2 processors, by chewson > Fri Sep 8 15:16:43 2023 > Using Petsc Release Version 3.19.5, unknown > > Max Max/Min Avg Total > Time (sec): 6.167e+00 1.001 6.164e+00 > Objects: 3.200e+01 1.000 3.200e+01 > Flops: 2.233e+09 1.000 2.233e+09 4.467e+09 > Flops/sec: 3.625e+08 1.001 3.623e+08 7.247e+08 > MPI Msg Count: 2.050e+02 1.000 2.050e+02 4.100e+02 > MPI Msg Len (bytes): 3.437e+07 1.000 1.676e+05 6.874e+07 > MPI Reductions: 4.580e+02 1.000 > > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total Count > %Total Avg %Total Count %Total > 0: Main Stage: 6.1642e+00 100.0% 4.4670e+09 100.0% 4.100e+02 > 100.0% 1.676e+05 100.0% 4.400e+02 96.1% > > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flop: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > AvgLen: average message length (bytes) > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %F - percent flop in this > phase > %M - percent messages in this phase %L - percent message lengths > in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over > all processors) > > ------------------------------------------------------------------------------------------------------------------------ > Event Count Time (sec) Flop > --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen > Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > BuildTwoSided 1 1.0 3.1824e-05 1.0 0.00e+00 0.0 2.0e+00 4.0e+00 > 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatMult 198 1.0 1.3480e+00 1.4 7.76e+08 1.0 4.0e+02 9.4e+04 > 0.0e+00 19 35 97 54 0 19 35 97 54 0 1151 > MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 > MatLUFactorNum 1 1.0 7.1852e-03 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 1789 > MatILUFactorSym 1 1.0 1.0472e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyBegin 1 1.0 9.8700e-07 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 1 1.0 6.8341e-03 1.1 0.00e+00 0.0 4.0e+00 2.3e+04 > 5.0e+00 0 0 1 0 1 0 0 1 0 1 0 > MatGetRowIJ 1 1.0 1.9930e-06 6.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 1.0 7.4472e-04 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLoad 1 1.0 9.8562e-02 1.0 0.00e+00 0.0 1.0e+01 2.7e+06 > 1.7e+01 2 0 2 39 4 2 0 2 39 4 0 > VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 > 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 > VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 > 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 > VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 > 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 > VecCopy 2 1.0 7.4971e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 202 1.0 8.0035e-02 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecAXPBYCZ 198 1.0 1.2889e-01 1.5 2.46e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 11 0 0 0 2 11 0 0 0 3811 > VecWAXPY 198 1.0 9.1526e-02 1.0 1.23e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 5 0 0 0 1 5 0 0 0 2683 > VecLoad 2 1.0 9.8983e-03 1.0 0.00e+00 0.0 4.0e+00 1.2e+06 > 1.6e+01 0 0 1 7 3 0 0 1 7 4 0 > VecScatterBegin 198 1.0 1.2941e-03 1.0 0.00e+00 0.0 4.0e+02 9.4e+04 > 0.0e+00 0 0 97 54 0 0 0 97 54 0 0 > VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 > SFSetGraph 1 1.0 7.6630e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SFSetUp 1 1.0 1.2410e-04 1.0 0.00e+00 0.0 4.0e+00 2.3e+04 > 1.0e+00 0 0 1 0 0 0 0 1 0 0 0 > SFPack 198 1.0 5.1814e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SFUnpack 198 1.0 3.8273e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSetUp 2 1.0 4.7077e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 6.0344e+00 1.0 2.23e+09 1.0 4.0e+02 9.4e+04 > 4.0e+02 98 100 97 54 87 98 100 97 54 90 738 > PCSetUp 2 1.0 1.8496e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 695 > PCSetUpOnBlocks 1 1.0 1.8435e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 697 > PCApply 199 1.0 9.5103e-01 1.1 7.75e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 15 35 0 0 0 15 35 0 0 0 1630 > > --- Event Stage 1: Unknown > > > ------------------------------------------------------------------------------------------------------------------------ > > Object Type Creations Destructions. Reports information only > for process 0. > > --- Event Stage 0: Main Stage > > Viewer 4 1 > Matrix 5 1 > Vector 13 2 > Index Set 5 2 > Star Forest Graph 1 0 > Krylov Solver 2 0 > Preconditioner 2 0 > > --- Event Stage 1: Unknown > > > ======================================================================================================================== > Average time to get PetscTime(): 2.47e-08 > Average time for MPI_Barrier(): 4.406e-07 > Average time for zero size MPI_Send(): 4.769e-06 > #PETSc Option Table entries: > -log_view # (source: command line) > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 > --download-mumps --download-scalapack --with-mpi=1 > --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 > ----------------------------------------- > Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office > Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 > Using PETSc directory: /opt/anl/petsc-3.19.5 > Using PETSc arch: > ----------------------------------------- > > Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow > -fstack-protector -fvisibility=hidden -O2 > Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall > -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch > -Wno-unused-dummy-argument -O2 > ----------------------------------------- > > Using include paths: -I/opt/anl/petsc-3.19.5/include > -I/opt/anl/mpich/include > ----------------------------------------- > > Using C linker: /opt/anl/mpich/bin/mpicc > Using Fortran linker: /opt/anl/mpich/bin/mpif90 > Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib > -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 > -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread > -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm > -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath > ----------------------------------------- > > Chris > > > On Fri, Sep 8, 2023 at 3:00?PM Barry Smith wrote: > >> >> It would be very helpful if you could run on 1 and 2 ranks with >> -log_view and send all the output. >> >> >> >> On Sep 8, 2023, at 4:52 PM, Chris Hewson wrote: >> >> Hi There, >> >> I am trying to solve a linear problem and am having an issue when I use >> more MPI processes with the KSPsolve slowing down considerably the more >> processes I add. >> >> The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I >> am using petsc version 3.19.5 and have tried with a couple different >> versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and >> v3.3.2 w/ ch3:sock). >> >> In testing, I've noticed the following trend for speed for the KSPSolve >> function call: >> 1 core: 4042 ms >> 2 core: 7085 ms >> 4 core: 26573 ms >> 8 core: 65745 ms >> 16 core: 149283 ms >> >> This was all done on a single node machine w/ 16 non-hyperthreaded cores. >> We solve quite a few different matrices with PETSc using MPI and haven't >> noticed an impact like this on performance before. >> >> I am very confused by this and am a little stumped at the moment as to >> why this was happening. I've been using the KSPBCGS solver to solve the >> problem. I have tried with multiple different solvers and pre-conditioners >> (we usually don't use a pre-conditioner for this part of our code). >> >> It did seem that using the piped BCGS solver did help improve the >> parallel speed slightly (maybe 15%), but it still doesn't come close to the >> single threaded speed. >> >> I'll attach a link to a folder that contains the specific A, x and b >> matrices for this problem, as well as a main.cpp file that I was using for >> testing. >> >> >> https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing >> >> I was testing this in our main code base, but don't include that here, >> and observe very similar speed results to the ones above. We do use Metis >> to graph partition in our own code and checked the vector and matrix >> partitioning and that all made sense. I could be doing the partitioning >> incorrectly in the example (not 100% sure how it works with the viewer/load >> functions). >> >> Any insight or thoughts on this would be greatly appreciated. >> >> Thanks, >> >> *Chris Hewson* >> Senior Reservoir Simulation Engineer >> ResFrac >> +1.587.575.9792 >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: MPIscaling.png Type: image/png Size: 53832 bytes Desc: not available URL: From junchao.zhang at gmail.com Fri Sep 8 17:38:54 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Fri, 8 Sep 2023 17:38:54 -0500 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: Hi, Chris, this is my result of running your test on a local machine (8 cores, 16 hardware threads). I use OpenMPI with command line like mpirun --bind-to core -n ./main np=1 Solve duration: 2132 np=2 Solve duration: 1116 np=4 Solve duration: 990 np=8 Solve duration: 1257 Note when I used $ mpirun -n 4 ./main Solve duration: 22693 It suggests binding is important. --Junchao Zhang On Fri, Sep 8, 2023 at 4:53?PM Barry Smith wrote: > > For the size problem you are running this is very unexpected. The > reductions should only start to dominate for thousands of MPI ranks, not 2. > > First thing I recommend is to run the streams benchmark. Then check the > binding that MPI is doing for the two processes. You want to bind to cores > in different NUMA regions. It could be that it is binding both processes to > cores that share the same cache. The MatSolve should be embarressingly > parallel but you are getting almost no speed up in it, so something very > "wrong" is happening. > > > > Event Count Time (sec) Flop > --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen > Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > > VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 > VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 > VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 > > VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 > 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 > VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 > 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 > VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 > 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 > VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 > > MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 > > > On Sep 8, 2023, at 5:22 PM, Chris Hewson wrote: > > Thanks for the quick response. > > The links to the log view files are below: > 2 ranks: > > https://drive.google.com/file/d/1PGRsiHypWtN5h3uxdJBKy9WzEkE0mUgO/view?usp=drive_link > > 1 rank: > > https://drive.google.com/file/d/1hB2XyoNtLMHseZUT7jCuiixTQeBi_tjJ/view?usp=drive_link > > I'll also attach them to this email: > **************************** 1 RANK ****************************** > ------------------------------------------------------------------ PETSc > Performance Summary: > ------------------------------------------------------------------ > > ./petsc-testing on a named ubuntu-office with 1 processor, by chewson Fri > Sep 8 15:16:51 2023 > Using Petsc Release Version 3.19.5, unknown > > Max Max/Min Avg Total > Time (sec): 2.746e+00 1.000 2.746e+00 > Objects: 2.100e+01 1.000 2.100e+01 > Flops: 4.117e+09 1.000 4.117e+09 4.117e+09 > Flops/sec: 1.499e+09 1.000 1.499e+09 1.499e+09 > MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00 > MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00 > MPI Reductions: 0.000e+00 0.000 > > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total Count > %Total Avg %Total Count %Total > 0: Main Stage: 2.7458e+00 100.0% 4.1167e+09 100.0% 0.000e+00 > 0.0% 0.000e+00 0.0% 0.000e+00 0.0% > > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flop: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > AvgLen: average message length (bytes) > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %F - percent flop in this > phase > %M - percent messages in this phase %L - percent message lengths > in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over > all processors) > > ------------------------------------------------------------------------------------------------------------------------ > Event Count Time (sec) Flop > --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen > Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > MatMult 182 1.0 8.0351e-01 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 29 35 0 0 0 29 35 0 0 0 1775 > MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > MatLUFactorNum 1 1.0 1.3892e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 934 > MatILUFactorSym 1 1.0 2.1567e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > MatAssemblyBegin 1 1.0 1.0420e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 1 1.0 6.9049e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetRowIJ 1 1.0 3.8500e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 1.0 1.7026e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLoad 1 1.0 6.6749e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 > VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 > VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 > VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 > VecCopy 2 1.0 6.8473e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 3 1.0 1.3256e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecAXPBYCZ 182 1.0 1.6542e-01 1.0 4.51e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 6 11 0 0 0 6 11 0 0 0 2729 > VecWAXPY 182 1.0 1.4476e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 5 5 0 0 0 5 5 0 0 0 1559 > VecLoad 2 1.0 1.0104e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSetUp 1 1.0 9.9204e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 2.6210e+00 1.0 4.10e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 95 100 0 0 0 95 100 0 0 0 1566 > PCSetUp 1 1.0 3.7232e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 349 > PCApply 183 1.0 1.0885e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 > 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 > > --- Event Stage 1: Unknown > > > ------------------------------------------------------------------------------------------------------------------------ > > Object Type Creations Destructions. Reports information only > for process 0. > > --- Event Stage 0: Main Stage > > Viewer 4 1 > Matrix 3 1 > Vector 9 1 > Krylov Solver 1 0 > Preconditioner 1 0 > Index Set 3 0 > > --- Event Stage 1: Unknown > > > ======================================================================================================================== > Average time to get PetscTime(): 1.51e-08 > #PETSc Option Table entries: > -log_view # (source: command line) > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 > --download-mumps --download-scalapack --with-mpi=1 > --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 > ----------------------------------------- > Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office > Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 > Using PETSc directory: /opt/anl/petsc-3.19.5 > Using PETSc arch: > ----------------------------------------- > > Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow > -fstack-protector -fvisibility=hidden -O2 > Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall > -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch > -Wno-unused-dummy-argument -O2 > ----------------------------------------- > > Using include paths: -I/opt/anl/petsc-3.19.5/include > -I/opt/anl/mpich/include > ----------------------------------------- > > Using C linker: /opt/anl/mpich/bin/mpicc > Using Fortran linker: /opt/anl/mpich/bin/mpif90 > Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib > -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 > -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread > -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm > -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath > ----------------------------------------- > > ************************* 2 RANKS ************************************ > ------------------------------------------------------------------ PETSc > Performance Summary: > ------------------------------------------------------------------ > > ./petsc-testing on a named ubuntu-office with 2 processors, by chewson > Fri Sep 8 15:16:43 2023 > Using Petsc Release Version 3.19.5, unknown > > Max Max/Min Avg Total > Time (sec): 6.167e+00 1.001 6.164e+00 > Objects: 3.200e+01 1.000 3.200e+01 > Flops: 2.233e+09 1.000 2.233e+09 4.467e+09 > Flops/sec: 3.625e+08 1.001 3.623e+08 7.247e+08 > MPI Msg Count: 2.050e+02 1.000 2.050e+02 4.100e+02 > MPI Msg Len (bytes): 3.437e+07 1.000 1.676e+05 6.874e+07 > MPI Reductions: 4.580e+02 1.000 > > Flop counting convention: 1 flop = 1 real number operation of type > (multiply/divide/add/subtract) > e.g., VecAXPY() for real vectors of length N > --> 2N flops > and VecAXPY() for complex vectors of length N > --> 8N flops > > Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages > --- -- Message Lengths -- -- Reductions -- > Avg %Total Avg %Total Count > %Total Avg %Total Count %Total > 0: Main Stage: 6.1642e+00 100.0% 4.4670e+09 100.0% 4.100e+02 > 100.0% 1.676e+05 100.0% 4.400e+02 96.1% > > > ------------------------------------------------------------------------------------------------------------------------ > See the 'Profiling' chapter of the users' manual for details on > interpreting output. > Phase summary info: > Count: number of times phase was executed > Time and Flop: Max - maximum over all processors > Ratio - ratio of maximum to minimum over all processors > Mess: number of messages sent > AvgLen: average message length (bytes) > Reduct: number of global reductions > Global: entire computation > Stage: stages of a computation. Set stages with PetscLogStagePush() and > PetscLogStagePop(). > %T - percent time in this phase %F - percent flop in this > phase > %M - percent messages in this phase %L - percent message lengths > in this phase > %R - percent reductions in this phase > Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time over > all processors) > > ------------------------------------------------------------------------------------------------------------------------ > Event Count Time (sec) Flop > --- Global --- --- Stage ---- Total > Max Ratio Max Ratio Max Ratio Mess AvgLen > Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s > > ------------------------------------------------------------------------------------------------------------------------ > > --- Event Stage 0: Main Stage > > BuildTwoSided 1 1.0 3.1824e-05 1.0 0.00e+00 0.0 2.0e+00 4.0e+00 > 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatMult 198 1.0 1.3480e+00 1.4 7.76e+08 1.0 4.0e+02 9.4e+04 > 0.0e+00 19 35 97 54 0 19 35 97 54 0 1151 > MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 > MatLUFactorNum 1 1.0 7.1852e-03 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 1789 > MatILUFactorSym 1 1.0 1.0472e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyBegin 1 1.0 9.8700e-07 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatAssemblyEnd 1 1.0 6.8341e-03 1.1 0.00e+00 0.0 4.0e+00 2.3e+04 > 5.0e+00 0 0 1 0 1 0 0 1 0 1 0 > MatGetRowIJ 1 1.0 1.9930e-06 6.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatGetOrdering 1 1.0 7.4472e-04 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > MatLoad 1 1.0 9.8562e-02 1.0 0.00e+00 0.0 1.0e+01 2.7e+06 > 1.7e+01 2 0 2 39 4 2 0 2 39 4 0 > VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 > 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 > VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 > 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 > VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 > 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 > VecCopy 2 1.0 7.4971e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > VecSet 202 1.0 8.0035e-02 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 > VecAXPBYCZ 198 1.0 1.2889e-01 1.5 2.46e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 2 11 0 0 0 2 11 0 0 0 3811 > VecWAXPY 198 1.0 9.1526e-02 1.0 1.23e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 1 5 0 0 0 1 5 0 0 0 2683 > VecLoad 2 1.0 9.8983e-03 1.0 0.00e+00 0.0 4.0e+00 1.2e+06 > 1.6e+01 0 0 1 7 3 0 0 1 7 4 0 > VecScatterBegin 198 1.0 1.2941e-03 1.0 0.00e+00 0.0 4.0e+02 9.4e+04 > 0.0e+00 0 0 97 54 0 0 0 97 54 0 0 > VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 > SFSetGraph 1 1.0 7.6630e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SFSetUp 1 1.0 1.2410e-04 1.0 0.00e+00 0.0 4.0e+00 2.3e+04 > 1.0e+00 0 0 1 0 0 0 0 1 0 0 0 > SFPack 198 1.0 5.1814e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > SFUnpack 198 1.0 3.8273e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSetUp 2 1.0 4.7077e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 > 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 > KSPSolve 1 1.0 6.0344e+00 1.0 2.23e+09 1.0 4.0e+02 9.4e+04 > 4.0e+02 98 100 97 54 87 98 100 97 54 90 738 > PCSetUp 2 1.0 1.8496e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 695 > PCSetUpOnBlocks 1 1.0 1.8435e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 > 0.0e+00 0 0 0 0 0 0 0 0 0 0 697 > PCApply 199 1.0 9.5103e-01 1.1 7.75e+08 1.0 0.0e+00 0.0e+00 > 0.0e+00 15 35 0 0 0 15 35 0 0 0 1630 > > --- Event Stage 1: Unknown > > > ------------------------------------------------------------------------------------------------------------------------ > > Object Type Creations Destructions. Reports information only > for process 0. > > --- Event Stage 0: Main Stage > > Viewer 4 1 > Matrix 5 1 > Vector 13 2 > Index Set 5 2 > Star Forest Graph 1 0 > Krylov Solver 2 0 > Preconditioner 2 0 > > --- Event Stage 1: Unknown > > > ======================================================================================================================== > Average time to get PetscTime(): 2.47e-08 > Average time for MPI_Barrier(): 4.406e-07 > Average time for zero size MPI_Send(): 4.769e-06 > #PETSc Option Table entries: > -log_view # (source: command line) > #End of PETSc Option Table entries > Compiled without FORTRAN kernels > Compiled with full precision matrices (default) > sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 > sizeof(PetscScalar) 8 sizeof(PetscInt) 4 > Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 > --download-mumps --download-scalapack --with-mpi=1 > --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 > ----------------------------------------- > Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office > Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 > Using PETSc directory: /opt/anl/petsc-3.19.5 > Using PETSc arch: > ----------------------------------------- > > Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow > -fstack-protector -fvisibility=hidden -O2 > Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall > -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch > -Wno-unused-dummy-argument -O2 > ----------------------------------------- > > Using include paths: -I/opt/anl/petsc-3.19.5/include > -I/opt/anl/mpich/include > ----------------------------------------- > > Using C linker: /opt/anl/mpich/bin/mpicc > Using Fortran linker: /opt/anl/mpich/bin/mpif90 > Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib > -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib > -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 > -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread > -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm > -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath > ----------------------------------------- > > Chris > > > On Fri, Sep 8, 2023 at 3:00?PM Barry Smith wrote: > >> >> It would be very helpful if you could run on 1 and 2 ranks with >> -log_view and send all the output. >> >> >> >> On Sep 8, 2023, at 4:52 PM, Chris Hewson wrote: >> >> Hi There, >> >> I am trying to solve a linear problem and am having an issue when I use >> more MPI processes with the KSPsolve slowing down considerably the more >> processes I add. >> >> The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I >> am using petsc version 3.19.5 and have tried with a couple different >> versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and >> v3.3.2 w/ ch3:sock). >> >> In testing, I've noticed the following trend for speed for the KSPSolve >> function call: >> 1 core: 4042 ms >> 2 core: 7085 ms >> 4 core: 26573 ms >> 8 core: 65745 ms >> 16 core: 149283 ms >> >> This was all done on a single node machine w/ 16 non-hyperthreaded cores. >> We solve quite a few different matrices with PETSc using MPI and haven't >> noticed an impact like this on performance before. >> >> I am very confused by this and am a little stumped at the moment as to >> why this was happening. I've been using the KSPBCGS solver to solve the >> problem. I have tried with multiple different solvers and pre-conditioners >> (we usually don't use a pre-conditioner for this part of our code). >> >> It did seem that using the piped BCGS solver did help improve the >> parallel speed slightly (maybe 15%), but it still doesn't come close to the >> single threaded speed. >> >> I'll attach a link to a folder that contains the specific A, x and b >> matrices for this problem, as well as a main.cpp file that I was using for >> testing. >> >> >> https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing >> >> I was testing this in our main code base, but don't include that here, >> and observe very similar speed results to the ones above. We do use Metis >> to graph partition in our own code and checked the vector and matrix >> partitioning and that all made sense. I could be doing the partitioning >> incorrectly in the example (not 100% sure how it works with the viewer/load >> functions). >> >> Any insight or thoughts on this would be greatly appreciated. >> >> Thanks, >> >> *Chris Hewson* >> Senior Reservoir Simulation Engineer >> ResFrac >> +1.587.575.9792 >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris at resfrac.com Fri Sep 8 17:52:10 2023 From: chris at resfrac.com (Chris Hewson) Date: Fri, 8 Sep 2023 16:52:10 -0600 Subject: [petsc-users] Slower performance using more MPI processes In-Reply-To: References: Message-ID: Thanks for the help. Yah, running the example again using core binding, I get similar results to Junchao as well: 1 core: 2808 ms 2 core: 1398 ms 4 core: 989 ms 8 core: 1083 ms On Fri, Sep 8, 2023 at 4:39?PM Junchao Zhang wrote: > Hi, Chris, > this is my result of running your test on a local machine (8 cores, 16 > hardware threads). I use OpenMPI with command line like > mpirun --bind-to core -n ./main > np=1 Solve duration: 2132 > np=2 Solve duration: 1116 > np=4 Solve duration: 990 > np=8 Solve duration: 1257 > > Note when I used > $ mpirun -n 4 ./main > Solve duration: 22693 > > It suggests binding is important. > > --Junchao Zhang > > > On Fri, Sep 8, 2023 at 4:53?PM Barry Smith wrote: > >> >> For the size problem you are running this is very unexpected. The >> reductions should only start to dominate for thousands of MPI ranks, not 2. >> >> First thing I recommend is to run the streams benchmark. Then check the >> binding that MPI is doing for the two processes. You want to bind to cores >> in different NUMA regions. It could be that it is binding both processes to >> cores that share the same cache. The MatSolve should be embarressingly >> parallel but you are getting almost no speed up in it, so something very >> "wrong" is happening. >> >> >> >> Event Count Time (sec) Flop >> --- Global --- --- Stage ---- Total >> Max Ratio Max Ratio Max Ratio Mess AvgLen >> Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s >> >> VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 >> VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 >> VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 >> >> VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 >> 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 >> VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 >> 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 >> VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 >> 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 >> VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 >> >> MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 >> 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 >> MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 >> >> >> On Sep 8, 2023, at 5:22 PM, Chris Hewson wrote: >> >> Thanks for the quick response. >> >> The links to the log view files are below: >> 2 ranks: >> >> https://drive.google.com/file/d/1PGRsiHypWtN5h3uxdJBKy9WzEkE0mUgO/view?usp=drive_link >> >> 1 rank: >> >> https://drive.google.com/file/d/1hB2XyoNtLMHseZUT7jCuiixTQeBi_tjJ/view?usp=drive_link >> >> I'll also attach them to this email: >> **************************** 1 RANK ****************************** >> ------------------------------------------------------------------ PETSc >> Performance Summary: >> ------------------------------------------------------------------ >> >> ./petsc-testing on a named ubuntu-office with 1 processor, by chewson >> Fri Sep 8 15:16:51 2023 >> Using Petsc Release Version 3.19.5, unknown >> >> Max Max/Min Avg Total >> Time (sec): 2.746e+00 1.000 2.746e+00 >> Objects: 2.100e+01 1.000 2.100e+01 >> Flops: 4.117e+09 1.000 4.117e+09 4.117e+09 >> Flops/sec: 1.499e+09 1.000 1.499e+09 1.499e+09 >> MPI Msg Count: 0.000e+00 0.000 0.000e+00 0.000e+00 >> MPI Msg Len (bytes): 0.000e+00 0.000 0.000e+00 0.000e+00 >> MPI Reductions: 0.000e+00 0.000 >> >> Flop counting convention: 1 flop = 1 real number operation of type >> (multiply/divide/add/subtract) >> e.g., VecAXPY() for real vectors of length N >> --> 2N flops >> and VecAXPY() for complex vectors of length N >> --> 8N flops >> >> Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages >> --- -- Message Lengths -- -- Reductions -- >> Avg %Total Avg %Total Count >> %Total Avg %Total Count %Total >> 0: Main Stage: 2.7458e+00 100.0% 4.1167e+09 100.0% 0.000e+00 >> 0.0% 0.000e+00 0.0% 0.000e+00 0.0% >> >> >> ------------------------------------------------------------------------------------------------------------------------ >> See the 'Profiling' chapter of the users' manual for details on >> interpreting output. >> Phase summary info: >> Count: number of times phase was executed >> Time and Flop: Max - maximum over all processors >> Ratio - ratio of maximum to minimum over all processors >> Mess: number of messages sent >> AvgLen: average message length (bytes) >> Reduct: number of global reductions >> Global: entire computation >> Stage: stages of a computation. Set stages with PetscLogStagePush() >> and PetscLogStagePop(). >> %T - percent time in this phase %F - percent flop in this >> phase >> %M - percent messages in this phase %L - percent message >> lengths in this phase >> %R - percent reductions in this phase >> Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time >> over all processors) >> >> ------------------------------------------------------------------------------------------------------------------------ >> Event Count Time (sec) Flop >> --- Global --- --- Stage ---- Total >> Max Ratio Max Ratio Max Ratio Mess AvgLen >> Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> --- Event Stage 0: Main Stage >> >> MatMult 182 1.0 8.0351e-01 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 >> 0.0e+00 29 35 0 0 0 29 35 0 0 0 1775 >> MatSolve 183 1.0 1.0882e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 >> 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 >> MatLUFactorNum 1 1.0 1.3892e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 934 >> MatILUFactorSym 1 1.0 2.1567e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >> MatAssemblyBegin 1 1.0 1.0420e-06 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatAssemblyEnd 1 1.0 6.9049e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatGetRowIJ 1 1.0 3.8500e-07 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatGetOrdering 1 1.0 1.7026e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatLoad 1 1.0 6.6749e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 2 0 0 0 0 2 0 0 0 0 0 >> VecDot 182 1.0 1.9998e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 7 5 0 0 0 7 5 0 0 0 1129 >> VecDotNorm2 91 1.0 6.6214e-02 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 2 5 0 0 0 2 5 0 0 0 3409 >> VecNorm 92 1.0 1.4790e-01 1.0 1.14e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 5 3 0 0 0 5 3 0 0 0 771 >> VecCopy 2 1.0 6.8473e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> VecSet 3 1.0 1.3256e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> VecAXPBYCZ 182 1.0 1.6542e-01 1.0 4.51e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 6 11 0 0 0 6 11 0 0 0 2729 >> VecWAXPY 182 1.0 1.4476e-01 1.0 2.26e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 5 5 0 0 0 5 5 0 0 0 1559 >> VecLoad 2 1.0 1.0104e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> KSPSetUp 1 1.0 9.9204e-03 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> KSPSolve 1 1.0 2.6210e+00 1.0 4.10e+09 1.0 0.0e+00 0.0e+00 >> 0.0e+00 95 100 0 0 0 95 100 0 0 0 1566 >> PCSetUp 1 1.0 3.7232e-02 1.0 1.30e+07 1.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 349 >> PCApply 183 1.0 1.0885e+00 1.0 1.43e+09 1.0 0.0e+00 0.0e+00 >> 0.0e+00 40 35 0 0 0 40 35 0 0 0 1318 >> >> --- Event Stage 1: Unknown >> >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> Object Type Creations Destructions. Reports information only >> for process 0. >> >> --- Event Stage 0: Main Stage >> >> Viewer 4 1 >> Matrix 3 1 >> Vector 9 1 >> Krylov Solver 1 0 >> Preconditioner 1 0 >> Index Set 3 0 >> >> --- Event Stage 1: Unknown >> >> >> ======================================================================================================================== >> Average time to get PetscTime(): 1.51e-08 >> #PETSc Option Table entries: >> -log_view # (source: command line) >> #End of PETSc Option Table entries >> Compiled without FORTRAN kernels >> Compiled with full precision matrices (default) >> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 >> sizeof(PetscScalar) 8 sizeof(PetscInt) 4 >> Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 >> --download-mumps --download-scalapack --with-mpi=1 >> --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 >> ----------------------------------------- >> Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office >> Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 >> Using PETSc directory: /opt/anl/petsc-3.19.5 >> Using PETSc arch: >> ----------------------------------------- >> >> Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings >> -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow >> -fstack-protector -fvisibility=hidden -O2 >> Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall >> -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch >> -Wno-unused-dummy-argument -O2 >> ----------------------------------------- >> >> Using include paths: -I/opt/anl/petsc-3.19.5/include >> -I/opt/anl/mpich/include >> ----------------------------------------- >> >> Using C linker: /opt/anl/mpich/bin/mpicc >> Using Fortran linker: /opt/anl/mpich/bin/mpif90 >> Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib >> -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib >> -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib >> -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 >> -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread >> -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm >> -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath >> ----------------------------------------- >> >> ************************* 2 RANKS ************************************ >> ------------------------------------------------------------------ PETSc >> Performance Summary: >> ------------------------------------------------------------------ >> >> ./petsc-testing on a named ubuntu-office with 2 processors, by chewson >> Fri Sep 8 15:16:43 2023 >> Using Petsc Release Version 3.19.5, unknown >> >> Max Max/Min Avg Total >> Time (sec): 6.167e+00 1.001 6.164e+00 >> Objects: 3.200e+01 1.000 3.200e+01 >> Flops: 2.233e+09 1.000 2.233e+09 4.467e+09 >> Flops/sec: 3.625e+08 1.001 3.623e+08 7.247e+08 >> MPI Msg Count: 2.050e+02 1.000 2.050e+02 4.100e+02 >> MPI Msg Len (bytes): 3.437e+07 1.000 1.676e+05 6.874e+07 >> MPI Reductions: 4.580e+02 1.000 >> >> Flop counting convention: 1 flop = 1 real number operation of type >> (multiply/divide/add/subtract) >> e.g., VecAXPY() for real vectors of length N >> --> 2N flops >> and VecAXPY() for complex vectors of length N >> --> 8N flops >> >> Summary of Stages: ----- Time ------ ----- Flop ------ --- Messages >> --- -- Message Lengths -- -- Reductions -- >> Avg %Total Avg %Total Count >> %Total Avg %Total Count %Total >> 0: Main Stage: 6.1642e+00 100.0% 4.4670e+09 100.0% 4.100e+02 >> 100.0% 1.676e+05 100.0% 4.400e+02 96.1% >> >> >> ------------------------------------------------------------------------------------------------------------------------ >> See the 'Profiling' chapter of the users' manual for details on >> interpreting output. >> Phase summary info: >> Count: number of times phase was executed >> Time and Flop: Max - maximum over all processors >> Ratio - ratio of maximum to minimum over all processors >> Mess: number of messages sent >> AvgLen: average message length (bytes) >> Reduct: number of global reductions >> Global: entire computation >> Stage: stages of a computation. Set stages with PetscLogStagePush() >> and PetscLogStagePop(). >> %T - percent time in this phase %F - percent flop in this >> phase >> %M - percent messages in this phase %L - percent message >> lengths in this phase >> %R - percent reductions in this phase >> Total Mflop/s: 10e-6 * (sum of flop over all processors)/(max time >> over all processors) >> >> ------------------------------------------------------------------------------------------------------------------------ >> Event Count Time (sec) Flop >> --- Global --- --- Stage ---- Total >> Max Ratio Max Ratio Max Ratio Mess AvgLen >> Reduct %T %F %M %L %R %T %F %M %L %R Mflop/s >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> --- Event Stage 0: Main Stage >> >> BuildTwoSided 1 1.0 3.1824e-05 1.0 0.00e+00 0.0 2.0e+00 4.0e+00 >> 1.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatMult 198 1.0 1.3480e+00 1.4 7.76e+08 1.0 4.0e+02 9.4e+04 >> 0.0e+00 19 35 97 54 0 19 35 97 54 0 1151 >> MatSolve 199 1.0 8.9666e-01 1.2 7.75e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 13 35 0 0 0 13 35 0 0 0 1729 >> MatLUFactorNum 1 1.0 7.1852e-03 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 1789 >> MatILUFactorSym 1 1.0 1.0472e-02 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatAssemblyBegin 1 1.0 9.8700e-07 1.4 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatAssemblyEnd 1 1.0 6.8341e-03 1.1 0.00e+00 0.0 4.0e+00 2.3e+04 >> 5.0e+00 0 0 1 0 1 0 0 1 0 1 0 >> MatGetRowIJ 1 1.0 1.9930e-06 6.3 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatGetOrdering 1 1.0 7.4472e-04 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> MatLoad 1 1.0 9.8562e-02 1.0 0.00e+00 0.0 1.0e+01 2.7e+06 >> 1.7e+01 2 0 2 39 4 2 0 2 39 4 0 >> VecDot 198 1.0 2.1037e+00 1.1 1.23e+08 1.0 0.0e+00 0.0e+00 >> 2.0e+02 33 5 0 0 43 33 5 0 0 45 117 >> VecDotNorm2 99 1.0 5.0169e-01 1.2 1.23e+08 1.0 0.0e+00 0.0e+00 >> 9.9e+01 7 5 0 0 22 7 5 0 0 22 489 >> VecNorm 100 1.0 1.3131e+00 1.0 6.20e+07 1.0 0.0e+00 0.0e+00 >> 1.0e+02 21 3 0 0 22 21 3 0 0 23 94 >> VecCopy 2 1.0 7.4971e-04 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> VecSet 202 1.0 8.0035e-02 1.5 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 1 0 0 0 0 1 0 0 0 0 0 >> VecAXPBYCZ 198 1.0 1.2889e-01 1.5 2.46e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 2 11 0 0 0 2 11 0 0 0 3811 >> VecWAXPY 198 1.0 9.1526e-02 1.0 1.23e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 1 5 0 0 0 1 5 0 0 0 2683 >> VecLoad 2 1.0 9.8983e-03 1.0 0.00e+00 0.0 4.0e+00 1.2e+06 >> 1.6e+01 0 0 1 7 3 0 0 1 7 4 0 >> VecScatterBegin 198 1.0 1.2941e-03 1.0 0.00e+00 0.0 4.0e+02 9.4e+04 >> 0.0e+00 0 0 97 54 0 0 0 97 54 0 0 >> VecScatterEnd 198 1.0 7.6160e-01 1.7 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 10 0 0 0 0 10 0 0 0 0 0 >> SFSetGraph 1 1.0 7.6630e-05 1.0 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> SFSetUp 1 1.0 1.2410e-04 1.0 0.00e+00 0.0 4.0e+00 2.3e+04 >> 1.0e+00 0 0 1 0 0 0 0 1 0 0 0 >> SFPack 198 1.0 5.1814e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> SFUnpack 198 1.0 3.8273e-05 1.3 0.00e+00 0.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> KSPSetUp 2 1.0 4.7077e-03 1.1 0.00e+00 0.0 0.0e+00 0.0e+00 >> 2.0e+00 0 0 0 0 0 0 0 0 0 0 0 >> KSPSolve 1 1.0 6.0344e+00 1.0 2.23e+09 1.0 4.0e+02 9.4e+04 >> 4.0e+02 98 100 97 54 87 98 100 97 54 90 738 >> PCSetUp 2 1.0 1.8496e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 695 >> PCSetUpOnBlocks 1 1.0 1.8435e-02 1.0 6.43e+06 1.0 0.0e+00 0.0e+00 >> 0.0e+00 0 0 0 0 0 0 0 0 0 0 697 >> PCApply 199 1.0 9.5103e-01 1.1 7.75e+08 1.0 0.0e+00 0.0e+00 >> 0.0e+00 15 35 0 0 0 15 35 0 0 0 1630 >> >> --- Event Stage 1: Unknown >> >> >> ------------------------------------------------------------------------------------------------------------------------ >> >> Object Type Creations Destructions. Reports information only >> for process 0. >> >> --- Event Stage 0: Main Stage >> >> Viewer 4 1 >> Matrix 5 1 >> Vector 13 2 >> Index Set 5 2 >> Star Forest Graph 1 0 >> Krylov Solver 2 0 >> Preconditioner 2 0 >> >> --- Event Stage 1: Unknown >> >> >> ======================================================================================================================== >> Average time to get PetscTime(): 2.47e-08 >> Average time for MPI_Barrier(): 4.406e-07 >> Average time for zero size MPI_Send(): 4.769e-06 >> #PETSc Option Table entries: >> -log_view # (source: command line) >> #End of PETSc Option Table entries >> Compiled without FORTRAN kernels >> Compiled with full precision matrices (default) >> sizeof(short) 2 sizeof(int) 4 sizeof(long) 8 sizeof(void*) 8 >> sizeof(PetscScalar) 8 sizeof(PetscInt) 4 >> Configure options: --with-debugging=0 --prefix=/opt/anl/petsc-3.19.5 >> --download-mumps --download-scalapack --with-mpi=1 >> --with-mpi-dir=/opt/anl/mpich COPTFLAGS=-O2 CXXOPTFLAGS=-O2 FOPTFLAGS=-O2 >> ----------------------------------------- >> Libraries compiled on 2023-09-08 16:27:49 on ubuntu-office >> Machine characteristics: Linux-6.2.0-26-generic-x86_64-with-glibc2.35 >> Using PETSc directory: /opt/anl/petsc-3.19.5 >> Using PETSc arch: >> ----------------------------------------- >> >> Using C compiler: /opt/anl/mpich/bin/mpicc -fPIC -Wall -Wwrite-strings >> -Wno-unknown-pragmas -Wno-lto-type-mismatch -Wno-stringop-overflow >> -fstack-protector -fvisibility=hidden -O2 >> Using Fortran compiler: /opt/anl/mpich/bin/mpif90 -fPIC -Wall >> -ffree-line-length-none -ffree-line-length-0 -Wno-lto-type-mismatch >> -Wno-unused-dummy-argument -O2 >> ----------------------------------------- >> >> Using include paths: -I/opt/anl/petsc-3.19.5/include >> -I/opt/anl/mpich/include >> ----------------------------------------- >> >> Using C linker: /opt/anl/mpich/bin/mpicc >> Using Fortran linker: /opt/anl/mpich/bin/mpif90 >> Using libraries: -Wl,-rpath,/opt/anl/petsc-3.19.5/lib >> -L/opt/anl/petsc-3.19.5/lib -lpetsc -Wl,-rpath,/opt/anl/petsc-3.19.5/lib >> -L/opt/anl/petsc-3.19.5/lib -Wl,-rpath,/opt/anl/mpich/lib >> -L/opt/anl/mpich/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11 >> -L/usr/lib/gcc/x86_64-linux-gnu/11 -ldmumps -lmumps_common -lpord -lpthread >> -lscalapack -llapack -lblas -lm -lX11 -lmpifort -lmpi -lgfortran -lm >> -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -lquadmath >> ----------------------------------------- >> >> Chris >> >> >> On Fri, Sep 8, 2023 at 3:00?PM Barry Smith wrote: >> >>> >>> It would be very helpful if you could run on 1 and 2 ranks with >>> -log_view and send all the output. >>> >>> >>> >>> On Sep 8, 2023, at 4:52 PM, Chris Hewson wrote: >>> >>> Hi There, >>> >>> I am trying to solve a linear problem and am having an issue when I use >>> more MPI processes with the KSPsolve slowing down considerably the more >>> processes I add. >>> >>> The matrix itself is 620100 X 620100 with ~5 million non-zero entries, I >>> am using petsc version 3.19.5 and have tried with a couple different >>> versions of mpich getting the same behavior (v4.1.2 w/ device ch4:ofi and >>> v3.3.2 w/ ch3:sock). >>> >>> In testing, I've noticed the following trend for speed for the KSPSolve >>> function call: >>> 1 core: 4042 ms >>> 2 core: 7085 ms >>> 4 core: 26573 ms >>> 8 core: 65745 ms >>> 16 core: 149283 ms >>> >>> This was all done on a single node machine w/ 16 non-hyperthreaded >>> cores. We solve quite a few different matrices with PETSc using MPI and >>> haven't noticed an impact like this on performance before. >>> >>> I am very confused by this and am a little stumped at the moment as to >>> why this was happening. I've been using the KSPBCGS solver to solve the >>> problem. I have tried with multiple different solvers and pre-conditioners >>> (we usually don't use a pre-conditioner for this part of our code). >>> >>> It did seem that using the piped BCGS solver did help improve the >>> parallel speed slightly (maybe 15%), but it still doesn't come close to the >>> single threaded speed. >>> >>> I'll attach a link to a folder that contains the specific A, x and b >>> matrices for this problem, as well as a main.cpp file that I was using for >>> testing. >>> >>> >>> https://drive.google.com/drive/folders/1CEDinKxu8ZbKpLtwmqKqP1ZIDG7JvDI1?usp=sharing >>> >>> I was testing this in our main code base, but don't include that here, >>> and observe very similar speed results to the ones above. We do use Metis >>> to graph partition in our own code and checked the vector and matrix >>> partitioning and that all made sense. I could be doing the partitioning >>> incorrectly in the example (not 100% sure how it works with the viewer/load >>> functions). >>> >>> Any insight or thoughts on this would be greatly appreciated. >>> >>> Thanks, >>> >>> *Chris Hewson* >>> Senior Reservoir Simulation Engineer >>> ResFrac >>> +1.587.575.9792 >>> >>> >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From inturu.srinivas2020 at vitstudent.ac.in Sat Sep 9 00:24:36 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Sat, 9 Sep 2023 10:54:36 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <58283126-56CF-4741-B264-3C7E68AA3655@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> <58283126-56CF-4741-B264-3C7E68AA3655@petsc.dev> Message-ID: I am sending the outputs available in the directory /usr/local/MATLAB/R2020b/extern/bin/glnxa64. Please find the attached files. Thanks and regards Srinivas On Fri, Sep 8, 2023 at 11:58?PM Barry Smith wrote: > > I expect a libmx.so in the > directory /usr/local/MATLAB/R2020b/extern/bin/glnxa64. Do an ls on that > directory and send all the output > > > > On Sep 8, 2023, at 10:33 AM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > Hi Barry, > > I tried to run Matlab Engine C example provided in the link " > https://in.mathworks.com/help/matlab/matlab_external/build-unix-engine-example.html > " > > *in Matlab:* copyfile(fullfile(matlabroot,'extern','examples','eng_mat','engdemo.c'),'.','f') > mex -v -client engine engdemo.c > > *in linux terminal :* LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 > > export LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH > > *./engdemo* > ./engdemo: error while loading shared libraries: libmx.so: cannot open shared object file: No such file or directory > > how to sort out this error? Is this the right way to check MatlabEngine with C? > > Thanks and regards > > Srinivas > > > > On Wed, Sep 6, 2023 at 11:47?PM Barry Smith wrote: > >> >> Ok, so the C++ binding for Matlab engine is working on your machine. >> PETSc uses the C binding which links against different libraries but, one >> would think the C binding would work for sure if the C++ binding works. Can >> you try a Matlab Engine C example provided by Matlab? >> >> >> >> >> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >> Hi Amneet, >> >> I repeated the same procedure again and this time it is working. >> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp >> -lMatlabDataArray -lMatlabEngine* >> >> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >> *$export LD_LIBRARY_PATH* >> *$./a.out* >> Square root of -2 is 0 + 1.41421i >> Square root of 2 is 1.41421 + 0i >> Square root of 6 is 2.44949 + 0i >> Square root of 8 is 2.82843 + 0i >> I don't know how it is working this time? >> >> Thanks and regards >> Srinivas >> >> >> On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >>> Hi Amneet, >>> I tried the following example to run a matlab engine. >>> >>> #include "MatlabDataArray.hpp" >>> #include "MatlabEngine.hpp" >>> #include >>> void callSQRT() { >>> >>> using namespace matlab::engine; >>> >>> // Start MATLAB engine synchronously >>> std::unique_ptr matlabPtr = startMATLAB(); >>> >>> //Create MATLAB data array factory >>> matlab::data::ArrayFactory factory; >>> >>> // Define a four-element typed array >>> matlab::data::TypedArray const argArray = >>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >>> >>> // Call MATLAB sqrt function on the data array >>> matlab::data::Array const results = matlabPtr->feval(u"sqrt", >>> argArray); >>> >>> // Display results >>> for (int i = 0; i < results.getNumberOfElements(); i++) { >>> double a = argArray[i]; >>> std::complex v = results[i]; >>> double realPart = v.real(); >>> double imgPart = v.imag(); >>> std::cout << "Square root of " << a << " is " << >>> realPart << " + " << imgPart << "i" << std::endl; >>> } >>> } >>> >>> int main() { >>> callSQRT(); >>> return 0; >>> } >>> >>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp >>> -lMatlabDataArray -lMatlabEngine* >>> >>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >>> *$export LD_LIBRARY_PATH* >>> *$./a.out* >>> Starting >>> Error: The import statement 'import matlab.internal.engine.input' cannot >>> be found or cannot be imported. Imported names must end with '.*' or be >>> fully qualified. >>> >>> terminate called after throwing an instance of >>> 'matlab::engine::EngineException' >>> what(): MATLAB process cannot be created. >>> Aborted (core dumped) >>> >>> I got the above error for Matlab R2020b. Please help me to sort out this. >>> >>> Thanks and regards >>> Srinivas >>> >>> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla >>> wrote: >>> >>>> BTW, what Barry is suggesting is the following: >>>> >>>> Compile a sample code with a command line this: >>>> >>>> >>>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>> >>>> >>>> This command is provided here: >>>> >>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>>> >>>> >>>> A sample MATLAB code is here: >>>> >>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>>> >>>> >>>> (You can just pick a few lines of code from here to create a barebone example) >>>> >>>> >>>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >>>> wrote: >>>> >>>>> Srinivas --- Do you have a different version of MATLAB that you can >>>>> install? If your organization has a MATLAB license, you can install recent >>>>> versions of MATLAB from mathworks.com >>>>> >>>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>>>> >>>>>> >>>>>> Ok, I have no suggestions. It seems to be more an issue with the >>>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>>>> (in the Matlab documentation) and try it to see if it works. >>>>>> >>>>>> Barry >>>>>> >>>>>> >>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>> >>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>> I got the same errors for petsc 3.17.5 >>>>>> >>>>>> >>>>>> *make all* >>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> MEX completed successfully. >>>>>> Building with 'gcc'. >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>> In function ?PetscBinaryWrite?: >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>> warning: ?err? may be used uninitialized in this function >>>>>> [-Wmaybe-uninitialized] >>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>> | ^ >>>>>> >>>>>> MEX completed successfully. >>>>>> ========================================= >>>>>> ========================================= >>>>>> Now to check if the libraries are working do: >>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>> >>>>>> *make test query=requires queryval=matlab >>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>> queryval=matlab query=requires >>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>> -------------------------------------------------------------- >>>>>> # [0]PETSC ERROR: Error in external library >>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>> shooting. >>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>> Tue Sep 5 21:39:22 2023 >>>>>> # [0]PETSC ERROR: Configure options >>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>> --known-64-bit-blas-indices=1 >>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>> # [0]PETSC ERROR: #9 main() at >>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>> # with errorcode 85. >>>>>> # >>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>> # You may or may not see output from other processes, depending on >>>>>> # exactly when Open MPI kills them. >>>>>> # >>>>>> -------------------------------------------------------------------------- >>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>> >>>>>> >>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>> # >>>>>> # To rerun failed tests: >>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>>>> >>>>>>> >>>>>>> The error is occuring during >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>>>> stdout and stdin from the Matlab session that is launched to the >>>>>>> executable. >>>>>>> >>>>>>> You can try the following. In 3.17.5 edit the >>>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>> >>>>>>> e->ep = engOpen(buffer); >>>>>>> >>>>>>> replace it with >>>>>>> >>>>>>> e->ep = engOpen(""); >>>>>>> >>>>>>> Now in the PETSc directory do make all (it should recompile one >>>>>>> file) and then run the >>>>>>> >>>>>>> make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>>>> >>>>>>> again >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via >>>>>>> petsc-users wrote: >>>>>>> >>>>>>> Hi Amneeth, >>>>>>> >>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>> >>>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>> >>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>> The version of PETSc you are using is out-of-date, we recommend >>>>>>> updating to the new release >>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>> https://petsc.org/release/download/ >>>>>>> >>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>> >>>>>>> ============================================================================================= >>>>>>> Configuring PETSc to compile on your system >>>>>>> >>>>>>> >>>>>>> ============================================================================================= >>>>>>> Compilers: >>>>>>> >>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>>>> -fvisibility=hidden -O3 >>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>> Linkers: >>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>> BlasLapack: >>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>

to control the number of threads >>>>>>> uses 8 byte integers >>>>>>> MPI: >>>>>>> Version: 3 >>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>> Implementation: openmpi >>>>>>> OMPI_VERSION: 4.0.3 >>>>>>> pthread: >>>>>>> cmake: >>>>>>> Version: 3.16.3 >>>>>>> /usr/bin/cmake >>>>>>> regex: >>>>>>> Matlab: >>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>> /usr/local/MATLAB/R2020b >>>>>>> MatlabEngine: >>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>> Language used to compile PETSc: C >>>>>>> PETSc: >>>>>>> PETSC_ARCH: linux-opt >>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>> Prefix: >>>>>>> Scalar type: real >>>>>>> Precision: double >>>>>>> Support for __float128 >>>>>>> Integer size: 4 bytes >>>>>>> Single library: yes >>>>>>> Shared libraries: yes >>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>> Using GNU make: /usr/bin/make >>>>>>> >>>>>>> xxx=========================================================================xxx >>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 >>>>>>> PETSC_ARCH=linux-opt all >>>>>>> >>>>>>> xxx=========================================================================xxx >>>>>>> >>>>>>> *$make* >>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> ========================================= >>>>>>> ========================================= >>>>>>> Now to check if the libraries are working do: >>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>>>> check >>>>>>> >>>>>>> *$make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>>> /usr/bin/python3 >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>>>> --testdir=./linux-opt/tests >>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>> queryval=matlab query=requires >>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> -------------------------------------------------------------- >>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>>> shooting. >>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Tue Sep 5 10:15:57 2023 >>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>> # [0]PETSC ERROR: #9 main() at >>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>> # with errorcode 85. >>>>>>> # >>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>> # You may or may not see output from other processes, depending on >>>>>>> # exactly when Open MPI kills them. >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>> >>>>>>> >>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> # >>>>>>> # To rerun failed tests: >>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> >>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>> >>>>>>> How to check error info and proceed further? >>>>>>> >>>>>>> Thanks and regards >>>>>>> Srinivas >>>>>>> >>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>>>> wrote: >>>>>>> >>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure >>>>>>>> options that Satish mentioned? >>>>>>>> >>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>>>> petsc-users wrote: >>>>>>>> >>>>>>>>> Sorry for missing that. >>>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>> -nosplash* >>>>>>>>> >>>>>>>>> < M A T L A B (R) > >>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>> November 23, 2020 >>>>>>>>> >>>>>>>>> >>>>>>>>> To get started, type doc. >>>>>>>>> For product information, visit www.mathworks.com. >>>>>>>>> >>>>>>>>> Thanks and regards >>>>>>>>> Srinivas >>>>>>>>> >>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> You are missing one more step: >>>>>>>>>> >>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>> >>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>> >>>>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>> >>>>>>>>>> Satish >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>> > Hi Sathish, >>>>>>>>>> > >>>>>>>>>> > I tried the following procedure >>>>>>>>>> > >>>>>>>>>> > *$make * >>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>> socket\n"); >>>>>>>>>> > | ^ >>>>>>>>>> > >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > Building with 'gcc'. >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>> socket\n"); >>>>>>>>>> > | ^ >>>>>>>>>> > >>>>>>>>>> > MEX completed successfully. >>>>>>>>>> > ========================================= >>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>>>> check >>>>>>>>>> > >>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>> queryval=matlab >>>>>>>>>> > query=requires >>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> > TEST >>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>> vit Mon Sep >>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>> vit Mon Sep >>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>> > >>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>>>> Violation, >>>>>>>>>> > probably memory access out of range >>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>>>> -on_error_attach_debugger >>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>>>> Apple Mac OS >>>>>>>>>> > X to find memory corruption errors >>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>>>> recompile, link, >>>>>>>>>> > and run >>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>> vit Mon Sep >>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in >>>>>>>>>> unknown file >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>> > # >>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>> processes. >>>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>>> on >>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>> > CC >>>>>>>>>> > >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>> > CLINKER >>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > TEST >>>>>>>>>> > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>> code: 124 >>>>>>>>>> > # Running problem 5 >>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>> MB108SMEC028 by >>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>> > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send entire >>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>> > # with errorcode 126076. >>>>>>>>>> > # >>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>> processes. >>>>>>>>>> > # You may or may not see output from other processes, depending >>>>>>>>>> on >>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>> > # >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>> Command failed >>>>>>>>>> > so no diff >>>>>>>>>> > >>>>>>>>>> > # ------------- >>>>>>>>>> > # Summary >>>>>>>>>> > # ------------- >>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>> > # >>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>> > # >>>>>>>>>> > # To rerun failed tests: >>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>> > # >>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec >>>>>>>>>> / 0.01 sec >>>>>>>>>> > >>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>> -Wwrite-strings >>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>> -Wno-strict-aliasing >>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>> matlab_ls_test.c >>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>>>>>> -lmex -lmx >>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>> -lmpi_mpifh >>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>> -lpthread -lquadmath >>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>> > >>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>> ./matlab_ls_test >>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>> processors = 1 >>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>> > Running problem 5 >>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>> 140155238476992 >>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>> command >>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>>> -nosplash >>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > [0]PETSC ERROR: See >>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > for trouble shooting. >>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send entire >>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>> > with errorcode 126076. >>>>>>>>>> > >>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>> processes. >>>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>> > >>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>> > >>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>>>> wrote: >>>>>>>>>> > >>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>> > > >>>>>>>>>> > > cd $HOME >>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>> > > >>>>>>>>> DATAFILESPATH - or set >>>>>>>>>> > > manually with make> >>>>>>>>>> > > >>>>>>>>>> > > make test query=requires queryval=matlab >>>>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>>>> > > >>>>>>>>>> > > Satish >>>>>>>>>> > > >>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>> > > >>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>>>> > > > >>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>> > > > > >>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I >>>>>>>>>> do not have >>>>>>>>>> > > any >>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>>>> help me how to >>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>> > > > > >>>>>>>>>> > > > >>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, >>>>>>>>>> we point to >>>>>>>>>> > > this >>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>>>> don't have those >>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>> > > > is why I suggested just using a different matrix, or >>>>>>>>>> running a problem >>>>>>>>>> > > you >>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>> > > > >>>>>>>>>> > > > Thanks, >>>>>>>>>> > > > >>>>>>>>>> > > > Matt >>>>>>>>>> > > > >>>>>>>>>> > > > >>>>>>>>>> > > > > Thanks and regards >>>>>>>>>> > > > > Srinivas. >>>>>>>>>> > > > > >>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>>>> knepley at gmail.com> >>>>>>>>>> > > wrote: >>>>>>>>>> > > > > >>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 >>>>>>>>>> via >>>>>>>>>> > > petsc-users < >>>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>>>> > > > >> >>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>>>> are giving me >>>>>>>>>> > > to >>>>>>>>>> > > > >>> sort this out. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed >>>>>>>>>> to build >>>>>>>>>> > > Petsc >>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$./configure >>>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> It appears you >>>>>>>>>> do not have >>>>>>>>>> > > valgrind >>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>>>> www.valgrind.org >>>>>>>>>> > > > >>> Or install >>>>>>>>>> > > valgrind-devel or >>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> =============================================================================== >>>>>>>>>> > > > >>> Compilers: >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> C Compiler: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > -fPIC >>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> > > > >>> C++ Compiler: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>> > > > >>> Fortran Compiler: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu >>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> > > > >>> Linkers: >>>>>>>>>> > > > >>> Shared linker: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > -shared >>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> Dynamic linker: >>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > -shared >>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>> > > > >>> make: >>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>>>> -lpthread >>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>> -omp_num_threads >>>>>>>>>> > >

to >>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>> > > > >>> MPI: >>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>> > > --oversubscribe >>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>> > > > >>> pthread: >>>>>>>>>> > > > >>> cmake: >>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>> > > > >>> regex: >>>>>>>>>> > > > >>> Matlab: >>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>> > > > >>> Library: >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>>>>>>>> -lmex -lmx -lmat >>>>>>>>>> > > -lut >>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>> > > > >>> PETSc: >>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>> > > > >>> Precision: double >>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries >>>>>>>>>> with: >>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>>>> -licui18n -licuuc as >>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$make* >>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>> to socket\n"); >>>>>>>>>> > > > >>> | ^ >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>> to socket\n"); >>>>>>>>>> > > > >>> | ^ >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>> > > > >>> ========================================= >>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>> > > > >>> =============================================== >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> > > > >>> TEST >>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > > > >>> >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>>>> defined, so it >>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of >>>>>>>>>> yours. >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> Thanks, >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> Matt >>>>>>>>>> > > > >> >>>>>>>>>> > > > >> >>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> for trouble >>>>>>>>>> > > > >>> shooting. >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>>> 2020 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>> > > Sun >>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() >>>>>>>>>> line 1444 in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line >>>>>>>>>> 1511 in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send >>>>>>>>>> > > > >>> entire error message to >>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>> MPI_COMM_SELF >>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>> MPI processes. >>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>> depending on >>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>>>> no diff >>>>>>>>>> > > > >>> CC >>>>>>>>>> > > > >>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>> > > > >>> CLINKER >>>>>>>>>> > > > >>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > > > >>> TEST >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> # Error >>>>>>>>>> > > code: 124 >>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>> > > > >>> >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> for trouble >>>>>>>>>> > > > >>> shooting. >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, >>>>>>>>>> 2020 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> --with-debugging=0 >>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>>>>>>> in >>>>>>>>>> > > > >>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>> -------send >>>>>>>>>> > > > >>> entire error message to >>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>> MPI_COMM_SELF >>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>> MPI processes. >>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>> depending on >>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>> SKIP Command >>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> # ------------- >>>>>>>>>> > > > >>> # Summary >>>>>>>>>> > > > >>> # ------------- >>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>> > > > >>> # >>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>>> 0.02 sec / >>>>>>>>>> > > 0.02 sec >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>> > > -Wwrite-strings >>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>> -fstack-protector >>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>> matlab_ls_test.c >>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>> > > > >>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>>>> -leng -lmex >>>>>>>>>> > > -lmx >>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>> -lpthread >>>>>>>>>> > > -lquadmath >>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b >>>>>>>>>> version. >>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. >>>>>>>>>> Please find the >>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>> > > > >>> Srinivas >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>>>> balay at mcs.anl.gov> >>>>>>>>>> > > wrote: >>>>>>>>>> > > > >>> >>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional >>>>>>>>>> info - and debug >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> Satish >>>>>>>>>> > > > >>>> ---------- >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>> > > -Wall >>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > -fstack-protector >>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>> > > > >>>> >>>>>>>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>>>> -lpthread -lm -leng >>>>>>>>>> > > -lmex >>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>>>> -ldl -lmpifort >>>>>>>>>> > > -lmpi >>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>> -lstdc++ -ldl -o >>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>> ./matlab_ls_test >>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>>>> number of >>>>>>>>>> > > processors >>>>>>>>>> > > > >>>> = 1 >>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely >>>>>>>>>> is NIS >>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: >>>>>>>>>> compute-386-07 >>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>> 1140850689 >>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>>>> with command >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>>>> string: >>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating >>>>>>>>>> Matlab string: >>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>> > > > >>>> 5 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>>>> works for you >>>>>>>>>> > > - on >>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>>>> MathWorks, Inc. >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) >>>>>>>>>> 64-bit (glnxa64) >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>>>> [reverting >>>>>>>>>> > > thread >>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>>> > > corresponding >>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on >>>>>>>>>> Ubuntu-20.04, >>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git >>>>>>>>>> branch >>>>>>>>>> > > > >>>> > main >>>>>>>>>> > > > >>>> > release >>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module >>>>>>>>>> load >>>>>>>>>> > > matlab/R2021a >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>>>> matlab >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>> ./configure >>>>>>>>>> > > > >>>> >>>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>> > > -Wall >>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > -fstack-protector >>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>> 9.4.0 >>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > -fstack-protector >>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>> 9.4.0 >>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>> > > -Wall >>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>> > > -shared -fPIC >>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>> > > > >>>> >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>> > > -shared -fPIC >>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ >>>>>>>>>> -ldl >>>>>>>>>> > > > >>>> > make: >>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>> > > > >>>> > Library: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>> -omp_num_threads >>>>>>>>>> > >

>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>> > > > >>>> > regex: >>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>> > > > >>>> > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>> > > > >>>> > Library: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries >>>>>>>>>> with: >>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>> writing to >>>>>>>>>> > > socket\n"); >>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>> function >>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>> writing to >>>>>>>>>> > > socket\n"); >>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>>> > > query=requires >>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed >>>>>>>>>> so no diff >>>>>>>>>> > > > >>>> > CC >>>>>>>>>> > > > >>>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>> > > > >>>> >>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>>> > not ok >>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>> > > code: >>>>>>>>>> > > > >>>> 1 >>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> # SKIP >>>>>>>>>> > > Command >>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make >>>>>>>>>> test >>>>>>>>>> > > query=requires >>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>> > > > >>>> > TEST >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>>> > ok >>>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>> > > > >>>> > # >>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>>>> 15.190000000000001 >>>>>>>>>> > > sec >>>>>>>>>> > > > >>>> > # >>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>> > > > >>>> > # >>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>> > > 7.54 >>>>>>>>>> > > > >>>> sec >>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>> > > > >>>> > >>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>>>> tried to >>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>>>> successful. After >>>>>>>>>> > > > >>>> running make >>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>>>> message. >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > not ok >>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error >>>>>>>>>> Message >>>>>>>>>> > > > >>>> > > >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>> Aug 01, 2020 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>>>> named >>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>> > > > >>>> > > --with-x=0 >>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>> line 67 in >>>>>>>>>> > > > >>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>> Message >>>>>>>>>> > > -------send >>>>>>>>>> > > > >>>> entire >>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>>> > > # >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>> MPI_COMM_SELF >>>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>>> > > > >>>> > > # >>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill >>>>>>>>>> all MPI >>>>>>>>>> > > > >>>> processes. >>>>>>>>>> > > > >>>> > > # You may or may not see output from other >>>>>>>>>> processes, depending >>>>>>>>>> > > on >>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>>> > > > >>>> > > # >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > Thanks >>>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>>>>>> > > > >>>> > > >>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > > >>>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>>> > > > >>>> > > > >>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > > >>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>>>>>> 20PHD0548 via >>>>>>>>>> > > > >>>> petsc-users < >>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>>>>>> > > > >>>> > > > >>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>>> > > > >>>> > > >> >>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>>>>>> balay at mcs.anl.gov> >>>>>>>>>> > > > >>>> wrote: >>>>>>>>>> > > > >>>> > > >> >>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if >>>>>>>>>> hypre will work >>>>>>>>>> > > > >>>> here]. >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> > > >>> ./configure >>>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>>> via >>>>>>>>>> > > petsc-users >>>>>>>>>> > > > >>>> wrote: >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>>> > > balay at mcs.anl.gov> >>>>>>>>>> > > > >>>> wrote: >>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work >>>>>>>>>> in this mode. >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>>>>>> dependency/conflicts >>>>>>>>>> > > across >>>>>>>>>> > > > >>>> packages] >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>>>>>> petsc-users wrote: >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit >>>>>>>>>> integers] conflict >>>>>>>>>> > > with >>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>>>>>> blas/lapack with >>>>>>>>>> > > > >>>> matlab - to >>>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>>>>>> 20PHD0548 via >>>>>>>>>> > > > >>>> petsc-users >>>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>>>>>> MATLAB is not >>>>>>>>>> > > > >>>> working. It is >>>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 >>>>>>>>>> versions. >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>>>>>> cluster with >>>>>>>>>> > > > >>>> libmesh and >>>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I >>>>>>>>>> tried without >>>>>>>>>> > > > >>>> linking >>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while >>>>>>>>>> configuring >>>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>>> > > > >>>> > > >>> that >>>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>>> > > > >>>> > > >>> > > > > was not found but >>>>>>>>>> --enable-petsc-required is >>>>>>>>>> > > specified. >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for >>>>>>>>>> libmesh with >>>>>>>>>> > > > >>>> PETSc and >>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for >>>>>>>>>> complicated >>>>>>>>>> > > geometries >>>>>>>>>> > > > >>>> it is >>>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh >>>>>>>>>> construct. >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these >>>>>>>>>> various >>>>>>>>>> > > things >>>>>>>>>> > > > >>>> and ended >>>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed >>>>>>>>>> further to do my >>>>>>>>>> > > > >>>> research work. >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon >>>>>>>>>> as possible. >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet >>>>>>>>>> Bhalla < >>>>>>>>>> > > > >>>> mail2amneet at gmail.com> >>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>>>>>>> libMesh for >>>>>>>>>> > > the >>>>>>>>>> > > > >>>> WEC >>>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that >>>>>>>>>> builds with >>>>>>>>>> > > > >>>> Matlab. >>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for >>>>>>>>>> wanting to build >>>>>>>>>> > > > >>>> libMesh? >>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM >>>>>>>>>> INTURU SRINIVAS >>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>> > > > >>>> > > >>> > > > > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 >>>>>>>>>> by removing all >>>>>>>>>> > > > >>>> occurrences >>>>>>>>>> > > > >>>> > > >>> of >>>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When >>>>>>>>>> I ran "make >>>>>>>>>> > > test" >>>>>>>>>> > > > >>>> got the >>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>> --------------------- Error >>>>>>>>>> > > Message >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>>>>> library >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>>>> MATLAB engine >>>>>>>>>> > > on >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > > > >>>> for >>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>>>> Version 3.13.4, >>>>>>>>>> > > Aug >>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test >>>>>>>>>> on a >>>>>>>>>> > > linux-debug >>>>>>>>>> > > > >>>> named >>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>>>>>>> --download-fblaslapack=1 >>>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>>>> PetscMatlabEngineCreate() >>>>>>>>>> > > line >>>>>>>>>> > > > >>>> 67 in >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line >>>>>>>>>> 126 in >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option >>>>>>>>>> Table entries: >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>> ----------------End of Error >>>>>>>>>> > > > >>>> Message >>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 >>>>>>>>>> in communicator >>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>>>> Open MPI to >>>>>>>>>> > > kill >>>>>>>>>> > > > >>>> all MPI >>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output >>>>>>>>>> from other >>>>>>>>>> > > processes, >>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>> --------------------- Error >>>>>>>>>> > > Message >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> >>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external >>>>>>>>>> library >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>>>> MATLAB engine >>>>>>>>>> > > on >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>> > > > >>>> for >>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>>>> Version 3.13.4, >>>>>>>>>> > > Aug >>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test >>>>>>>>>> on a >>>>>>>>>> > > linux-opt >>>>>>>>>> > > > >>>> named >>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>>>> PetscMatlabEngineCreate() >>>>>>>>>> > > line >>>>>>>>>> > > > >>>> 67 in >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line >>>>>>>>>> 126 in >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option >>>>>>>>>> Table entries: >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>> ----------------End of Error >>>>>>>>>> > > > >>>> Message >>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 >>>>>>>>>> in communicator >>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>>>> Open MPI to >>>>>>>>>> > > kill >>>>>>>>>> > > > >>>> all MPI >>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output >>>>>>>>>> from other >>>>>>>>>> > > processes, >>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc >>>>>>>>>> 3.17.5 >>>>>>>>>> > > version. I >>>>>>>>>> > > > >>>> am >>>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both >>>>>>>>>> petsc 3.13.4 and >>>>>>>>>> > > > >>>> petsc >>>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM >>>>>>>>>> Satish Balay < >>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not >>>>>>>>>> petsc's >>>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you >>>>>>>>>> have: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>> > > -leng >>>>>>>>>> > > > >>>> -lmex >>>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and >>>>>>>>>> matlab-R2022a) - we are >>>>>>>>>> > > seeing: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n >>>>>>>>>> -licuuc" are not >>>>>>>>>> > > > >>>> preset here. >>>>>>>>>> > > > >>>> > > >>> This >>>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab >>>>>>>>>> versions. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>>>>>>> -licudata >>>>>>>>>> > > -licui18n >>>>>>>>>> > > > >>>> -licuuc" >>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU >>>>>>>>>> SRINIVAS 20PHD0548 >>>>>>>>>> > > via >>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while >>>>>>>>>> building >>>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building >>>>>>>>>> libmesh with >>>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>>>> > > successfully. >>>>>>>>>> > > > >>>> But >>>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>>>>>>> Satish Balay < >>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log >>>>>>>>>> from both >>>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the >>>>>>>>>> logs >>>>>>>>>> > > friendly to >>>>>>>>>> > > > >>>> mailing >>>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with >>>>>>>>>> 3.17? [or >>>>>>>>>> > > 3.19?] >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU >>>>>>>>>> SRINIVAS >>>>>>>>>> > > 20PHD0548 >>>>>>>>>> > > > >>>> via >>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log >>>>>>>>>> file while >>>>>>>>>> > > building >>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment >>>>>>>>>> and do the >>>>>>>>>> > > needful. >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at >>>>>>>>>> 10:19?AM INTURU >>>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>>>>>>> > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. >>>>>>>>>> During >>>>>>>>>> > > building >>>>>>>>>> > > > >>>> of >>>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at >>>>>>>>>> 9:43?PM Satish >>>>>>>>>> > > > >>>> Balay < >>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> https://ibamr.github.io/linux says >>>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>>>>>>> petsc-3.17.5? >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, >>>>>>>>>> INTURU SRINIVAS >>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc >>>>>>>>>> with MATLAB for >>>>>>>>>> > > > >>>> working on >>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>>>>>>> building the >>>>>>>>>> > > PETSc, >>>>>>>>>> > > > >>>> using the >>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export >>>>>>>>>> PETSC_ARCH=linux-debug >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> --download-fblaslapack=1 \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following >>>>>>>>>> error >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>>>> `EvaluateResidual': >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>>>> `EvaluateJacobian': >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> > > >>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld >>>>>>>>>> returned 1 exit >>>>>>>>>> > > > >>>> status >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>>>>>>> [gmakefile.test:185: >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>> > > > >>>> >>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>>>>>>> unfinished >>>>>>>>>> > > jobs.... >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve >>>>>>>>>> this issue >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent >>>>>>>>>> from Vellore >>>>>>>>>> > > > >>>> Institute of >>>>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may >>>>>>>>>> contain legally >>>>>>>>>> > > > >>>> protected >>>>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>>>>>>> Institute of >>>>>>>>>> > > > >>>> Technology?. >>>>>>>>>> > > > >>>> > > >>> If >>>>>>>>>> > > > >>>> > > >>> > > you are >>>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you >>>>>>>>>> should not >>>>>>>>>> > > > >>>> disseminate, >>>>>>>>>> > > > >>>> > > >>> distribute >>>>>>>>>> > > > >>>> > > >>> > > or copy >>>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. 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If >>>>>>> you have received this email in error, please promptly notify the sender by >>>>>>> reply email and delete the original email and any backup copies without >>>>>>> reading them.* >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> *Disclaimer:This message was sent from Vellore Institute of >>>>>> Technology. The contents of this email may contain legally protected >>>>>> confidential or privileged information of ?Vellore Institute of >>>>>> Technology?. If you are not the intended recipient, you should not >>>>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>>>> immediately and destroy all copies of this message and any attachments. If >>>>>> you have received this email in error, please promptly notify the sender by >>>>>> reply email and delete the original email and any backup copies without >>>>>> reading them.* >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> --Amneet >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> --Amneet >>>> >>>> >>>> >>>> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> >> >> > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? 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Name: libMatlabDataArray.so Type: application/octet-stream Size: 130176 bytes Desc: not available URL: From mfadams at lbl.gov Sat Sep 9 07:40:19 2023 From: mfadams at lbl.gov (Mark Adams) Date: Sat, 9 Sep 2023 08:40:19 -0400 Subject: [petsc-users] Compute integral using DMPlexComputeIntegralFEM In-Reply-To: References: Message-ID: PetscFECreateLagrange(comm, dim, 1, simplex, 1, PETSC_DETERMINE, &fe); The default may be qorder = 0. Replace PETSC_DETERMINE with 1, 2, etc, and see. Thanks, Mark On Fri, Sep 8, 2023 at 6:26?PM David Andrs wrote: > Hi all! > > I am trying to use DMPlexComputeIntegralFEM to compute an integral > $\int_\Omega u d\Omega$. My domain is a square (-1, 1)^2 (2x2 QUAD4 > elements), I add first order Lagrange FE field on it, set the solution > vector (computed by a previous simulation). > > The value I am seeing computed by PETSc is -4, but the hand-calculated > value of this integral is -4.6. I also checked this in paraview using the > ?Integrate Variables? filter and it also returns -4.6 (this was to double > check that my hand-calculated value is correct). > > So, I must be missing something obvious in my code. Attached is the > minimal PETSc code to show what I am doing. This is against PETSc 3.19.4. > > Thanks in advance for your help, > > David > > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrsd at gmail.com Sat Sep 9 08:01:06 2023 From: andrsd at gmail.com (David Andrs) Date: Sat, 9 Sep 2023 07:01:06 -0600 Subject: [petsc-users] Compute integral using DMPlexComputeIntegralFEM In-Reply-To: References: Message-ID: Hi Mark! > On Sep 9, 2023, at 06:40, Mark Adams wrote: > > PetscFECreateLagrange(comm, dim, 1, simplex, 1, PETSC_DETERMINE, &fe); > > The default may be qorder = 0. > Replace PETSC_DETERMINE with 1, 2, etc, and see. With PETSC_DETERMINE, I see 4 evaluations of the function per element, so I think that works as expected. Even if I force a higher quadrature order, I still see the wrong value. ? David > > Thanks, > Mark > > > On Fri, Sep 8, 2023 at 6:26?PM David Andrs > wrote: >> Hi all! >> >> I am trying to use DMPlexComputeIntegralFEM to compute an integral $\int_\Omega u d\Omega$. My domain is a square (-1, 1)^2 (2x2 QUAD4 elements), I add first order Lagrange FE field on it, set the solution vector (computed by a previous simulation). >> >> The value I am seeing computed by PETSc is -4, but the hand-calculated value of this integral is -4.6. I also checked this in paraview using the ?Integrate Variables? filter and it also returns -4.6 (this was to double check that my hand-calculated value is correct). >> >> So, I must be missing something obvious in my code. Attached is the minimal PETSc code to show what I am doing. This is against PETSc 3.19.4. >> >> Thanks in advance for your help, >> >> David >> >> -- >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Sat Sep 9 13:21:59 2023 From: bsmith at petsc.dev (Barry Smith) Date: Sat, 9 Sep 2023 14:21:59 -0400 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> <58283126-56CF-4741-B264-3C7E68AA3655@petsc.dev> Message-ID: <3AF4D6DD-D536-4A17-8C07-2F7FBB34078A@petsc.dev> I don't understand. The directory only has two files in it? They begin with libMatlab? My directory has over 100 files. Barry > On Sep 9, 2023, at 1:24 AM, INTURU SRINIVAS 20PHD0548 wrote: > > I am sending the outputs available in the directory /usr/local/MATLAB/R2020b/extern/bin/glnxa64. > Please find the attached files. > > > Thanks and regards > Srinivas > > On Fri, Sep 8, 2023 at 11:58?PM Barry Smith > wrote: >> >> I expect a libmx.so in the directory /usr/local/MATLAB/R2020b/extern/bin/glnxa64. Do an ls on that directory and send all the output >> >> >> >>> On Sep 8, 2023, at 10:33 AM, INTURU SRINIVAS 20PHD0548 > wrote: >>> >>> Hi Barry, >>> >>> I tried to run Matlab Engine C example provided in the link "https://in.mathworks.com/help/matlab/matlab_external/build-unix-engine-example.html" >>> in Matlab: copyfile(fullfile(matlabroot,'extern','examples','eng_mat','engdemo.c'),'.','f') >>> mex -v -client engine engdemo.c >>> in linux terminal : LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>> >>> export LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH >>> >>> ./engdemo >>> ./engdemo: error while loading shared libraries: libmx.so: cannot open shared object file: No such file or directory >>> >>> how to sort out this error? Is this the right way to check MatlabEngine with C? >>> >>> Thanks and regards >>> Srinivas >>> >>> >>> On Wed, Sep 6, 2023 at 11:47?PM Barry Smith > wrote: >>>> >>>> Ok, so the C++ binding for Matlab engine is working on your machine. PETSc uses the C binding which links against different libraries but, one would think the C binding would work for sure if the C++ binding works. Can you try a Matlab Engine C example provided by Matlab? >>>> >>>> >>>> >>>> >>>>> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 > wrote: >>>>> >>>>> Hi Amneet, >>>>> >>>>> I repeated the same procedure again and this time it is working. >>>>> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp -lMatlabDataArray -lMatlabEngine >>>>> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>> $export LD_LIBRARY_PATH >>>>> $./a.out >>>>> Square root of -2 is 0 + 1.41421i >>>>> Square root of 2 is 1.41421 + 0i >>>>> Square root of 6 is 2.44949 + 0i >>>>> Square root of 8 is 2.82843 + 0i >>>>> I don't know how it is working this time? >>>>> >>>>> Thanks and regards >>>>> Srinivas >>>>> >>>>> >>>>> On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 > wrote: >>>>>> Hi Amneet, >>>>>> I tried the following example to run a matlab engine. >>>>>> >>>>>> #include "MatlabDataArray.hpp" >>>>>> #include "MatlabEngine.hpp" >>>>>> #include >>>>>> void callSQRT() { >>>>>> >>>>>> using namespace matlab::engine; >>>>>> >>>>>> // Start MATLAB engine synchronously >>>>>> std::unique_ptr matlabPtr = startMATLAB(); >>>>>> >>>>>> //Create MATLAB data array factory >>>>>> matlab::data::ArrayFactory factory; >>>>>> >>>>>> // Define a four-element typed array >>>>>> matlab::data::TypedArray const argArray = >>>>>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >>>>>> >>>>>> // Call MATLAB sqrt function on the data array >>>>>> matlab::data::Array const results = matlabPtr->feval(u"sqrt", argArray); >>>>>> >>>>>> // Display results >>>>>> for (int i = 0; i < results.getNumberOfElements(); i++) { >>>>>> double a = argArray[i]; >>>>>> std::complex v = results[i]; >>>>>> double realPart = v.real(); >>>>>> double imgPart = v.imag(); >>>>>> std::cout << "Square root of " << a << " is " << >>>>>> realPart << " + " << imgPart << "i" << std::endl; >>>>>> } >>>>>> } >>>>>> >>>>>> int main() { >>>>>> callSQRT(); >>>>>> return 0; >>>>>> } >>>>>> >>>>>> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>>>> $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>> $export LD_LIBRARY_PATH >>>>>> $./a.out >>>>>> Starting >>>>>> Error: The import statement 'import matlab.internal.engine.input' cannot be found or cannot be imported. Imported names must end with '.*' or be fully qualified. >>>>>> >>>>>> terminate called after throwing an instance of 'matlab::engine::EngineException' >>>>>> what(): MATLAB process cannot be created. >>>>>> Aborted (core dumped) >>>>>> >>>>>> I got the above error for Matlab R2020b. Please help me to sort out this. >>>>>> >>>>>> Thanks and regards >>>>>> Srinivas >>>>>> >>>>>> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla > wrote: >>>>>>> BTW, what Barry is suggesting is the following: >>>>>>> >>>>>>> Compile a sample code with a command line this: >>>>>>> >>>>>>> g++ -std=c++11 -I matlabroot/extern/include/ -L matlabroot/extern/bin/glnxa64/ >>>>>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>>>>> >>>>>>> This command is provided here: >>>>>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>>>>>> >>>>>>> A sample MATLAB code is here: >>>>>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>>>>>> >>>>>>> (You can just pick a few lines of code from here to create a barebone example) >>>>>>> >>>>>>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla > wrote: >>>>>>>> Srinivas --- Do you have a different version of MATLAB that you can install? If your organization has a MATLAB license, you can install recent versions of MATLAB from mathworks.com >>>>>>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith > wrote: >>>>>>>>> >>>>>>>>> Ok, I have no suggestions. It seems to be more an issue with the Matlab than PETSc. You could find a pure Matlab example of using the engine (in the Matlab documentation) and try it to see if it works. >>>>>>>>> >>>>>>>>> Barry >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 > wrote: >>>>>>>>>> >>>>>>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>>>>>> I got the same errors for petsc 3.17.5 >>>>>>>>>> >>>>>>>>>> make all >>>>>>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>> | ^ >>>>>>>>>> >>>>>>>>>> MEX completed successfully. >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> MEX completed successfully. >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> MEX completed successfully. >>>>>>>>>> Building with 'gcc'. >>>>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>> | ^ >>>>>>>>>> >>>>>>>>>> MEX completed successfully. >>>>>>>>>> ========================================= >>>>>>>>>> ========================================= >>>>>>>>>> Now to check if the libraries are working do: >>>>>>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>>>>> >>>>>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 21:39:22 2023 >>>>>>>>>> # [0]PETSC ERROR: Configure options --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 >>>>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>> # -------------------------------------------------------------------------- >>>>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>> # with errorcode 85. >>>>>>>>>> # >>>>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>>>> # exactly when Open MPI kills them. >>>>>>>>>> # -------------------------------------------------------------------------- >>>>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>> # >>>>>>>>>> # To rerun failed tests: >>>>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>> >>>>>>>>>> Thanks and regards >>>>>>>>>> Srinivas >>>>>>>>>> >>>>>>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith > wrote: >>>>>>>>>>> >>>>>>>>>>> The error is occuring during >>>>>>>>>>> >>>>>>>>>>> e->ep = engOpen(buffer); >>>>>>>>>>> >>>>>>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to assume the problem is occuring when engOpen() is attempting to connect the stdout and stdin from the Matlab session that is launched to the executable. >>>>>>>>>>> >>>>>>>>>>> You can try the following. In 3.17.5 edit the file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>>>>>> >>>>>>>>>>> e->ep = engOpen(buffer); >>>>>>>>>>> >>>>>>>>>>> replace it with >>>>>>>>>>> >>>>>>>>>>> e->ep = engOpen(""); >>>>>>>>>>> >>>>>>>>>>> Now in the PETSc directory do make all (it should recompile one file) and then run the >>>>>>>>>>> >>>>>>>>>>> make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>>> >>>>>>>>>>> again >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>>>>>> >>>>>>>>>>>> Hi Amneeth, >>>>>>>>>>>> >>>>>>>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>>>>>>> >>>>>>>>>>>> ./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>>>>>> The version of PETSc you are using is out-of-date, we recommend updating to the new release >>>>>>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>>>>>>> https://petsc.org/release/download/ >>>>>>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>>>>>> ============================================================================================= >>>>>>>>>>>> Configuring PETSc to compile on your system >>>>>>>>>>>> ============================================================================================= >>>>>>>>>>>> Compilers: >>>>>>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>> Linkers: >>>>>>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>>> BlasLapack: >>>>>>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads

to control the number of threads >>>>>>>>>>>> uses 8 byte integers >>>>>>>>>>>> MPI: >>>>>>>>>>>> Version: 3 >>>>>>>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>>>>>>> Implementation: openmpi >>>>>>>>>>>> OMPI_VERSION: 4.0.3 >>>>>>>>>>>> pthread: >>>>>>>>>>>> cmake: >>>>>>>>>>>> Version: 3.16.3 >>>>>>>>>>>> /usr/bin/cmake >>>>>>>>>>>> regex: >>>>>>>>>>>> Matlab: >>>>>>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>> /usr/local/MATLAB/R2020b >>>>>>>>>>>> MatlabEngine: >>>>>>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 -L/usr/local/MATLAB/R2020b/bin/glnxa64 -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>>>>>>> Language used to compile PETSc: C >>>>>>>>>>>> PETSc: >>>>>>>>>>>> PETSC_ARCH: linux-opt >>>>>>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>>>>>> Prefix: >>>>>>>>>>>> Scalar type: real >>>>>>>>>>>> Precision: double >>>>>>>>>>>> Support for __float128 >>>>>>>>>>>> Integer size: 4 bytes >>>>>>>>>>>> Single library: yes >>>>>>>>>>>> Shared libraries: yes >>>>>>>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>>> Using GNU make: /usr/bin/make >>>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt all >>>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>>> >>>>>>>>>>>> $make >>>>>>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>> Building with 'gcc'. >>>>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>> | ^ >>>>>>>>>>>> >>>>>>>>>>>> MEX completed successfully. >>>>>>>>>>>> Building with 'gcc'. >>>>>>>>>>>> MEX completed successfully. >>>>>>>>>>>> Building with 'gcc'. >>>>>>>>>>>> MEX completed successfully. >>>>>>>>>>>> Building with 'gcc'. >>>>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: In function ?PetscBinaryWrite?: >>>>>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: warning: ?err? may be used uninitialized in this function [-Wmaybe-uninitialized] >>>>>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>> | ^ >>>>>>>>>>>> >>>>>>>>>>>> MEX completed successfully. >>>>>>>>>>>> ========================================= >>>>>>>>>>>> ========================================= >>>>>>>>>>>> Now to check if the libraries are working do: >>>>>>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>>>>>>> >>>>>>>>>>>> $make test query=requires queryval=matlab DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>>>> /usr/bin/python3 /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt --testdir=./linux-opt/tests >>>>>>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab query=requires >>>>>>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>>>>>> # [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- >>>>>>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>>>>>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue Sep 5 10:15:57 2023 >>>>>>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b --with-blaslapack-dir=/usr/local/MATLAB/R2020b --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>>>>>> # [0]PETSC ERROR: #9 main() at /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>> # -------------------------------------------------------------------------- >>>>>>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>>>> # with errorcode 85. >>>>>>>>>>>> # >>>>>>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>>>>>> # exactly when Open MPI kills them. >>>>>>>>>>>> # -------------------------------------------------------------------------- >>>>>>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>> # >>>>>>>>>>>> # To rerun failed tests: >>>>>>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>>> >>>>>>>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>>>>>>> >>>>>>>>>>>> How to check error info and proceed further? >>>>>>>>>>>> >>>>>>>>>>>> Thanks and regards >>>>>>>>>>>> Srinivas >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla > wrote: >>>>>>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure options that Satish mentioned? >>>>>>>>>>>>> >>>>>>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via petsc-users > wrote: >>>>>>>>>>>>>> Sorry for missing that. >>>>>>>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>>> >>>>>>>>>>>>>> < M A T L A B (R) > >>>>>>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>>>>>>> November 23, 2020 >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> To get started, type doc. >>>>>>>>>>>>>> For product information, visit www.mathworks.com . >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks and regards >>>>>>>>>>>>>> Srinivas >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay > wrote: >>>>>>>>>>>>>>> You are missing one more step: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Satish >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > Hi Sathish, >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > I tried the following procedure >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > *$make * >>>>>>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>>>> > | ^ >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>>>> > | ^ >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>>>>>> > ========================================= >>>>>>>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab >>>>>>>>>>>>>>> > query=requires >>>>>>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>>>>>> > ------------------------------------------------------------------------ >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, >>>>>>>>>>>>>>> > probably memory access out of range >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger >>>>>>>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS >>>>>>>>>>>>>>> > X to find memory corruption errors >>>>>>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, >>>>>>>>>>>>>>> > and run >>>>>>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep >>>>>>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file >>>>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>>>>>>> > # >>>>>>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>>>>> > CC >>>>>>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>>>>>> > CLINKER >>>>>>>>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>>>> > TEST >>>>>>>>>>>>>>> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 >>>>>>>>>>>>>>> > # Running problem 5 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>>>> > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by >>>>>>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>>>> > # with errorcode 126076. >>>>>>>>>>>>>>> > # >>>>>>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>>>> > # You may or may not see output from other processes, depending on >>>>>>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > # -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed >>>>>>>>>>>>>>> > so no diff >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > # ------------- >>>>>>>>>>>>>>> > # Summary >>>>>>>>>>>>>>> > # ------------- >>>>>>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>>>>>>> > # >>>>>>>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>>>>>>> > # >>>>>>>>>>>>>>> > # To rerun failed tests: >>>>>>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>>>>>> > # >>>>>>>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx >>>>>>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh >>>>>>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath >>>>>>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 >>>>>>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>>>>>> > Running problem 5 >>>>>>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 >>>>>>>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>>>> > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > for trouble shooting. >>>>>>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send entire >>>>>>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>>>> > with errorcode 126076. >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>>>> > You may or may not see output from other processes, depending on >>>>>>>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay > wrote: >>>>>>>>>>>>>>> > >>>>>>>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>>>>>>> > > >>>>>>>>>>>>>>> > > cd $HOME >>>>>>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>>>>>>> > > >>>>>>>>>>>>>> > > manually with make> >>>>>>>>>>>>>>> > > >>>>>>>>>>>>>>> > > make test query=requires queryval=matlab DATAFILESPATH=$HOME/datafiles >>>>>>>>>>>>>>> > > >>>>>>>>>>>>>>> > > Satish >>>>>>>>>>>>>>> > > >>>>>>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>>>>>>> > > >>>>>>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in > wrote: >>>>>>>>>>>>>>> > > > >>>>>>>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>>>>>>> > > > > >>>>>>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do not have >>>>>>>>>>>>>>> > > any >>>>>>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please help me how to >>>>>>>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>>>>>>> > > > > >>>>>>>>>>>>>>> > > > >>>>>>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we point to >>>>>>>>>>>>>>> > > this >>>>>>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You don't have those >>>>>>>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>>>>>>> > > > is why I suggested just using a different matrix, or running a problem >>>>>>>>>>>>>>> > > you >>>>>>>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>>>>>>> > > > >>>>>>>>>>>>>>> > > > Thanks, >>>>>>>>>>>>>>> > > > >>>>>>>>>>>>>>> > > > Matt >>>>>>>>>>>>>>> > > > >>>>>>>>>>>>>>> > > > >>>>>>>>>>>>>>> > > > > Thanks and regards >>>>>>>>>>>>>>> > > > > Srinivas. >>>>>>>>>>>>>>> > > > > >>>>>>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley > >>>>>>>>>>>>>>> > > wrote: >>>>>>>>>>>>>>> > > > > >>>>>>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>>>> > > petsc-users < >>>>>>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>>>>>> > > > >> >>>>>>>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you are giving me >>>>>>>>>>>>>>> > > to >>>>>>>>>>>>>>> > > > >>> sort this out. >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> I tried to follow the same procedure which you followed to build >>>>>>>>>>>>>>> > > Petsc >>>>>>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>>>> > > > >>> Configuring PETSc to compile on your system >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>>>> > > > >>> It appears you do not have >>>>>>>>>>>>>>> > > valgrind >>>>>>>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from www.valgrind.org >>>>>>>>>>>>>>> > > > >>> Or install >>>>>>>>>>>>>>> > > valgrind-devel or >>>>>>>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > =============================================================================== >>>>>>>>>>>>>>> > > > >>> Compilers: >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>>>> > > -fPIC >>>>>>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>>>> > > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>>>>>> > > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>>>> > > > >>> Linkers: >>>>>>>>>>>>>>> > > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>>>> > > -shared >>>>>>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>>>> > > -shared >>>>>>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>>>>>> > > > >>> make: >>>>>>>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread >>>>>>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>>>>>> > >

to >>>>>>>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>>>>>>> > > > >>> MPI: >>>>>>>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>>>>>>> > > --oversubscribe >>>>>>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>>>>>>> > > > >>> pthread: >>>>>>>>>>>>>>> > > > >>> cmake: >>>>>>>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>>>>>>> > > > >>> regex: >>>>>>>>>>>>>>> > > > >>> Matlab: >>>>>>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>>>>>>> > > > >>> Library: >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>>>>>>>>>> > > -lut >>>>>>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>>>>>>> > > > >>> PETSc: >>>>>>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>>>>>>> > > > >>> Precision: double >>>>>>>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as >>>>>>>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> *$make* >>>>>>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>>>>>> > > > >>> ========================================= >>>>>>>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check >>>>>>>>>>>>>>> > > > >>> =============================================== >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>>>>> > > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >> >>>>>>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH defined, so it >>>>>>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of yours. >>>>>>>>>>>>>>> > > > >> >>>>>>>>>>>>>>> > > > >> Thanks, >>>>>>>>>>>>>>> > > > >> >>>>>>>>>>>>>>> > > > >> Matt >>>>>>>>>>>>>>> > > > >> >>>>>>>>>>>>>>> > > > >> >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>>>>>>>>>> > > Sun >>>>>>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>>>>> > > > >>> CC >>>>>>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>>>>>> > > > >>> CLINKER >>>>>>>>>>>>>>> > > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>>>> > > > >>> TEST >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>>>>>> > > code: 124 >>>>>>>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > > > >>> -------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble >>>>>>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>>>>>>>>>> > > > >>> # You may or may not see output from other processes, depending on >>>>>>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command >>>>>>>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>>>>>> > > > >>> # Summary >>>>>>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>>>>>> > > > >>> # >>>>>>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / >>>>>>>>>>>>>>> > > 0.02 sec >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>>>>>> > > -Wwrite-strings >>>>>>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c >>>>>>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex >>>>>>>>>>>>>>> > > -lmx >>>>>>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread >>>>>>>>>>>>>>> > > -lquadmath >>>>>>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version. >>>>>>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please find the >>>>>>>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>>>>>>> > > > >>> Srinivas >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay > >>>>>>>>>>>>>>> > > wrote: >>>>>>>>>>>>>>> > > > >>> >>>>>>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional info - and debug >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> Satish >>>>>>>>>>>>>>> > > > >>>> ---------- >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>>>>>> > > -Wall >>>>>>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > -fstack-protector >>>>>>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>>>>>> > > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng >>>>>>>>>>>>>>> > > -lmex >>>>>>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort >>>>>>>>>>>>>>> > > -lmpi >>>>>>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o >>>>>>>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>>>>>>> > > processors >>>>>>>>>>>>>>> > > > >>>> = 1 >>>>>>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07 >>>>>>>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689 >>>>>>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string: >>>>>>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string: >>>>>>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>>>>>> > > > >>>> 5 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually works for you >>>>>>>>>>>>>>> > > - on >>>>>>>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> Copyright 1984-2021 The MathWorks, Inc. >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64) >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com . >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting >>>>>>>>>>>>>>> > > thread >>>>>>>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the >>>>>>>>>>>>>>> > > corresponding >>>>>>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04, >>>>>>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch >>>>>>>>>>>>>>> > > > >>>> > main >>>>>>>>>>>>>>> > > > >>>> > release >>>>>>>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load >>>>>>>>>>>>>>> > > matlab/R2021a >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure >>>>>>>>>>>>>>> > > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>>>>>> > > -Wall >>>>>>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > -fstack-protector >>>>>>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > -fstack-protector >>>>>>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>>>>>>> > > -Wall >>>>>>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>>>>>>> > > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>>>>>> > > > >>>> > make: >>>>>>>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>>>>>>>> > >

>>>>>>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>>>>>>> > > > >>>> > regex: >>>>>>>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>>>>>> > > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc >>>>>>>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries with: >>>>>>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > xxx=========================================================================xxx >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>>>>>> > > socket\n"); >>>>>>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this function >>>>>>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>>>>>> > > socket\n"); >>>>>>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check >>>>>>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test >>>>>>>>>>>>>>> > > query=requires >>>>>>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>>>>>>> > > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>>>> > > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>>>>>> > > code: >>>>>>>>>>>>>>> > > > >>>> 1 >>>>>>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>>>>>> > > Command >>>>>>>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test >>>>>>>>>>>>>>> > > query=requires >>>>>>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>>>>>>> > > > >>>> > # >>>>>>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 >>>>>>>>>>>>>>> > > sec >>>>>>>>>>>>>>> > > > >>>> > # >>>>>>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>>>>>>> > > 7.54 >>>>>>>>>>>>>>> > > > >>>> sec >>>>>>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>>>>>>> > > > >>>> > >>>>>>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have tried to >>>>>>>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After >>>>>>>>>>>>>>> > > > >>>> running make >>>>>>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error message. >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>>>>>> > > > >>>> > > -------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>>>>>> > > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>>>>>> > > -------send >>>>>>>>>>>>>>> > > > >>>> entire >>>>>>>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>>>>>> > > > >>>> processes. >>>>>>>>>>>>>>> > > > >>>> > > # You may or may not see output from other processes, depending >>>>>>>>>>>>>>> > > on >>>>>>>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> > > Thanks >>>>>>>>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>>>>>>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>>>> > > > >>>> petsc-users < >>>>>>>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov > wrote: >>>>>>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay > >>>>>>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work >>>>>>>>>>>>>>> > > > >>>> here]. >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>>>> > > petsc-users >>>>>>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>>>>>>>> > > balay at mcs.anl.gov > >>>>>>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work in this mode. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such dependency/conflicts >>>>>>>>>>>>>>> > > across >>>>>>>>>>>>>>> > > > >>>> packages] >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict >>>>>>>>>>>>>>> > > with >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with >>>>>>>>>>>>>>> > > > >>>> matlab - to >>>>>>>>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via >>>>>>>>>>>>>>> > > > >>>> petsc-users >>>>>>>>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not >>>>>>>>>>>>>>> > > > >>>> working. It is >>>>>>>>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with >>>>>>>>>>>>>>> > > > >>>> libmesh and >>>>>>>>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without >>>>>>>>>>>>>>> > > > >>>> linking >>>>>>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring >>>>>>>>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>>>>>>>> > > > >>>> > > >>> that >>>>>>>>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is >>>>>>>>>>>>>>> > > specified. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with >>>>>>>>>>>>>>> > > > >>>> PETSc and >>>>>>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated >>>>>>>>>>>>>>> > > geometries >>>>>>>>>>>>>>> > > > >>>> it is >>>>>>>>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these various >>>>>>>>>>>>>>> > > things >>>>>>>>>>>>>>> > > > >>>> and ended >>>>>>>>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to do my >>>>>>>>>>>>>>> > > > >>>> research work. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as possible. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla < >>>>>>>>>>>>>>> > > > >>>> mail2amneet at gmail.com > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need libMesh for >>>>>>>>>>>>>>> > > the >>>>>>>>>>>>>>> > > > >>>> WEC >>>>>>>>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with >>>>>>>>>>>>>>> > > > >>>> Matlab. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build >>>>>>>>>>>>>>> > > > >>>> libMesh? >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS >>>>>>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all >>>>>>>>>>>>>>> > > > >>>> occurrences >>>>>>>>>>>>>>> > > > >>>> > > >>> of >>>>>>>>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make >>>>>>>>>>>>>>> > > test" >>>>>>>>>>>>>>> > > > >>>> got the >>>>>>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>>>>>> > > Message >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>>>>>> > > on >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > > > >>>> for >>>>>>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>>>>>> > > Aug >>>>>>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>>>>>> > > linux-debug >>>>>>>>>>>>>>> > > > >>>> named >>>>>>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1 >>>>>>>>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>>>>>> > > line >>>>>>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>>>>>> > > > >>>> Message >>>>>>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>>>>>> > > kill >>>>>>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>>>>>> > > processes, >>>>>>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>>>>>> > > Message >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> -------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine >>>>>>>>>>>>>>> > > on >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>>>>>> > > > >>>> for >>>>>>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>>>>>> > > Aug >>>>>>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>>>>>> > > linux-opt >>>>>>>>>>>>>>> > > > >>>> named >>>>>>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>>>>>> > > line >>>>>>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>>>>>> > > > >>>> Message >>>>>>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>>>>>> > > kill >>>>>>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from other >>>>>>>>>>>>>>> > > processes, >>>>>>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -------------------------------------------------------------------------- >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 >>>>>>>>>>>>>>> > > version. I >>>>>>>>>>>>>>> > > > >>>> am >>>>>>>>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and >>>>>>>>>>>>>>> > > > >>>> petsc >>>>>>>>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM Satish Balay < >>>>>>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's >>>>>>>>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>>>>>> > > -leng >>>>>>>>>>>>>>> > > > >>>> -lmex >>>>>>>>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are >>>>>>>>>>>>>>> > > seeing: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not >>>>>>>>>>>>>>> > > > >>>> preset here. >>>>>>>>>>>>>>> > > > >>>> > > >>> This >>>>>>>>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata >>>>>>>>>>>>>>> > > -licui18n >>>>>>>>>>>>>>> > > > >>>> -licuuc" >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>>>>>>>> > > via >>>>>>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while building >>>>>>>>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh with >>>>>>>>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done >>>>>>>>>>>>>>> > > successfully. >>>>>>>>>>>>>>> > > > >>>> But >>>>>>>>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM Satish Balay < >>>>>>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both >>>>>>>>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs >>>>>>>>>>>>>>> > > friendly to >>>>>>>>>>>>>>> > > > >>>> mailing >>>>>>>>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or >>>>>>>>>>>>>>> > > 3.19?] >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS >>>>>>>>>>>>>>> > > 20PHD0548 >>>>>>>>>>>>>>> > > > >>>> via >>>>>>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while >>>>>>>>>>>>>>> > > building >>>>>>>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the >>>>>>>>>>>>>>> > > needful. >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19?AM INTURU >>>>>>>>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in > >>>>>>>>>>>>>>> > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During >>>>>>>>>>>>>>> > > building >>>>>>>>>>>>>>> > > > >>>> of >>>>>>>>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43?PM Satish >>>>>>>>>>>>>>> > > > >>>> Balay < >>>>>>>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says >>>>>>>>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5? >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS >>>>>>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for >>>>>>>>>>>>>>> > > > >>>> working on >>>>>>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the >>>>>>>>>>>>>>> > > PETSc, >>>>>>>>>>>>>>> > > > >>>> using the >>>>>>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual': >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian': >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> >>>>>>>>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit >>>>>>>>>>>>>>> > > > >>>> status >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185: >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>>>>>> > > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished >>>>>>>>>>>>>>> > > jobs.... >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>>>>>> > > > >>>> > > >>> > > > > >> 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The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. >> > > Disclaimer: > This message was sent from Vellore Institute of Technology. The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From maruthinh at gmail.com Sun Sep 10 04:54:23 2023 From: maruthinh at gmail.com (Maruthi NH) Date: Sun, 10 Sep 2023 15:24:23 +0530 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU Message-ID: Hi all, I am trying to accelerate the linear solver with PETSc GPU backend. For testing I have a simple 1D heat diffusion solver, here are some observations. 1. If I use -pc_type gamg it throws the following error ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) had an illegal value: NULL pointer [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: GPU error [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : invalid value [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-959-g92f1e92e88 GIT Date: 2023-08-13 19:43:04 +0000 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes about 105.9 seconds on a GPU. Similar observations with pc_type asm I have NVIDIA RTX A2000 8GB Laptop GPU 3. What I could be missing? Also, are there any general guidelines for better GPU performance using PETSc? Regards, Maruthi -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Sun Sep 10 12:47:27 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Sun, 10 Sep 2023 17:47:27 +0000 Subject: [petsc-users] Coupled system of equations on unstructured mesh Message-ID: Hello, I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions. Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns, A = [A00 A01 A10 A11] the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor. Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations? -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide. Kind regards, Karthik. -- Karthik Chockalingam, Ph.D. Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk [signature_3970890138] -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sun Sep 10 13:02:40 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 10 Sep 2023 14:02:40 -0400 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via petsc-users wrote: > Hello, > > > > I have so far solved scalar field problems using finite elements on a > given (*unstructured*) mesh. I made use of MATMPIAIJ to create matrixes, > MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to > set boundary conditions. > > > > Now, I would like to solve a coupled system of equations for the > quantities u1 and u2 on the (*unstructured*) mesh. I.e., the matrix > should get the double number of rows and columns, > > > > A = [A00 A01 > > A10 A11] > This is usually not a good way to think of it. This division means that all variables of one field come before all those of another. It is much more common to group together all the unknowns at a given point. You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location. Thanks, Matt > the vectors contain twice the number of entries (e.g. first all u1s and > then all u2s). I would like to be sure that the entries of u1 and u2, which > are associated with the same element are located on the same processor. > > > > Is a pre-defined structure already available within PETSc to enlarge such > a single equation to store the entries of coupled equations? > > > > -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 > > -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 > > > > Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently > to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); > > > > I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ > and MatSetValues to create and assign values to matrix entries > respectively. I would be grateful if you could provide the stepwise guide. > > > > Kind regards, > > Karthik. > > > > -- > > *Karthik Chockalingam, Ph.D.* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > [image: signature_3970890138] > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Sun Sep 10 13:07:16 2023 From: bsmith at petsc.dev (Barry Smith) Date: Sun, 10 Sep 2023 14:07:16 -0400 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: References: Message-ID: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> > On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: > > Hi all, > > I am trying to accelerate the linear solver with PETSc GPU backend. For testing I have a simple 1D heat diffusion solver, here are some observations. > 1. If I use -pc_type gamg it throws the following error > ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) had an illegal value: NULL pointer > > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: GPU error > [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : invalid value > [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-959-g92f1e92e88 GIT Date: 2023-08-13 19:43:04 +0000 > Can you share the code that triggers this? > 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes about 105.9 seconds on a GPU. Similar observations with pc_type asm > I have NVIDIA RTX A2000 8GB Laptop GPU This is expected. The triangular solves sequentialize on the GPU so naturally are extremely slow since they cannot take advantage of the massive parallelism of the GPU. > > 3. What I could be missing? Also, are there any general guidelines for better GPU performance using PETSc? > > Regards, > Maruthi -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Sun Sep 10 14:01:31 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Sun, 10 Sep 2023 19:01:31 +0000 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: I will solve the coupled problem in a non-linear fashion using SNES, so I will have one residual for each variable R(u1) and R(u2) and the resulting Jacobian matrix J = [J11 J12 J21 J22] for each element. For first-order Lagrange elements (in 2D) will have four nodes, then J would be of size 8 x 8. Let's say the variables are u and v. The order would be [u1 u2 u3 u4 v1 v2 v3 v4]. Or should I rearrange the above entr?es in the element Jacobian so as to have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will not have block ordering I guess. In my case, the discretization of the u and v are from the same element space. Can you please elaborate when you say, ?Just enlarge the block size of your matrix?? I have never used block size before and not sure what it accomplishes. Do you mean to say, I should use MATBAIJ instead of MATAIJ? Kind regards, Karthik. From: Matthew Knepley Date: Sunday, 10 September 2023 at 19:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: Hello, I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions. Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns, A = [A00 A01 A10 A11] This is usually not a good way to think of it. This division means that all variables of one field come before all those of another. It is much more common to group together all the unknowns at a given point. You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location. Thanks, Matt the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor. Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations? -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide. Kind regards, Karthik. -- Karthik Chockalingam, Ph.D. Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sun Sep 10 14:09:13 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 10 Sep 2023 15:09:13 -0400 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > I will solve the coupled problem in a non-linear fashion using SNES, so I > will have one residual for each variable R(u1) and R(u2) and the resulting > Jacobian matrix > > > > J = [J11 J12 > > J21 J22] for each element. > > > > For first-order Lagrange elements (in 2D) will have four nodes, then J > would be of size 8 x 8. Let's say the variables are u and v. The order > would be [u1 u2 u3 u4 v1 v2 v3 v4]. > > > > Or should I rearrange the above entr?es in the element Jacobian so as to > have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will > not have block ordering I guess. > This is the correct order to get block matrices. > In my case, the discretization of the u and v are from the same element > space. > > Can you please elaborate when you say, ?Just enlarge the block size of > your matrix?? > > I have never used block size before and not sure what it accomplishes. > > Do you mean to say, I should use MATBAIJ instead of MATAIJ? > You do not need to change the type, just give the AIJ matrix a blocksize of 2. Thanks, Matt > Kind regards, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 19:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > Hello, > > > > I have so far solved scalar field problems using finite elements on a > given (*unstructured*) mesh. I made use of MATMPIAIJ to create matrixes, > MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to > set boundary conditions. > > > > Now, I would like to solve a coupled system of equations for the > quantities u1 and u2 on the (*unstructured*) mesh. I.e., the matrix > should get the double number of rows and columns, > > > > A = [A00 A01 > > A10 A11] > > > > This is usually not a good way to think of it. This division means that > all variables of one field come before > > all those of another. It is much more common to group together all the > unknowns at a given point. > > > > You could, if the discretizations of u1 and u2 are the same, just enlarge > the blocksize of your matrix. Then you set u1 and u2 for each vec location, > or a 2x2 block for each Jacobian location. > > > > Thanks, > > > > Matt > > > > the vectors contain twice the number of entries (e.g. first all u1s and > then all u2s). I would like to be sure that the entries of u1 and u2, which > are associated with the same element are located on the same processor. > > > > Is a pre-defined structure already available within PETSc to enlarge such > a single equation to store the entries of coupled equations? > > > > -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 > > -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 > > > > Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently > to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); > > > > I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ > and MatSetValues to create and assign values to matrix entries > respectively. I would be grateful if you could provide the stepwise guide. > > > > Kind regards, > > Karthik. > > > > -- > > *Karthik Chockalingam, Ph.D.* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Sun Sep 10 14:15:18 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Sun, 10 Sep 2023 19:15:18 +0000 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: I don?t see an option to give block size. https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ Many thanks, Karthik. From: Matthew Knepley Date: Sunday, 10 September 2023 at 20:09 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I will solve the coupled problem in a non-linear fashion using SNES, so I will have one residual for each variable R(u1) and R(u2) and the resulting Jacobian matrix J = [J11 J12 J21 J22] for each element. For first-order Lagrange elements (in 2D) will have four nodes, then J would be of size 8 x 8. Let's say the variables are u and v. The order would be [u1 u2 u3 u4 v1 v2 v3 v4]. Or should I rearrange the above entr?es in the element Jacobian so as to have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will not have block ordering I guess. This is the correct order to get block matrices. In my case, the discretization of the u and v are from the same element space. Can you please elaborate when you say, ?Just enlarge the block size of your matrix?? I have never used block size before and not sure what it accomplishes. Do you mean to say, I should use MATBAIJ instead of MATAIJ? You do not need to change the type, just give the AIJ matrix a blocksize of 2. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 19:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: Hello, I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions. Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns, A = [A00 A01 A10 A11] This is usually not a good way to think of it. This division means that all variables of one field come before all those of another. It is much more common to group together all the unknowns at a given point. You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location. Thanks, Matt the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor. Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations? -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide. Kind regards, Karthik. -- Karthik Chockalingam, Ph.D. Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sun Sep 10 14:17:50 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 10 Sep 2023 15:17:50 -0400 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > I don?t see an option to give block size. > > https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ > https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ Thanks, Matt > > > Many thanks, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:09 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I will solve the coupled problem in a non-linear fashion using SNES, so I > will have one residual for each variable R(u1) and R(u2) and the resulting > Jacobian matrix > > > > J = [J11 J12 > > J21 J22] for each element. > > > > For first-order Lagrange elements (in 2D) will have four nodes, then J > would be of size 8 x 8. Let's say the variables are u and v. The order > would be [u1 u2 u3 u4 v1 v2 v3 v4]. > > > > Or should I rearrange the above entr?es in the element Jacobian so as to > have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will > not have block ordering I guess. > > > > This is the correct order to get block matrices. > > > > In my case, the discretization of the u and v are from the same element > space. > > Can you please elaborate when you say, ?Just enlarge the block size of > your matrix?? > > I have never used block size before and not sure what it accomplishes. > > Do you mean to say, I should use MATBAIJ instead of MATAIJ? > > > > You do not need to change the type, just give the AIJ matrix a blocksize > of 2. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 19:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > Hello, > > > > I have so far solved scalar field problems using finite elements on a > given (*unstructured*) mesh. I made use of MATMPIAIJ to create matrixes, > MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to > set boundary conditions. > > > > Now, I would like to solve a coupled system of equations for the > quantities u1 and u2 on the (*unstructured*) mesh. I.e., the matrix > should get the double number of rows and columns, > > > > A = [A00 A01 > > A10 A11] > > > > This is usually not a good way to think of it. This division means that > all variables of one field come before > > all those of another. It is much more common to group together all the > unknowns at a given point. > > > > You could, if the discretizations of u1 and u2 are the same, just enlarge > the blocksize of your matrix. Then you set u1 and u2 for each vec location, > or a 2x2 block for each Jacobian location. > > > > Thanks, > > > > Matt > > > > the vectors contain twice the number of entries (e.g. first all u1s and > then all u2s). I would like to be sure that the entries of u1 and u2, which > are associated with the same element are located on the same processor. > > > > Is a pre-defined structure already available within PETSc to enlarge such > a single equation to store the entries of coupled equations? > > > > -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 > > -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 > > > > Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently > to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); > > > > I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ > and MatSetValues to create and assign values to matrix entries > respectively. I would be grateful if you could provide the stepwise guide. > > > > Kind regards, > > Karthik. > > > > -- > > *Karthik Chockalingam, Ph.D.* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From birocloudstemp at gmail.com Sun Sep 10 15:10:52 2023 From: birocloudstemp at gmail.com (Biro Clouds) Date: Sun, 10 Sep 2023 21:10:52 +0100 Subject: [petsc-users] Generally constrained solvers with FenicsX Message-ID: Hi all, I've been struggling for some time now trying to get a generally constrained solver (ideally ALMM, but PDIPM might work too) to work in python, specifically with FEniCS X. My model is an incremental variational approach to plasticity and normally requires two lagrange multipliers alongside the energy functional terms. However, through experimentation outside of this environment, I found that dealing with these lagrange multipliers as non linear constraints in the SciPy optimise function worked very well and has allowed me to achieve some good results. I'd like to implement an approach as similar as possible to this with a TAO solver, and ALMM method looks the most similar to me. I have looked in the Fenics discourse forum and there is vanishingly small amounts of PETSc TAO content there, and I've found no good example of ALMM solvers in python, or even the setEqualityConstraint() function anywhere. I'm relatively new to all this and cannot read C code unfortunately, so the constrained example in C is not much help to me, especially as the implementation seems completely different to python. Kind regards, Magnus -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Sun Sep 10 15:16:03 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Sun, 10 Sep 2023 20:16:03 +0000 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: Thank you. I almost got it and have a couple of questions. Let me summarize, I have an element Jacobian matrix of size 8 x 8 for QAUD4 (for variables u and v) ordered such that the degrees of freedom at a node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4]. Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not have an on-diagonal and off-diagonal block structure? Does it not matter? When assembling the element Jacobian into the system matrix A, I would make use of MatSetValues. For each element, I presume m = 8 and n = 8 along with idxm and idxn, are passed to MatSetValues. Meaning I have to figure out the global index (say idxm) set of size 8 corresponding to the system matrix A. Q2) What does setting the block size bs = 2 accomplish? Because the way to assemble the Jacobian into the system matrix A seems to me no different than I did for the single variable scalar problem. Kind regards, Karthik. From: Matthew Knepley Date: Sunday, 10 September 2023 at 20:18 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I don?t see an option to give block size. https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ Thanks, Matt Many thanks, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 20:09 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I will solve the coupled problem in a non-linear fashion using SNES, so I will have one residual for each variable R(u1) and R(u2) and the resulting Jacobian matrix J = [J11 J12 J21 J22] for each element. For first-order Lagrange elements (in 2D) will have four nodes, then J would be of size 8 x 8. Let's say the variables are u and v. The order would be [u1 u2 u3 u4 v1 v2 v3 v4]. Or should I rearrange the above entr?es in the element Jacobian so as to have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will not have block ordering I guess. This is the correct order to get block matrices. In my case, the discretization of the u and v are from the same element space. Can you please elaborate when you say, ?Just enlarge the block size of your matrix?? I have never used block size before and not sure what it accomplishes. Do you mean to say, I should use MATBAIJ instead of MATAIJ? You do not need to change the type, just give the AIJ matrix a blocksize of 2. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 19:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: Hello, I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions. Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns, A = [A00 A01 A10 A11] This is usually not a good way to think of it. This division means that all variables of one field come before all those of another. It is much more common to group together all the unknowns at a given point. You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location. Thanks, Matt the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor. Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations? -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide. Kind regards, Karthik. -- Karthik Chockalingam, Ph.D. Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sun Sep 10 15:22:52 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sun, 10 Sep 2023 16:22:52 -0400 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: On Sun, Sep 10, 2023 at 4:16?PM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > Thank you. I almost got it and have a couple of questions. > > > > Let me summarize, I have an element Jacobian matrix of size 8 x 8 for > QAUD4 (for variables u and v) ordered such that the degrees of freedom at > a node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4]. > > > > Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not > have an on-diagonal and off-diagonal block structure? Does it not matter? > It does have block structure in that each entry in your original matrix is now a 2x2 block entry in the matrix for 2 fields. When assembling the element Jacobian into the system matrix A, I would make > use of MatSetValues. For each element, I *presume* m = 8 and n = 8 along > with idxm and idxn, are passed to MatSetValues. Meaning I have to figure > out the global index (say idxm) set of size 8 corresponding to the system > matrix A. > What you can do is call https://petsc.org/main/manualpages/Mat/MatSetValuesBlocked/ and give the same indices that you would have given for the original matrix, but instead of a value at each location, we now have a 2x2 block. > Q2) What does setting the block size bs = 2 accomplish? Because the way to > assemble the Jacobian into the system matrix A seems to me no different > than I did for the single variable scalar problem. > This is answered above. Thanks, Matt > Kind regards, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:18 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I don?t see an option to give block size. > > https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ > > > > https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ > > > > Thanks, > > > > Matt > > > > > > Many thanks, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:09 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I will solve the coupled problem in a non-linear fashion using SNES, so I > will have one residual for each variable R(u1) and R(u2) and the resulting > Jacobian matrix > > > > J = [J11 J12 > > J21 J22] for each element. > > > > For first-order Lagrange elements (in 2D) will have four nodes, then J > would be of size 8 x 8. Let's say the variables are u and v. The order > would be [u1 u2 u3 u4 v1 v2 v3 v4]. > > > > Or should I rearrange the above entr?es in the element Jacobian so as to > have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will > not have block ordering I guess. > > > > This is the correct order to get block matrices. > > > > In my case, the discretization of the u and v are from the same element > space. > > Can you please elaborate when you say, ?Just enlarge the block size of > your matrix?? > > I have never used block size before and not sure what it accomplishes. > > Do you mean to say, I should use MATBAIJ instead of MATAIJ? > > > > You do not need to change the type, just give the AIJ matrix a blocksize > of 2. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 19:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > Hello, > > > > I have so far solved scalar field problems using finite elements on a > given (*unstructured*) mesh. I made use of MATMPIAIJ to create matrixes, > MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to > set boundary conditions. > > > > Now, I would like to solve a coupled system of equations for the > quantities u1 and u2 on the (*unstructured*) mesh. I.e., the matrix > should get the double number of rows and columns, > > > > A = [A00 A01 > > A10 A11] > > > > This is usually not a good way to think of it. This division means that > all variables of one field come before > > all those of another. It is much more common to group together all the > unknowns at a given point. > > > > You could, if the discretizations of u1 and u2 are the same, just enlarge > the blocksize of your matrix. Then you set u1 and u2 for each vec location, > or a 2x2 block for each Jacobian location. > > > > Thanks, > > > > Matt > > > > the vectors contain twice the number of entries (e.g. first all u1s and > then all u2s). I would like to be sure that the entries of u1 and u2, which > are associated with the same element are located on the same processor. > > > > Is a pre-defined structure already available within PETSc to enlarge such > a single equation to store the entries of coupled equations? > > > > -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 > > -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 > > > > Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently > to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); > > > > I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ > and MatSetValues to create and assign values to matrix entries > respectively. I would be grateful if you could provide the stepwise guide. > > > > Kind regards, > > Karthik. > > > > -- > > *Karthik Chockalingam, Ph.D.* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From maruthinh at gmail.com Mon Sep 11 11:52:55 2023 From: maruthinh at gmail.com (Maruthi NH) Date: Mon, 11 Sep 2023 22:22:55 +0530 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> References: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> Message-ID: Hi Barry Smith, Thanks for the quick response. Here is the code I used to test PETSc on GPU. This is the command I used to run mpiexec.hydra -n 1 ./heat_diff_cu -Nx 10000000 -ksp_type gmres -mat_type aijcusparse -vec_type cuda -use_gpu_aware_mpi 0 -pc_type gamg -ksp_converged_reason Regards, Maruthi On Sun, Sep 10, 2023 at 11:37?PM Barry Smith wrote: > > > On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: > > Hi all, > > I am trying to accelerate the linear solver with PETSc GPU backend. For > testing I have a simple 1D heat diffusion solver, here are some > observations. > 1. If I use -pc_type gamg it throws the following error > ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) had > an illegal value: NULL pointer > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: GPU error > [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : > invalid value > [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-959-g92f1e92e88 > GIT Date: 2023-08-13 19:43:04 +0000 > > Can you share the code that triggers this? > > 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes > about 105.9 seconds on a GPU. Similar observations with pc_type asm > I have NVIDIA RTX A2000 8GB Laptop GPU > > > This is expected. The triangular solves sequentialize on the GPU so > naturally are extremely slow since they cannot take advantage of the > massive parallelism of the GPU. > > > 3. What I could be missing? Also, are there any general guidelines for > better GPU performance using PETSc? > > Regards, > Maruthi > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: heat_diff_cu.cu Type: application/octet-stream Size: 6772 bytes Desc: not available URL: From junchao.zhang at gmail.com Mon Sep 11 14:39:29 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Mon, 11 Sep 2023 14:39:29 -0500 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: References: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> Message-ID: Hi, Maruthi, I could run your example on my machine. BTW, I added these at the end of main() to free petsc objects. VecDestroy(&vout); VecDestroy(&x); VecDestroy(&b); VecDestroy(&u); MatDestroy(&A); VecScatterDestroy(&ctx); KSPDestroy(&ksp); If you use cuda-12.2, maybe the problem is already fixed by MR https://gitlab.com/petsc/petsc/-/merge_requests/6828 You can use petsc/main branch to try. Note your petsc version is from Date: 2023-08-13 Thanks. --Junchao Zhang On Mon, Sep 11, 2023 at 12:10?PM Maruthi NH wrote: > Hi Barry Smith, > > Thanks for the quick response. > > Here is the code I used to test PETSc on GPU. > This is the command I used to run > mpiexec.hydra -n 1 ./heat_diff_cu -Nx 10000000 -ksp_type gmres -mat_type > aijcusparse -vec_type cuda -use_gpu_aware_mpi 0 -pc_type gamg > -ksp_converged_reason > > Regards, > Maruthi > > > > On Sun, Sep 10, 2023 at 11:37?PM Barry Smith wrote: > >> >> >> On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: >> >> Hi all, >> >> I am trying to accelerate the linear solver with PETSc GPU backend. For >> testing I have a simple 1D heat diffusion solver, here are some >> observations. >> 1. If I use -pc_type gamg it throws the following error >> ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) >> had an illegal value: NULL pointer >> >> [0]PETSC ERROR: --------------------- Error Message >> -------------------------------------------------------------- >> [0]PETSC ERROR: GPU error >> [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : >> invalid value >> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-959-g92f1e92e88 >> GIT Date: 2023-08-13 19:43:04 +0000 >> >> Can you share the code that triggers this? >> >> 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes >> about 105.9 seconds on a GPU. Similar observations with pc_type asm >> I have NVIDIA RTX A2000 8GB Laptop GPU >> >> >> This is expected. The triangular solves sequentialize on the GPU so >> naturally are extremely slow since they cannot take advantage of the >> massive parallelism of the GPU. >> >> >> 3. What I could be missing? Also, are there any general guidelines for >> better GPU performance using PETSc? >> >> Regards, >> Maruthi >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From maruthinh at gmail.com Tue Sep 12 10:15:19 2023 From: maruthinh at gmail.com (Maruthi NH) Date: Tue, 12 Sep 2023 20:45:19 +0530 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: References: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> Message-ID: Hi Junchao Zhang, Thanks for the help. Updating PETSc fixed the problem. However, if I use boomeramg from hypre as follows, I get a similar error. ./heat_diff_cu --ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) had an illegal value: NULL pointer CUSPARSE ERROR (code = 3, invalid value) at csr_matrix_cuda_utils.c:57 Regards, Maruthi On Tue, Sep 12, 2023 at 1:09?AM Junchao Zhang wrote: > Hi, Maruthi, > I could run your example on my machine. BTW, I added these at the end > of main() to free petsc objects. > VecDestroy(&vout); > VecDestroy(&x); > VecDestroy(&b); > VecDestroy(&u); > MatDestroy(&A); > VecScatterDestroy(&ctx); > KSPDestroy(&ksp); > > If you use cuda-12.2, maybe the problem is already fixed by MR > https://gitlab.com/petsc/petsc/-/merge_requests/6828 > You can use petsc/main branch to try. Note your petsc version is from > Date: 2023-08-13 > > Thanks. > --Junchao Zhang > > > On Mon, Sep 11, 2023 at 12:10?PM Maruthi NH wrote: > >> Hi Barry Smith, >> >> Thanks for the quick response. >> >> Here is the code I used to test PETSc on GPU. >> This is the command I used to run >> mpiexec.hydra -n 1 ./heat_diff_cu -Nx 10000000 -ksp_type gmres -mat_type >> aijcusparse -vec_type cuda -use_gpu_aware_mpi 0 -pc_type gamg >> -ksp_converged_reason >> >> Regards, >> Maruthi >> >> >> >> On Sun, Sep 10, 2023 at 11:37?PM Barry Smith wrote: >> >>> >>> >>> On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: >>> >>> Hi all, >>> >>> I am trying to accelerate the linear solver with PETSc GPU backend. For >>> testing I have a simple 1D heat diffusion solver, here are some >>> observations. >>> 1. If I use -pc_type gamg it throws the following error >>> ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) >>> had an illegal value: NULL pointer >>> >>> [0]PETSC ERROR: --------------------- Error Message >>> -------------------------------------------------------------- >>> [0]PETSC ERROR: GPU error >>> [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : >>> invalid value >>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. >>> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-959-g92f1e92e88 >>> GIT Date: 2023-08-13 19:43:04 +0000 >>> >>> Can you share the code that triggers this? >>> >>> 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes >>> about 105.9 seconds on a GPU. Similar observations with pc_type asm >>> I have NVIDIA RTX A2000 8GB Laptop GPU >>> >>> >>> This is expected. The triangular solves sequentialize on the GPU so >>> naturally are extremely slow since they cannot take advantage of the >>> massive parallelism of the GPU. >>> >>> >>> 3. What I could be missing? Also, are there any general guidelines for >>> better GPU performance using PETSc? >>> >>> Regards, >>> Maruthi >>> >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From junchao.zhang at gmail.com Tue Sep 12 11:49:59 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Tue, 12 Sep 2023 11:49:59 -0500 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: References: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> Message-ID: Which version of hypre do you use? I used petsc's --download-hypre, which automatically installed hypre-2.29.0. I did not see the error. $ ./heat_diff_cu -ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda The start and end indices of mat for each rank: 0 100 Total time taken for KSP solve: rank: 0 0.0112464 --Junchao Zhang On Tue, Sep 12, 2023 at 10:15?AM Maruthi NH wrote: > Hi Junchao Zhang, > > Thanks for the help. Updating PETSc fixed the problem. However, if I use > boomeramg from hypre as follows, I get a similar error. > > ./heat_diff_cu --ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg > -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda > > ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) had > an illegal value: NULL pointer > > CUSPARSE ERROR (code = 3, invalid value) at csr_matrix_cuda_utils.c:57 > > Regards, > Maruthi > > > > > > On Tue, Sep 12, 2023 at 1:09?AM Junchao Zhang > wrote: > >> Hi, Maruthi, >> I could run your example on my machine. BTW, I added these at the end >> of main() to free petsc objects. >> VecDestroy(&vout); >> VecDestroy(&x); >> VecDestroy(&b); >> VecDestroy(&u); >> MatDestroy(&A); >> VecScatterDestroy(&ctx); >> KSPDestroy(&ksp); >> >> If you use cuda-12.2, maybe the problem is already fixed by MR >> https://gitlab.com/petsc/petsc/-/merge_requests/6828 >> You can use petsc/main branch to try. Note your petsc version is from >> Date: 2023-08-13 >> >> Thanks. >> --Junchao Zhang >> >> >> On Mon, Sep 11, 2023 at 12:10?PM Maruthi NH wrote: >> >>> Hi Barry Smith, >>> >>> Thanks for the quick response. >>> >>> Here is the code I used to test PETSc on GPU. >>> This is the command I used to run >>> mpiexec.hydra -n 1 ./heat_diff_cu -Nx 10000000 -ksp_type gmres -mat_type >>> aijcusparse -vec_type cuda -use_gpu_aware_mpi 0 -pc_type gamg >>> -ksp_converged_reason >>> >>> Regards, >>> Maruthi >>> >>> >>> >>> On Sun, Sep 10, 2023 at 11:37?PM Barry Smith wrote: >>> >>>> >>>> >>>> On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: >>>> >>>> Hi all, >>>> >>>> I am trying to accelerate the linear solver with PETSc GPU backend. For >>>> testing I have a simple 1D heat diffusion solver, here are some >>>> observations. >>>> 1. If I use -pc_type gamg it throws the following error >>>> ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) >>>> had an illegal value: NULL pointer >>>> >>>> [0]PETSC ERROR: --------------------- Error Message >>>> -------------------------------------------------------------- >>>> [0]PETSC ERROR: GPU error >>>> [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : >>>> invalid value >>>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>> shooting. >>>> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-959-g92f1e92e88 >>>> GIT Date: 2023-08-13 19:43:04 +0000 >>>> >>>> Can you share the code that triggers this? >>>> >>>> 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes >>>> about 105.9 seconds on a GPU. Similar observations with pc_type asm >>>> I have NVIDIA RTX A2000 8GB Laptop GPU >>>> >>>> >>>> This is expected. The triangular solves sequentialize on the GPU so >>>> naturally are extremely slow since they cannot take advantage of the >>>> massive parallelism of the GPU. >>>> >>>> >>>> 3. What I could be missing? Also, are there any general guidelines for >>>> better GPU performance using PETSc? >>>> >>>> Regards, >>>> Maruthi >>>> >>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From maruthinh at gmail.com Wed Sep 13 01:06:27 2023 From: maruthinh at gmail.com (Maruthi NH) Date: Wed, 13 Sep 2023 11:36:27 +0530 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: References: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> Message-ID: Hi Junchao Zhang, I also build petsc with --download-hypre and I too have 2.29.0 version. Not sure why I am facing this issue. This is the configuration file I created for building petsc. #!/usr/bin/env python3 import os petsc_hash_pkgs=os.path.join(os.getenv('HOME'),'petsc-hash-pkgs') if __name__ == '__main__': import sys import os sys.path.insert(0, os.path.abspath('config')) import configure configure_options = [ '--package-prefix-hash='+petsc_hash_pkgs, '--with-debugging=0', '--with-shared-libraries=0', '--with-cc=mpiicc', '--with-cxx=mpiicpc', '--with-fc=mpiifort', '--with-mpiexec=mpiexec.hydra', '--with-cudac=nvcc', # nvcc-12.2 via ccache '--with-cuda-dir=/usr/local/cuda-12.2', # Intel compilers enable GCC/clangs equivalent of -ffast-math *by default*. This is # bananas, so we make sure they use the same model as everyone else 'COPTFLAGS=-O3 -fPIE -fp-model=precise', 'FOPTFLAGS=-O3 -fPIE -fp-model=precise', 'CXXOPTFLAGS=-O3 -fPIE -fp-model=precise', 'CUDAOPTFLAGS=-O3', '--with-precision=double', '--with-blaslapack-dir='+os.environ['MKLROOT'], '--with-mkl_pardiso-dir='+os.environ['MKLROOT'], '--with-mkl_cpardiso-dir='+os.environ['MKLROOT'], '--download-hypre', ] configure.petsc_configure(configure_options) Regards, Maruthi On Tue, Sep 12, 2023 at 10:20?PM Junchao Zhang wrote: > Which version of hypre do you use? I used petsc's --download-hypre, which > automatically installed hypre-2.29.0. I did not see the error. > > $ ./heat_diff_cu -ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg > -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda > The start and end indices of mat for each rank: 0 100 > Total time taken for KSP solve: rank: 0 0.0112464 > > --Junchao Zhang > > > On Tue, Sep 12, 2023 at 10:15?AM Maruthi NH wrote: > >> Hi Junchao Zhang, >> >> Thanks for the help. Updating PETSc fixed the problem. However, if I use >> boomeramg from hypre as follows, I get a similar error. >> >> ./heat_diff_cu --ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg >> -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda >> >> ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) had >> an illegal value: NULL pointer >> >> CUSPARSE ERROR (code = 3, invalid value) at csr_matrix_cuda_utils.c:57 >> >> Regards, >> Maruthi >> >> >> >> >> >> On Tue, Sep 12, 2023 at 1:09?AM Junchao Zhang >> wrote: >> >>> Hi, Maruthi, >>> I could run your example on my machine. BTW, I added these at the >>> end of main() to free petsc objects. >>> VecDestroy(&vout); >>> VecDestroy(&x); >>> VecDestroy(&b); >>> VecDestroy(&u); >>> MatDestroy(&A); >>> VecScatterDestroy(&ctx); >>> KSPDestroy(&ksp); >>> >>> If you use cuda-12.2, maybe the problem is already fixed by MR >>> https://gitlab.com/petsc/petsc/-/merge_requests/6828 >>> You can use petsc/main branch to try. Note your petsc version is from >>> Date: 2023-08-13 >>> >>> Thanks. >>> --Junchao Zhang >>> >>> >>> On Mon, Sep 11, 2023 at 12:10?PM Maruthi NH wrote: >>> >>>> Hi Barry Smith, >>>> >>>> Thanks for the quick response. >>>> >>>> Here is the code I used to test PETSc on GPU. >>>> This is the command I used to run >>>> mpiexec.hydra -n 1 ./heat_diff_cu -Nx 10000000 -ksp_type gmres >>>> -mat_type aijcusparse -vec_type cuda -use_gpu_aware_mpi 0 -pc_type gamg >>>> -ksp_converged_reason >>>> >>>> Regards, >>>> Maruthi >>>> >>>> >>>> >>>> On Sun, Sep 10, 2023 at 11:37?PM Barry Smith wrote: >>>> >>>>> >>>>> >>>>> On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: >>>>> >>>>> Hi all, >>>>> >>>>> I am trying to accelerate the linear solver with PETSc GPU backend. >>>>> For testing I have a simple 1D heat diffusion solver, here are some >>>>> observations. >>>>> 1. If I use -pc_type gamg it throws the following error >>>>> ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) >>>>> had an illegal value: NULL pointer >>>>> >>>>> [0]PETSC ERROR: --------------------- Error Message >>>>> -------------------------------------------------------------- >>>>> [0]PETSC ERROR: GPU error >>>>> [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) : >>>>> invalid value >>>>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>> shooting. >>>>> [0]PETSC ERROR: Petsc Development GIT revision: >>>>> v3.19.4-959-g92f1e92e88 GIT Date: 2023-08-13 19:43:04 +0000 >>>>> >>>>> Can you share the code that triggers this? >>>>> >>>>> 2. Default pc ilu takes about 1.2 seconds on a single CPU and it takes >>>>> about 105.9 seconds on a GPU. Similar observations with pc_type asm >>>>> I have NVIDIA RTX A2000 8GB Laptop GPU >>>>> >>>>> >>>>> This is expected. The triangular solves sequentialize on the GPU so >>>>> naturally are extremely slow since they cannot take advantage of the >>>>> massive parallelism of the GPU. >>>>> >>>>> >>>>> 3. What I could be missing? Also, are there any general guidelines for >>>>> better GPU performance using PETSc? >>>>> >>>>> Regards, >>>>> Maruthi >>>>> >>>>> >>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From junchao.zhang at gmail.com Wed Sep 13 13:42:08 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Wed, 13 Sep 2023 13:42:08 -0500 Subject: [petsc-users] Error while running with -pc_type gamg on NVIDIA GPU In-Reply-To: References: <2BD6A1C5-B64F-4E77-AE33-16AD68352968@petsc.dev> Message-ID: Hi, Maruthi, I could not reproduce it. I used the attached slightly modified code (note the added PetscFunctionBeginUser; PetscFunctionReturn(PETSC_SUCCESS); in bc_const_temp_both_sides) Could you try it? --Junchao Zhang On Wed, Sep 13, 2023 at 1:07?AM Maruthi NH wrote: > Hi Junchao Zhang, > > I also build petsc with --download-hypre and I too have 2.29.0 version. > Not sure why I am facing this issue. This is the configuration file I > created for building petsc. > > #!/usr/bin/env python3 > > import os > petsc_hash_pkgs=os.path.join(os.getenv('HOME'),'petsc-hash-pkgs') > > if __name__ == '__main__': > import sys > import os > sys.path.insert(0, os.path.abspath('config')) > import configure > configure_options = [ > '--package-prefix-hash='+petsc_hash_pkgs, > '--with-debugging=0', > '--with-shared-libraries=0', > '--with-cc=mpiicc', > '--with-cxx=mpiicpc', > '--with-fc=mpiifort', > '--with-mpiexec=mpiexec.hydra', > '--with-cudac=nvcc', # nvcc-12.2 via ccache > '--with-cuda-dir=/usr/local/cuda-12.2', > # Intel compilers enable GCC/clangs equivalent of -ffast-math *by > default*. This is > # bananas, so we make sure they use the same model as everyone else > 'COPTFLAGS=-O3 -fPIE -fp-model=precise', > 'FOPTFLAGS=-O3 -fPIE -fp-model=precise', > 'CXXOPTFLAGS=-O3 -fPIE -fp-model=precise', > 'CUDAOPTFLAGS=-O3', > '--with-precision=double', > '--with-blaslapack-dir='+os.environ['MKLROOT'], > '--with-mkl_pardiso-dir='+os.environ['MKLROOT'], > '--with-mkl_cpardiso-dir='+os.environ['MKLROOT'], > '--download-hypre', > ] > configure.petsc_configure(configure_options) > > Regards, > Maruthi > > On Tue, Sep 12, 2023 at 10:20?PM Junchao Zhang > wrote: > >> Which version of hypre do you use? I used petsc's --download-hypre, >> which automatically installed hypre-2.29.0. I did not see the error. >> >> $ ./heat_diff_cu -ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg >> -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda >> The start and end indices of mat for each rank: 0 100 >> Total time taken for KSP solve: rank: 0 0.0112464 >> >> --Junchao Zhang >> >> >> On Tue, Sep 12, 2023 at 10:15?AM Maruthi NH wrote: >> >>> Hi Junchao Zhang, >>> >>> Thanks for the help. Updating PETSc fixed the problem. However, if I use >>> boomeramg from hypre as follows, I get a similar error. >>> >>> ./heat_diff_cu --ksp_type gmres -pc_type hypre -pc_hypre_type boomeramg >>> -use_gpu_aware_mpi 0 -mat_type aijcusparse -vec_type cuda >>> >>> ** On entry to cusparseCreateCsr() parameter number 5 (csrRowOffsets) >>> had an illegal value: NULL pointer >>> >>> CUSPARSE ERROR (code = 3, invalid value) at csr_matrix_cuda_utils.c:57 >>> >>> Regards, >>> Maruthi >>> >>> >>> >>> >>> >>> On Tue, Sep 12, 2023 at 1:09?AM Junchao Zhang >>> wrote: >>> >>>> Hi, Maruthi, >>>> I could run your example on my machine. BTW, I added these at the >>>> end of main() to free petsc objects. >>>> VecDestroy(&vout); >>>> VecDestroy(&x); >>>> VecDestroy(&b); >>>> VecDestroy(&u); >>>> MatDestroy(&A); >>>> VecScatterDestroy(&ctx); >>>> KSPDestroy(&ksp); >>>> >>>> If you use cuda-12.2, maybe the problem is already fixed by MR >>>> https://gitlab.com/petsc/petsc/-/merge_requests/6828 >>>> You can use petsc/main branch to try. Note your petsc version is from >>>> Date: 2023-08-13 >>>> >>>> Thanks. >>>> --Junchao Zhang >>>> >>>> >>>> On Mon, Sep 11, 2023 at 12:10?PM Maruthi NH >>>> wrote: >>>> >>>>> Hi Barry Smith, >>>>> >>>>> Thanks for the quick response. >>>>> >>>>> Here is the code I used to test PETSc on GPU. >>>>> This is the command I used to run >>>>> mpiexec.hydra -n 1 ./heat_diff_cu -Nx 10000000 -ksp_type gmres >>>>> -mat_type aijcusparse -vec_type cuda -use_gpu_aware_mpi 0 -pc_type gamg >>>>> -ksp_converged_reason >>>>> >>>>> Regards, >>>>> Maruthi >>>>> >>>>> >>>>> >>>>> On Sun, Sep 10, 2023 at 11:37?PM Barry Smith wrote: >>>>> >>>>>> >>>>>> >>>>>> On Sep 10, 2023, at 5:54 AM, Maruthi NH wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I am trying to accelerate the linear solver with PETSc GPU backend. >>>>>> For testing I have a simple 1D heat diffusion solver, here are some >>>>>> observations. >>>>>> 1. If I use -pc_type gamg it throws the following error >>>>>> ** On entry to cusparseCreateCsr() parameter number 5 >>>>>> (csrRowOffsets) had an illegal value: NULL pointer >>>>>> >>>>>> [0]PETSC ERROR: --------------------- Error Message >>>>>> -------------------------------------------------------------- >>>>>> [0]PETSC ERROR: GPU error >>>>>> [0]PETSC ERROR: cuSPARSE errorcode 3 (CUSPARSE_STATUS_INVALID_VALUE) >>>>>> : invalid value >>>>>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>> shooting. >>>>>> [0]PETSC ERROR: Petsc Development GIT revision: >>>>>> v3.19.4-959-g92f1e92e88 GIT Date: 2023-08-13 19:43:04 +0000 >>>>>> >>>>>> Can you share the code that triggers this? >>>>>> >>>>>> 2. Default pc ilu takes about 1.2 seconds on a single CPU and it >>>>>> takes about 105.9 seconds on a GPU. Similar observations with pc_type asm >>>>>> I have NVIDIA RTX A2000 8GB Laptop GPU >>>>>> >>>>>> >>>>>> This is expected. The triangular solves sequentialize on the GPU so >>>>>> naturally are extremely slow since they cannot take advantage of the >>>>>> massive parallelism of the GPU. >>>>>> >>>>>> >>>>>> 3. What I could be missing? Also, are there any general guidelines >>>>>> for better GPU performance using PETSc? >>>>>> >>>>>> Regards, >>>>>> Maruthi >>>>>> >>>>>> >>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: heat_diff_cu.cu Type: application/octet-stream Size: 6990 bytes Desc: not available URL: From gongding at cn.cogenda.com Thu Sep 14 04:35:14 2023 From: gongding at cn.cogenda.com (Gong Ding) Date: Thu, 14 Sep 2023 17:35:14 +0800 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix Message-ID: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> Hi all I find such a nonlinear problem, the jacobian matrix is ill conditioned. Solve the jacobian matrix by 64bit LU? solver, the Newton method failed to convergence. However, when solve the jacobian matrix by 128bit LU solver , Newton iteration will convergence. I think this phenomena indicate that , the jacobian matrix is ill conditioned. The question is, if I do a precondition as M*J*dx = -M*f(x), here M is the precondition matrix, . then I solve the matrix A=M*J by a LU solver. Can I expect that solve A=M*J has a better precision result that help the convergence of Newton iteration? Gong Ding From mfadams at lbl.gov Thu Sep 14 05:35:30 2023 From: mfadams at lbl.gov (Mark Adams) Date: Thu, 14 Sep 2023 06:35:30 -0400 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix In-Reply-To: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> References: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> Message-ID: I would first verify that you are happy with the solution that works. Next, I would worry about losing accuracy in computing M*J, but you could try it and search for any related work. There may be some tricks. And MUMPS is good at high accuracy, you might try that and if it fails look at the MUMPS docs for any flags for high-accuracy. Good luck, Mark On Thu, Sep 14, 2023 at 5:35?AM Gong Ding wrote: > Hi all > > I find such a nonlinear problem, the jacobian matrix is ill conditioned. > > Solve the jacobian matrix by 64bit LU solver, the Newton method failed > to convergence. > > However, when solve the jacobian matrix by 128bit LU solver , Newton > iteration will convergence. > > I think this phenomena indicate that , the jacobian matrix is ill > conditioned. > > > The question is, if I do a precondition as M*J*dx = -M*f(x), here M is > the precondition matrix, . then I solve the matrix A=M*J by a LU solver. > > Can I expect that solve A=M*J has a better precision result that help > the convergence of Newton iteration? > > Gong Ding > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hzhang at mcs.anl.gov Thu Sep 14 10:05:06 2023 From: hzhang at mcs.anl.gov (Zhang, Hong) Date: Thu, 14 Sep 2023 15:05:06 +0000 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix In-Reply-To: References: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> Message-ID: Gong Ding, When you use a LU solver, the preconditioner M = inv(LU) = inv (J) on theory. I suspect your jacobian evaluation by 64bit might be inaccurate. What LU solver did you use? Run your code with option '-snes_view -snes_monitor -ksp_monitor' and compare the displays. Hong ________________________________ From: petsc-users on behalf of Mark Adams Sent: Thursday, September 14, 2023 5:35 AM To: Gong Ding Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Is precondition works for ill-conditioned jacobian matrix I would first verify that you are happy with the solution that works. Next, I would worry about losing accuracy in computing M*J, but you could try it and search for any related work. There may be some tricks. And MUMPS is good at high accuracy, you might try that and if it fails look at the MUMPS docs for any flags for high-accuracy. Good luck, Mark On Thu, Sep 14, 2023 at 5:35?AM Gong Ding > wrote: Hi all I find such a nonlinear problem, the jacobian matrix is ill conditioned. Solve the jacobian matrix by 64bit LU solver, the Newton method failed to convergence. However, when solve the jacobian matrix by 128bit LU solver , Newton iteration will convergence. I think this phenomena indicate that , the jacobian matrix is ill conditioned. The question is, if I do a precondition as M*J*dx = -M*f(x), here M is the precondition matrix, . then I solve the matrix A=M*J by a LU solver. Can I expect that solve A=M*J has a better precision result that help the convergence of Newton iteration? Gong Ding -------------- next part -------------- An HTML attachment was scrubbed... URL: From gongding at cn.cogenda.com Thu Sep 14 11:30:22 2023 From: gongding at cn.cogenda.com (Gong Ding) Date: Fri, 15 Sep 2023 00:30:22 +0800 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix In-Reply-To: References: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> Message-ID: <714c6329-3a55-1222-6853-85436e1f483d@cn.cogenda.com> The physical problem itself is ill-conditioned since there are floating regions in the simulation domain. I use MUMPS as 64 bit LU solver, and a special improved SuperLU as 128 bit LU solver (https://github.com/cogenda/superlu, added float128 support). Although 128 bit solver works, it is 10x slower. I'd like to try, if? jacobian can be processed under 64 bit precision while keeps the Newton iteration convergence. Method 1: Use a block inversion of the main diagonal of jacobian as preconditioner? (or ILU? ). Then factorize M*J. Both the precondition matrix and jacobian matrix are 64 bit. Method 2: Do a 64 bit LU factorization of jacobian matrix, and use the factorization result as a preconditioner for higher precision krylov solver (such as iterative refinement) On 2023/9/14 23:05, Zhang, Hong wrote: > Gong Ding, > When you use a LU solver, the preconditioner M = inv(LU) = inv (J) on > theory. I suspect your jacobian evaluation by?64bit might be > inaccurate. What LU solver did you use? Run your code with option > '-snes_view -snes_monitor -ksp_monitor' and compare the displays. > Hong > ------------------------------------------------------------------------ > *From:* petsc-users on behalf of > Mark Adams > *Sent:* Thursday, September 14, 2023 5:35 AM > *To:* Gong Ding > *Cc:* petsc-users at mcs.anl.gov > *Subject:* Re: [petsc-users] Is precondition works for ill-conditioned > jacobian matrix > I would first verify that you are happy with the solution that works. > > Next, I would worry about losing accuracy in computing M*J, but you > could try it and search for any related work. There may be some tricks. > > And MUMPS is good at high accuracy, you might try that and if it fails > look at the MUMPS docs for any flags for high-accuracy. > > Good luck, > Mark > > On Thu, Sep 14, 2023 at 5:35?AM Gong Ding wrote: > > Hi all > > I find such a nonlinear problem, the jacobian matrix is ill > conditioned. > > Solve the jacobian matrix by 64bit LU? solver, the Newton method > failed > to convergence. > > However, when solve the jacobian matrix by 128bit LU solver , Newton > iteration will convergence. > > I think this phenomena indicate that , the jacobian matrix is ill > conditioned. > > > The question is, if I do a precondition as M*J*dx = -M*f(x), here > M is > the precondition matrix, . then I solve the matrix A=M*J by a LU > solver. > > Can I expect that solve A=M*J has a better precision result that help > the convergence of Newton iteration? > > Gong Ding > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Thu Sep 14 12:37:46 2023 From: bsmith at petsc.dev (Barry Smith) Date: Thu, 14 Sep 2023 13:37:46 -0400 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix In-Reply-To: <714c6329-3a55-1222-6853-85436e1f483d@cn.cogenda.com> References: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> <714c6329-3a55-1222-6853-85436e1f483d@cn.cogenda.com> Message-ID: Method 1 and 2 are unlikely to work. It sounds like your matrix is (in exact precision) singular, but using 128 bit floats allows a "stable" factorization to go through giving you a descent direction for Newton. I think you really need to fix the singularity at the modeling level, it is not robust to fix it at the numerical algorithm level. If you know the exact form of the null spaces you can use MatSetNullSpace() but you cannot use a direct solver for the system since the factorization will still see the singular matrix. Barry > On Sep 14, 2023, at 12:30 PM, Gong Ding wrote: > > The physical problem itself is ill-conditioned since there are floating regions in the simulation domain. > I use MUMPS as 64 bit LU solver, and a special improved SuperLU as 128 bit LU solver (https://github.com/cogenda/superlu, added float128 support). > Although 128 bit solver works, it is 10x slower. > > I'd like to try, if jacobian can be processed under 64 bit precision while keeps the Newton iteration convergence. > > > Method 1: > Use a block inversion of the main diagonal of jacobian as preconditioner (or ILU? ). Then factorize M*J. > Both the precondition matrix and jacobian matrix are 64 bit. > > Method 2: > Do a 64 bit LU factorization of jacobian matrix, and use the factorization result as a preconditioner for higher precision krylov solver (such as iterative refinement) > > > > On 2023/9/14 23:05, Zhang, Hong wrote: >> Gong Ding, >> When you use a LU solver, the preconditioner M = inv(LU) = inv (J) on theory. I suspect your jacobian evaluation by 64bit might be inaccurate. What LU solver did you use? Run your code with option '-snes_view -snes_monitor -ksp_monitor' and compare the displays. >> Hong >> From: petsc-users on behalf of Mark Adams >> Sent: Thursday, September 14, 2023 5:35 AM >> To: Gong Ding >> Cc: petsc-users at mcs.anl.gov >> Subject: Re: [petsc-users] Is precondition works for ill-conditioned jacobian matrix >> >> I would first verify that you are happy with the solution that works. >> >> Next, I would worry about losing accuracy in computing M*J, but you could try it and search for any related work. There may be some tricks. >> >> And MUMPS is good at high accuracy, you might try that and if it fails look at the MUMPS docs for any flags for high-accuracy. >> >> Good luck, >> Mark >> >> On Thu, Sep 14, 2023 at 5:35?AM Gong Ding > wrote: >> Hi all >> >> I find such a nonlinear problem, the jacobian matrix is ill conditioned. >> >> Solve the jacobian matrix by 64bit LU solver, the Newton method failed >> to convergence. >> >> However, when solve the jacobian matrix by 128bit LU solver , Newton >> iteration will convergence. >> >> I think this phenomena indicate that , the jacobian matrix is ill >> conditioned. >> >> >> The question is, if I do a precondition as M*J*dx = -M*f(x), here M is >> the precondition matrix, . then I solve the matrix A=M*J by a LU solver. >> >> Can I expect that solve A=M*J has a better precision result that help >> the convergence of Newton iteration? >> >> Gong Ding -------------- next part -------------- An HTML attachment was scrubbed... URL: From gongding at cn.cogenda.com Thu Sep 14 22:29:41 2023 From: gongding at cn.cogenda.com (Gong Ding) Date: Fri, 15 Sep 2023 11:29:41 +0800 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix In-Reply-To: References: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> <714c6329-3a55-1222-6853-85436e1f483d@cn.cogenda.com> Message-ID: <78420c93-8b38-f382-16f3-10155bbe6ef5@cn.cogenda.com> The matrix has a bad condition number, but not singular. It comes from real physical problem and the floating zone is weekly controlled by remote boundary condition. Yes, I am also afraid that with 64 bit floating number, the matrix is numerically singular since the construction of jacaobian has already lost precision. Anyway, I can build the jacobian at 128 bit precision and then truncate to 64 bit. Our solution x and function f can also be evaluated at 128 bit precision. The main purpose is, always do LU factorization at 64 bit for performance issue. Method 1 tries to "precondition" a direct solver. I don't know if possible. Method 2 wants to use post refinement to improve the accuracy of a direct solver. Theoretically, I think it should work. On 2023/9/15 01:37, Barry Smith wrote: > > ? Method 1 and 2 are unlikely to work. > > ? It sounds like your matrix is (in exact precision) singular, but > using 128 bit floats allows a "stable" factorization to go through > giving you a descent direction for Newton. > > ? I think you really need to fix the singularity at the modeling > level, it is not robust to fix it at the numerical algorithm level. If > you know the exact form of the null spaces you can use > MatSetNullSpace() but you cannot use a direct solver for the system > since the factorization will still see the singular matrix. > > ? ?Barry > > >> On Sep 14, 2023, at 12:30 PM, Gong Ding wrote: >> >> The physical problem itself is ill-conditioned since there are >> floating regions in the simulation domain. >> I use MUMPS as 64 bit LU solver, and a special improved SuperLU as >> 128 bit LU solver (https://github.com/cogenda/superlu, added float128 >> support). >> Although 128 bit solver works, it is 10x slower. >> >> I'd like to try, if? jacobian can be processed under 64 bit precision >> while keeps the Newton iteration convergence. >> >> >> Method 1: >> Use a block inversion of the main diagonal of jacobian as >> preconditioner? (or ILU? ). Then factorize M*J. >> Both the precondition matrix and jacobian matrix are 64 bit. >> >> Method 2: >> Do a 64 bit LU factorization of jacobian matrix, and use the >> factorization result as a preconditioner for higher precision krylov >> solver (such as iterative refinement) >> >> >> >> On 2023/9/14 23:05, Zhang, Hong wrote: >>> Gong Ding, >>> When you use a LU solver, the preconditioner M = inv(LU) = inv (J) >>> on theory. I suspect your jacobian evaluation by?64bit might be >>> inaccurate. What LU solver did you use? Run your code with option >>> '-snes_view -snes_monitor -ksp_monitor' and compare the displays. >>> Hong >>> ------------------------------------------------------------------------ >>> *From:*petsc-userson behalf of Mark >>> Adams >>> *Sent:*Thursday, September 14, 2023 5:35 AM >>> *To:*Gong Ding >>> *Cc:*petsc-users at mcs.anl.gov >>> *Subject:*Re: [petsc-users] Is precondition works for >>> ill-conditioned jacobian matrix >>> I would first verify that you are happy with the solution that works. >>> >>> Next, I would worry about losing accuracy in computing M*J, but you >>> could try it and search for any related work. There may be some tricks. >>> >>> And MUMPS is good at high accuracy, you might try that and if it >>> fails look at the MUMPS docs for any flags for high-accuracy. >>> >>> Good luck, >>> Mark >>> >>> On Thu, Sep 14, 2023 at 5:35?AM Gong Ding >>> wrote: >>> >>> Hi all >>> >>> I find such a nonlinear problem, the jacobian matrix is ill >>> conditioned. >>> >>> Solve the jacobian matrix by 64bit LU? solver, the Newton method >>> failed >>> to convergence. >>> >>> However, when solve the jacobian matrix by 128bit LU solver , Newton >>> iteration will convergence. >>> >>> I think this phenomena indicate that , the jacobian matrix is ill >>> conditioned. >>> >>> >>> The question is, if I do a precondition as M*J*dx = -M*f(x), >>> here M is >>> the precondition matrix, . then I solve the matrix A=M*J by a LU >>> solver. >>> >>> Can I expect that solve A=M*J has a better precision result that >>> help >>> the convergence of Newton iteration? >>> >>> Gong Ding >>> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hzhang at mcs.anl.gov Fri Sep 15 09:27:12 2023 From: hzhang at mcs.anl.gov (Zhang, Hong) Date: Fri, 15 Sep 2023 14:27:12 +0000 Subject: [petsc-users] Is precondition works for ill-conditioned jacobian matrix In-Reply-To: <78420c93-8b38-f382-16f3-10155bbe6ef5@cn.cogenda.com> References: <6fd3e32d-f38e-e6fc-1191-671b8e75f00b@cn.cogenda.com> <714c6329-3a55-1222-6853-85436e1f483d@cn.cogenda.com> <78420c93-8b38-f382-16f3-10155bbe6ef5@cn.cogenda.com> Message-ID: Gong, Iterative refinement might help, i.e., more than one MatSolve ( LU x = b) is applied. If you use superlu_dist, this operation can be activated at runtime by the option '-pc_type lu -pc_factor_mat_solver_type superlu_dist -mat_superlu_dist_iterrefine' (run your code withe '-help' for available options). Using mumps, the iterative refinement can be activated by -mat_mumps_icntl_10: : ICNTL(10): max num of refinements (None) i.e., '-mat_mumps_icntl_10 1' applies one refinement. I suspect the LU solver would be called again if one MatSolve() does not reach the required tolerance. Check your runs with '-snes_monitor -ksp_monitor' to get more understanding. Hong ________________________________ From: petsc-users on behalf of Gong Ding Sent: Thursday, September 14, 2023 10:29 PM To: Barry Smith Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Is precondition works for ill-conditioned jacobian matrix The matrix has a bad condition number, but not singular. It comes from real physical problem and the floating zone is weekly controlled by remote boundary condition. Yes, I am also afraid that with 64 bit floating number, the matrix is numerically singular since the construction of jacaobian has already lost precision. Anyway, I can build the jacobian at 128 bit precision and then truncate to 64 bit. Our solution x and function f can also be evaluated at 128 bit precision. The main purpose is, always do LU factorization at 64 bit for performance issue. Method 1 tries to "precondition" a direct solver. I don't know if possible. Method 2 wants to use post refinement to improve the accuracy of a direct solver. Theoretically, I think it should work. On 2023/9/15 01:37, Barry Smith wrote: Method 1 and 2 are unlikely to work. It sounds like your matrix is (in exact precision) singular, but using 128 bit floats allows a "stable" factorization to go through giving you a descent direction for Newton. I think you really need to fix the singularity at the modeling level, it is not robust to fix it at the numerical algorithm level. If you know the exact form of the null spaces you can use MatSetNullSpace() but you cannot use a direct solver for the system since the factorization will still see the singular matrix. Barry On Sep 14, 2023, at 12:30 PM, Gong Ding wrote: The physical problem itself is ill-conditioned since there are floating regions in the simulation domain. I use MUMPS as 64 bit LU solver, and a special improved SuperLU as 128 bit LU solver (https://github.com/cogenda/superlu, added float128 support). Although 128 bit solver works, it is 10x slower. I'd like to try, if jacobian can be processed under 64 bit precision while keeps the Newton iteration convergence. Method 1: Use a block inversion of the main diagonal of jacobian as preconditioner (or ILU? ). Then factorize M*J. Both the precondition matrix and jacobian matrix are 64 bit. Method 2: Do a 64 bit LU factorization of jacobian matrix, and use the factorization result as a preconditioner for higher precision krylov solver (such as iterative refinement) On 2023/9/14 23:05, Zhang, Hong wrote: Gong Ding, When you use a LU solver, the preconditioner M = inv(LU) = inv (J) on theory. I suspect your jacobian evaluation by 64bit might be inaccurate. What LU solver did you use? Run your code with option '-snes_view -snes_monitor -ksp_monitor' and compare the displays. Hong ________________________________ From: petsc-users on behalf of Mark Adams Sent: Thursday, September 14, 2023 5:35 AM To: Gong Ding Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Is precondition works for ill-conditioned jacobian matrix I would first verify that you are happy with the solution that works. Next, I would worry about losing accuracy in computing M*J, but you could try it and search for any related work. There may be some tricks. And MUMPS is good at high accuracy, you might try that and if it fails look at the MUMPS docs for any flags for high-accuracy. Good luck, Mark On Thu, Sep 14, 2023 at 5:35?AM Gong Ding > wrote: Hi all I find such a nonlinear problem, the jacobian matrix is ill conditioned. Solve the jacobian matrix by 64bit LU solver, the Newton method failed to convergence. However, when solve the jacobian matrix by 128bit LU solver , Newton iteration will convergence. I think this phenomena indicate that , the jacobian matrix is ill conditioned. The question is, if I do a precondition as M*J*dx = -M*f(x), here M is the precondition matrix, . then I solve the matrix A=M*J by a LU solver. Can I expect that solve A=M*J has a better precision result that help the convergence of Newton iteration? Gong Ding -------------- next part -------------- An HTML attachment was scrubbed... URL: From bubu.cattaneo at gmail.com Fri Sep 15 17:50:36 2023 From: bubu.cattaneo at gmail.com (Alberto Cattaneo) Date: Fri, 15 Sep 2023 16:50:36 -0600 Subject: [petsc-users] Having some trouble creating a library Message-ID: Greetings I hope this email reaches you well. I'm afraid I'm having a bit of trouble using PETSC for a library I'm writing for myself, and I was hoping for some clarification/help. I've been writing PETSC C code and compiling it using the included makefiles in the tutorial section as that was sufficient. However, I decided since there are a few functions I keep using it would be beneficial to write them and make them into a little library for myself. However, I'm having some difficulty understanding what I need to include when trying to compile something as a library with PETSC stuff. The makefiles are rather complicated, so I thought it may be more prudent to just ask. I'm trying to use #include and #include to have access to the PETSC data types (PetscScalar, PetscInt) but I can't find where those files are located, and I wanted to check if just using gcc with those added was sufficient or if I needed some other compiler flags and options. Please forgive me if this is a silly question, but makefiles have always been tricky for me. Respectfully: Alberto -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Fri Sep 15 23:07:47 2023 From: bsmith at petsc.dev (Barry Smith) Date: Sat, 16 Sep 2023 00:07:47 -0400 Subject: [petsc-users] Having some trouble creating a library In-Reply-To: References: Message-ID: <6B493203-4179-4C0D-80FE-055344AA32BE@petsc.dev> There are multiple ways to do this. See https://petsc.org/release/manual/getting_started/#sec-writing-application-codes in particular Select an application build process. The PETSC_DIR (and PETSC_ARCH if the --prefix=directoryname option was not used when configuring PETSc) environmental variable(s) must be set for any of these approaches. make (recommended). Copy $PETSC_DIR/share/petsc/Makefile.user or $PETSC_DIR/share/petsc/Makefile.basic.user to your directory, for example, cp $PETSC_DIR/share/petsc/Makefile.user makefile Examine the comments in your makefile Makefile.user uses the pkg-config tool and is the recommended approach. These makefile automatically set certain make variables that handle setting the locations of the include files for you. The comments in the makefiles tell you how to proceed. > On Sep 15, 2023, at 6:50 PM, Alberto Cattaneo wrote: > > Greetings > I hope this email reaches you well. I'm afraid I'm having a bit of trouble using PETSC for a library I'm writing for myself, and I was hoping for some clarification/help. I've been writing PETSC C code and compiling it using the included makefiles in the tutorial section as that was sufficient. However, I decided since there are a few functions I keep using it would be beneficial to write them and make them into a little library for myself. However, I'm having some difficulty understanding what I need to include when trying to compile something as a library with PETSC stuff. The makefiles are rather complicated, so I thought it may be more prudent to just ask. > > I'm trying to use #include and #include to have access to the PETSC data types (PetscScalar, PetscInt) but I can't find where those files are located, and I wanted to check if just using gcc with those added was sufficient or if I needed some other compiler flags and options. > > Please forgive me if this is a silly question, but makefiles have always been tricky for me. > > Respectfully: > Alberto -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wick.1980 at gmail.com Sat Sep 16 09:19:51 2023 From: michael.wick.1980 at gmail.com (Michael Wick) Date: Sat, 16 Sep 2023 22:19:51 +0800 Subject: [petsc-users] compiler preprocessor for PETSc Message-ID: Hi PETSc team: What is an appropriate compiler preprocessor to tell the code PETSc has been initialized? Mike -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Sep 16 09:37:50 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 16 Sep 2023 10:37:50 -0400 Subject: [petsc-users] [petsc-maint] compiler preprocessor for PETSc In-Reply-To: References: Message-ID: On Sat, Sep 16, 2023 at 10:20?AM Michael Wick wrote: > Hi PETSc team: > > What is an appropriate compiler preprocessor to tell the code PETSc has > been initialized? > https://petsc.org/main/manualpages/Sys/PetscInitialized/ Thanks, Matt > Mike > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.khurana22 at imperial.ac.uk Mon Sep 18 10:15:58 2023 From: p.khurana22 at imperial.ac.uk (Khurana, Parv) Date: Mon, 18 Sep 2023 15:15:58 +0000 Subject: [petsc-users] Looking for PETSc Example: Poisson Equation in 2D using FEM - scale upto 1000 procs Message-ID: Hello PETSc users, Thank you for this very active community of users and the mailing list. I am looking for a PETSc example which solves the Poisson equation on a 2D domain using FEM (or HO-FEM if possible). I would like the following: 1. The example should be formulated fully on PETSc, and to be solved with KSP objects in PETSc. 2. The problem should scale up to a few hundred processors (ideally 1000 procs). 3. Ideally on a unit square with either Square or Triangle element discretization. 4. There should be an option to specify Dirichlet/Neumann-type BCs on the boundaries. I was wondering if someone could point me to such an example as I am relatively new to PETSc - and I am trying to avoid reinventing the wheel. I have had a look at Examples 29,32,50 and 66 in the PETSc tutorials - while they are very close to what I need I am not sure if they scale to a few hundred processors. Furthermore, I am aware that I can formulate such a problem with FENICS/Firedrake with relative ease and these software interfaces with PETSc quite well. However, I am just trying to see if such an application already exists purely in PETSc. Thanks, and Best Parv -------------- next part -------------- An HTML attachment was scrubbed... URL: From mfadams at lbl.gov Mon Sep 18 11:38:57 2023 From: mfadams at lbl.gov (Mark Adams) Date: Mon, 18 Sep 2023 12:38:57 -0400 Subject: [petsc-users] Looking for PETSc Example: Poisson Equation in 2D using FEM - scale upto 1000 procs In-Reply-To: References: Message-ID: There are several but I am updating *src/snes/tests/ex13.c * now, in branch adams/gamg-fast-filter . but main is fine (it should get merged very soon). It does what you want scales forever, but it does not have Neumann BCs. I might be able to add that, but not today. Mark On Mon, Sep 18, 2023 at 11:16?AM Khurana, Parv wrote: > Hello PETSc users, > > > > Thank you for this very active community of users and the mailing list. > > > > I am looking for a PETSc example which solves the Poisson equation on a 2D > domain using FEM (or HO-FEM if possible). I would like the following: > > 1. The example should be formulated fully on PETSc, and to be solved > with KSP objects in PETSc. > 2. The problem should scale up to a few hundred processors (ideally > 1000 procs). > 3. Ideally on a unit square with either Square or Triangle element > discretization. > 4. There should be an option to specify Dirichlet/Neumann-type BCs on > the boundaries. > > > > I was wondering if someone could point me to such an example as I am > relatively new to PETSc ? and I am trying to avoid reinventing the wheel. I > have had a look at Examples 29,32,50 and 66 in the PETSc tutorials ? while > they are very close to what I need I am not sure if they scale to a few > hundred processors. Furthermore, I am aware that I can formulate such a > problem with FENICS/Firedrake with relative ease and these software > interfaces with PETSc quite well. However, I am just trying to see if such > an application already exists purely in PETSc. > > > > Thanks, and Best > > Parv > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mfadams at lbl.gov Mon Sep 18 14:03:56 2023 From: mfadams at lbl.gov (Mark Adams) Date: Mon, 18 Sep 2023 15:03:56 -0400 Subject: [petsc-users] Looking for PETSc Example: Poisson Equation in 2D using FEM - scale upto 1000 procs In-Reply-To: References: Message-ID: Well, I think you can do Neumann problems with ex13 with a small code change: ** run on a unit cube/square with: -dm_plex_box_upper 1,1,1 -dm_plex_box_lower 0,0,0 ** use a svd coarse grid solver: -mg_coarse_pc_type svd ** change one line in this example to get a Neumann problem on around 97 you comment this out: //PetscCall(DMAddBoundary(dm, DM_BC_ESSENTIAL, "wall", label, 1, &id, 0, 0, NULL, (void (*)(void))trig_u, NULL, user, NULL)); This is what I see and the solution : (new_py-env) 14:46 86 adams/gamg-fast-filter *= ~/Codes/petsc/src/snes/tests$ ./ex13 -dm_plex_dim 2 -benchmark_it 0 -dm_plex_simplex 1 -dm_plex_box_faces 2,2,1 -dm_refine 2 -petscpartitioner_simple_node_grid 1,1,1 -petscpartitioner_simple_process_grid 2,2,1 -potential_petscspace_degree 2 -petscpartitioner_type simple -snes_type ksponly -dm_view -ksp_type cg -ksp_rtol 1e-12 -snes_lag_jacobian -2 -dm_plex_box_upper 1,1 -dm_plex_box_lower 0,0 -pc_type gamg -pc_gamg_process_eq_limit 200 -pc_gamg_coarse_eq_limit 1000 -pc_gamg_esteig_ksp_type cg -mg_levels_ksp_chebyshev_esteig 0,0.2,0,1.05 -pc_gamg_reuse_interpolation true -pc_gamg_aggressive_square_graph true -pc_gamg_threshold 0.04 -pc_gamg_threshold_scale .25 -pc_gamg_aggressive_coarsening 2 -pc_gamg_mis_k_minimum_degree_ordering true -ksp_monitor -ksp_norm_type unpreconditioned -dm_view hdf5:sol.h5 -potential_view hdf5:sol.h5::append -ksp_converged_reason -mg_coarse_pc_type svd Number equations N = 289 0 KSP Residual norm 2.775536542048e+00 1 KSP Residual norm 2.631487127409e+00 2 KSP Residual norm 5.145745091100e-01 3 KSP Residual norm 9.031411480985e-02 4 KSP Residual norm 1.120911726117e-02 5 KSP Residual norm 1.869571597808e-03 6 KSP Residual norm 2.861476924898e-04 7 KSP Residual norm 6.168949367531e-05 8 KSP Residual norm 1.098972695713e-05 9 KSP Residual norm 1.510979924319e-06 10 KSP Residual norm 1.958281010810e-07 11 KSP Residual norm 2.648997408740e-08 12 KSP Residual norm 3.191829696292e-09 13 KSP Residual norm 4.003245254269e-10 14 KSP Residual norm 6.645229161624e-11 15 KSP Residual norm 1.055754552827e-11 16 KSP Residual norm 9.104749948055e-13 Linear solve converged due to CONVERGED_RTOL iterations 16 On Mon, Sep 18, 2023 at 12:38?PM Mark Adams wrote: > There are several but I am updating *src/snes/tests/ex13.c * > now, in > branch adams/gamg-fast-filter > . but main > is fine (it should get merged very soon). > It does what you want scales forever, but it does not have Neumann BCs. > I might be able to add that, but not today. > > Mark > > On Mon, Sep 18, 2023 at 11:16?AM Khurana, Parv > wrote: > >> Hello PETSc users, >> >> >> >> Thank you for this very active community of users and the mailing list. >> >> >> >> I am looking for a PETSc example which solves the Poisson equation on a >> 2D domain using FEM (or HO-FEM if possible). I would like the following: >> >> 1. The example should be formulated fully on PETSc, and to be solved >> with KSP objects in PETSc. >> 2. The problem should scale up to a few hundred processors (ideally >> 1000 procs). >> 3. Ideally on a unit square with either Square or Triangle element >> discretization. >> 4. There should be an option to specify Dirichlet/Neumann-type BCs on >> the boundaries. >> >> >> >> I was wondering if someone could point me to such an example as I am >> relatively new to PETSc ? and I am trying to avoid reinventing the wheel. I >> have had a look at Examples 29,32,50 and 66 in the PETSc tutorials ? while >> they are very close to what I need I am not sure if they scale to a few >> hundred processors. Furthermore, I am aware that I can formulate such a >> problem with FENICS/Firedrake with relative ease and these software >> interfaces with PETSc quite well. However, I am just trying to see if such >> an application already exists purely in PETSc. >> >> >> >> Thanks, and Best >> >> Parv >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot 2023-09-18 at 3.03.44 PM.png Type: image/png Size: 238805 bytes Desc: not available URL: From knepley at gmail.com Mon Sep 18 15:23:18 2023 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 18 Sep 2023 21:23:18 +0100 Subject: [petsc-users] Looking for PETSc Example: Poisson Equation in 2D using FEM - scale upto 1000 procs In-Reply-To: References: Message-ID: On Mon, Sep 18, 2023 at 4:16?PM Khurana, Parv wrote: > Hello PETSc users, > > > > Thank you for this very active community of users and the mailing list. > > > > I am looking for a PETSc example which solves the Poisson equation on a 2D > domain using FEM (or HO-FEM if possible). I would like the following: > > 1. The example should be formulated fully on PETSc, and to be solved > with KSP objects in PETSc. > 2. The problem should scale up to a few hundred processors (ideally > 1000 procs). > 3. Ideally on a unit square with either Square or Triangle element > discretization. > 4. There should be an option to specify Dirichlet/Neumann-type BCs on > the boundaries. > > > > I was wondering if someone could point me to such an example as I am > relatively new to PETSc ? and I am trying to avoid reinventing the wheel. I > have had a look at Examples 29,32,50 and 66 in the PETSc tutorials ? while > they are very close to what I need I am not sure if they scale to a few > hundred processors. Furthermore, I am aware that I can formulate such a > problem with FENICS/Firedrake with relative ease and these software > interfaces with PETSc quite well. However, I am just trying to see if such > an application already exists purely in PETSc. > > > It looks like Mark has everything working. However, if you have problems getting that to run, I am here at ICL this week. Thanks, Matt > Thanks, and Best > > Parv > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From bui at calcreek.com Mon Sep 18 17:26:49 2023 From: bui at calcreek.com (Thuc Bui) Date: Mon, 18 Sep 2023 15:26:49 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 Message-ID: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> Dear Petsc users and experts, If someone can direct me how to track this bug, I would really appreciate it. The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. Should I install the latest Intel MKL to work with Petsc 3.19.4? Many thanks in advance for your help, Thuc Bui Senior R&D Engineer Calabazas Creek Research, Inc (650) 948-5361 ############################################### [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 BLASdot() [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:23 7 [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:31 8 [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:11 0 [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:22 7 [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:107 0 job aborted: [ranks] message [0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Mon Sep 18 17:42:59 2023 From: bsmith at petsc.dev (Barry Smith) Date: Mon, 18 Sep 2023 18:42:59 -0400 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> Message-ID: <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? Barry > On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote: > > Dear Petsc users and experts, > > If someone can direct me how to track this bug, I would really appreciate it. > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > Many thanks in advance for your help, > Thuc Bui > Senior R&D Engineer > Calabazas Creek Research, Inc > (650) 948-5361 > > > ############################################### > > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > [0]PETSC ERROR: #1 BLASdot() > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > job aborted: > [ranks] message > > [0] application aborted > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bui at calcreek.com Mon Sep 18 18:24:25 2023 From: bui at calcreek.com (Thuc Bui) Date: Mon, 18 Sep 2023 16:24:25 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> Message-ID: <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. Best regards, Thuc From: Barry Smith [mailto:bsmith at petsc.dev] Sent: Monday, September 18, 2023 3:43 PM To: Thuc Bui Cc: PETSc users list Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? Barry On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote: Dear Petsc users and experts, If someone can direct me how to track this bug, I would really appreciate it. The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. Should I install the latest Intel MKL to work with Petsc 3.19.4? Many thanks in advance for your help, Thuc Bui Senior R&D Engineer Calabazas Creek Research, Inc (650) 948-5361 ############################################### [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 BLASdot() [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:23 7 [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:31 8 [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:11 0 [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:22 7 [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:107 0 job aborted: [ranks] message [0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bui at calcreek.com Tue Sep 19 01:04:16 2023 From: bui at calcreek.com (Thuc Bui) Date: Mon, 18 Sep 2023 23:04:16 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> Message-ID: <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> Hi Barry, Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don't remember for sure, but I don't think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. Thanks for your help, Thuc [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 BLASdot() [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2. c:216 [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvecto r.c:237 [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvecto r.c:318 [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmre s.c:111 [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmre s.c:228 [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc .c:899 [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc .c:1071 job aborted: [ranks] message [0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui Sent: Monday, September 18, 2023 4:24 PM To: 'Barry Smith' Cc: 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. Best regards, Thuc From: Barry Smith [mailto:bsmith at petsc.dev] Sent: Monday, September 18, 2023 3:43 PM To: Thuc Bui Cc: PETSc users list Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? Barry On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote: Dear Petsc users and experts, If someone can direct me how to track this bug, I would really appreciate it. The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. Should I install the latest Intel MKL to work with Petsc 3.19.4? Many thanks in advance for your help, Thuc Bui Senior R&D Engineer Calabazas Creek Research, Inc (650) 948-5361 ############################################### [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 BLASdot() [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:23 7 [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:31 8 [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:11 0 [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:22 7 [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:107 0 job aborted: [ranks] message [0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Tue Sep 19 01:38:17 2023 From: knepley at gmail.com (Matthew Knepley) Date: Tue, 19 Sep 2023 07:38:17 +0100 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> Message-ID: On Tue, Sep 19, 2023 at 7:04?AM Thuc Bui wrote: > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built > with VS 2022 also crashes at the same place. The same errors are shown > below. I don?t remember for sure, but I don?t think I was able to configure > Petsc 3.19.4 with VS 2019. However, I will still try that next. > It is so easy to hate VS. This suggests that VS is secretly linking to another BLAS, perhaps with different calling semantics. Thanks, Matt > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and > https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always > exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > *From:* petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] *On Behalf > Of *Thuc Bui > *Sent:* Monday, September 18, 2023 4:24 PM > *To:* 'Barry Smith' > *Cc:* 'PETSc users list' > *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have > suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > *From:* Barry Smith [mailto:bsmith at petsc.dev] > *Sent:* Monday, September 18, 2023 3:43 PM > *To:* Thuc Bui > *Cc:* PETSc users list > *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc > and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same > older PETSc version? If that works could you try with the old Visual Studio > version but the new PETSc version? > > > > Barry > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate > it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual > Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The > same code works fine with Petsc 3.18.6 using the same versions of MS MPI > and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to > PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), > PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = > PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong > to Intel MKL, and its library does not contain debug information. After the > code exits, the errors are shown below the hash line. > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > Many thanks in advance for your help, > > Thuc Bui > > Senior R&D Engineer > > Calabazas Creek Research, Inc > > (650) 948-5361 > > > > > > ############################################### > > > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and > https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always > exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > [0]PETSC ERROR: #3 VecNorm() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > [0]PETSC ERROR: #7 KSPSolve_Private() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > [0]PETSC ERROR: #8 KSPSolve() at > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Tue Sep 19 09:29:40 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Tue, 19 Sep 2023 09:29:40 -0500 (CDT) Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> Message-ID: <022b0df1-de28-becc-fbc8-1af076d72950@mcs.anl.gov> On Tue, 19 Sep 2023, Matthew Knepley wrote: > On Tue, Sep 19, 2023 at 7:04?AM Thuc Bui wrote: > > > Hi Barry, > > > > > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built > > with VS 2022 also crashes at the same place. The same errors are shown > > below. I don?t remember for sure, but I don?t think I was able to configure > > Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > It is so easy to hate VS. This suggests that VS is secretly linking to > another BLAS, perhaps with different calling semantics. There could be multiple issues: - code bugs - that show up in different settings - Intel Compilers/OneAPI are have tight dependency on native compilers [on linux and windows] So perhaps the current install is over VS19 - and not VS22. If this is the case - a reinstall [of Intel Compilers] over VS22 might help? Or there could be different compiler dlls in VS vs Intel installs - and one of them is misbehaving.. [so reorder PATH location for Intel/MS?] - MLK bugs that show up in some setups? [here using alternate blas - aka fblaslapack might help?] - Latest VS with latest OneAPI might help? [however our test setup is with older versions of these compilers.. >>> Compilers: C Compiler: /cygdrive/e/svcpetsc/builds/Cw-cvdV3/0/petsc/petsc/lib/petsc/bin/win32fe/win_cl -GF -MD -wd4996 -Zc:preprocessor -O2 Version: Win32 Development Tool Front End, version 1.11.4 Fri, Sep 10, 2021 6:33:40 PM\nMicrosoft (R) C/C++ Optimizing Compiler Version 19.32.31329 for x64 C++ Compiler: /cygdrive/e/svcpetsc/builds/Cw-cvdV3/0/petsc/petsc/lib/petsc/bin/win32fe/win_cl -GF -MD -GR -EHsc -Zc:preprocessor -Zc:__cplusplus -O2 -Zm200 -std:c++20 -TP Version: Win32 Development Tool Front End, version 1.11.4 Fri, Sep 10, 2021 6:33:40 PM\nMicrosoft (R) C/C++ Optimizing Compiler Version 19.32.31329 for x64 Fortran Compiler: /cygdrive/e/svcpetsc/builds/Cw-cvdV3/0/petsc/petsc/lib/petsc/bin/win32fe/win_ifort -MD -O3 -fpp Version: Win32 Development Tool Front End, version 1.11.4 Fri, Sep 10, 2021 6:33:40 PM\nIntel(R) Fortran Intel(R) 64 Compiler Classic for applications running on Intel(R) 64, Version 2021.6.0 Build 20220226_000000 <<< Satish > > Thanks, > > Matt > > > > Thanks for your help, > > > > Thuc > > > > > > > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > probably memory access out of range > > > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and > > https://petsc.org/release/faq/ > > > > [0]PETSC ERROR: --------------------- Stack Frames > > ------------------------------------ > > > > [0]PETSC ERROR: The line numbers in the error traceback are not always > > exact. > > > > [0]PETSC ERROR: #1 BLASdot() > > > > [0]PETSC ERROR: #2 VecNorm_Seq() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > > > [0]PETSC ERROR: #3 VecNorm() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > > > [0]PETSC ERROR: #4 VecNormalize() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > > > [0]PETSC ERROR: #7 KSPSolve_Private() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > > > [0]PETSC ERROR: #8 KSPSolve() at > > D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > > > > > job aborted: > > > > [ranks] message > > > > > > > > [0] application aborted > > > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > > > > > > > > > *From:* petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] *On Behalf > > Of *Thuc Bui > > *Sent:* Monday, September 18, 2023 4:24 PM > > *To:* 'Barry Smith' > > *Cc:* 'PETSc users list' > > *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > > > Thanks a lot Barry, for getting back to me. Will do what you have > > suggested, and get back with the results. > > > > > > > > Best regards, > > > > Thuc > > > > > > > > *From:* Barry Smith [mailto:bsmith at petsc.dev] > > *Sent:* Monday, September 18, 2023 3:43 PM > > *To:* Thuc Bui > > *Cc:* PETSc users list > > *Subject:* Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > > > > > > > Ok, two things are being changed at the same time: the version of PETSc > > and the version of Visual Studio. > > > > > > > > Could you please try with the new Visual Studio version but the same > > older PETSc version? If that works could you try with the old Visual Studio > > version but the new PETSc version? > > > > > > > > Barry > > > > > > > > > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui wrote: > > > > > > > > Dear Petsc users and experts, > > > > > > > > If someone can direct me how to track this bug, I would really appreciate > > it. > > > > > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual > > Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The > > same code works fine with Petsc 3.18.6 using the same versions of MS MPI > > and Intel MKL, and built with Visual Studio 2019. > > > > > > > > When my code calls PetscCall(KSPSolve(...)), it gets to > > PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), > > PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = > > PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong > > to Intel MKL, and its library does not contain debug information. After the > > code exits, the errors are shown below the hash line. > > > > > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > > > > > Many thanks in advance for your help, > > > > Thuc Bui > > > > Senior R&D Engineer > > > > Calabazas Creek Research, Inc > > > > (650) 948-5361 > > > > > > > > > > > > ############################################### > > > > > > > > [0]PETSC ERROR: > > ------------------------------------------------------------------------ > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > probably memory access out of range > > > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and > > https://petsc.org/release/faq/ > > > > [0]PETSC ERROR: --------------------- Stack Frames > > ------------------------------------ > > > > [0]PETSC ERROR: The line numbers in the error traceback are not always > > exact. > > > > [0]PETSC ERROR: #1 BLASdot() > > > > [0]PETSC ERROR: #2 VecNorm_Seq() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > > > [0]PETSC ERROR: #3 VecNorm() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > > > [0]PETSC ERROR: #4 VecNormalize() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > > > [0]PETSC ERROR: #5 KSPGMRESCycle() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > > > [0]PETSC ERROR: #7 KSPSolve_Private() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > > > [0]PETSC ERROR: #8 KSPSolve() at > > D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > > > > > job aborted: > > > > [ranks] message > > > > > > > > [0] application aborted > > > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > > From bsmith at petsc.dev Tue Sep 19 10:24:22 2023 From: bsmith at petsc.dev (Barry Smith) Date: Tue, 19 Sep 2023 11:24:22 -0400 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> Message-ID: <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). Barry > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > Hi Barry, > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. > > Thanks for your help, > Thuc > > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > [0]PETSC ERROR: #1 BLASdot() > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > job aborted: > [ranks] message > > [0] application aborted > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui > Sent: Monday, September 18, 2023 4:24 PM > To: 'Barry Smith' > Cc: 'PETSc users list' > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. > > Best regards, > Thuc > > From: Barry Smith [mailto:bsmith at petsc.dev] > Sent: Monday, September 18, 2023 3:43 PM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. > > Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? > > Barry > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui > wrote: > > Dear Petsc users and experts, > > If someone can direct me how to track this bug, I would really appreciate it. > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > Many thanks in advance for your help, > Thuc Bui > Senior R&D Engineer > Calabazas Creek Research, Inc > (650) 948-5361 > > > ############################################### > > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > [0]PETSC ERROR: #1 BLASdot() > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > job aborted: > [ranks] message > > [0] application aborted > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Tue Sep 19 10:30:30 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Tue, 19 Sep 2023 10:30:30 -0500 (CDT) Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> Message-ID: BTW: Can check if you are using threaded MKL? We default to: Libraries: -L/cygdrive/c/PROGRA~2/Intel/oneAPI/mkl/2022.1.0/lib/intel64 mkl_intel_lp64_dll.lib mkl_sequential_dll.lib mkl_core_dll.lib If using threaded MKL - try using env variable "OMP_NUM_THREADS=1" and see that makes a difference Satish On Tue, 19 Sep 2023, Barry Smith wrote: > > Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler > > > It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). > > Barry > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui > > Sent: Monday, September 18, 2023 4:24 PM > > To: 'Barry Smith' > > Cc: 'PETSc users list' > > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [mailto:bsmith at petsc.dev] > > Sent: Monday, September 18, 2023 3:43 PM > > To: Thuc Bui > > Cc: PETSc users list > > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? > > > > Barry > > > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui > wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > Many thanks in advance for your help, > > Thuc Bui > > Senior R&D Engineer > > Calabazas Creek Research, Inc > > (650) 948-5361 > > > > > > ############################################### > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > From bui at calcreek.com Tue Sep 19 11:53:36 2023 From: bui at calcreek.com (Thuc Bui) Date: Tue, 19 Sep 2023 09:53:36 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> Message-ID: <013201d9eb19$d55d94d0$8018be70$@calcreek.com> Hi Barry, Thanks for getting back to me. The diagnostics were generated when tracing under the VS debugger. To use the option ?no_signal_handler, I believe I will need to reconfigure PETSc with this additional option. I will try it now. Thuc From: Barry Smith [mailto:bsmith at petsc.dev] Sent: Tuesday, September 19, 2023 8:24 AM To: Thuc Bui Cc: PETSc users list Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). Barry On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: Hi Barry, Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. Thanks for your help, Thuc [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 BLASdot() [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 job aborted: [ranks] message [0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 From: petsc-users [ mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui Sent: Monday, September 18, 2023 4:24 PM To: 'Barry Smith' Cc: 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. Best regards, Thuc From: Barry Smith [ mailto:bsmith at petsc.dev] Sent: Monday, September 18, 2023 3:43 PM To: Thuc Bui Cc: PETSc users list Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? Barry On Sep 18, 2023, at 6:26 PM, Thuc Bui < bui at calcreek.com> wrote: Dear Petsc users and experts, If someone can direct me how to track this bug, I would really appreciate it. The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. Should I install the latest Intel MKL to work with Petsc 3.19.4? Many thanks in advance for your help, Thuc Bui Senior R&D Engineer Calabazas Creek Research, Inc (650) 948-5361 ############################################### [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [0]PETSC ERROR: The line numbers in the error traceback are not always exact. [0]PETSC ERROR: #1 BLASdot() [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 job aborted: [ranks] message [0] application aborted aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Tue Sep 19 12:00:57 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Tue, 19 Sep 2023 12:00:57 -0500 (CDT) Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <013201d9eb19$d55d94d0$8018be70$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> <013201d9eb19$d55d94d0$8018be70$@calcreek.com> Message-ID: <9aac59cc-e175-0a7a-6193-53c0f5443cd8@mcs.anl.gov> Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing under the VS debugger. To use the option ?no_signal_handler, I believe I will need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsmith at petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > From: petsc-users [ mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui > Sent: Monday, September 18, 2023 4:24 PM > To: 'Barry Smith' > Cc: 'PETSc users list' > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [ mailto:bsmith at petsc.dev] > Sent: Monday, September 18, 2023 3:43 PM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? > > > > Barry > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui < bui at calcreek.com> wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > Many thanks in advance for your help, > > Thuc Bui > > Senior R&D Engineer > > Calabazas Creek Research, Inc > > (650) 948-5361 > > > > > > ############################################### > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > From srvenkat at utexas.edu Tue Sep 19 15:42:49 2023 From: srvenkat at utexas.edu (Sreeram R Venkat) Date: Tue, 19 Sep 2023 15:42:49 -0500 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP Message-ID: I have a custom implementation of a matrix-vector product that inherently relies on a 2D processor partitioning of the matrix. That is, if the matrix looks like: A B C D E F G H I J K L in block form, we use 12 processors, each having one block. The input vector is partitioned across each row, and the output vector is partitioned across each column. Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a COL_COMM. The ROW/COL communicators are used to do reductions over rows/columns of processors. With this setup, I am a bit confused about how to set up the matrix shell. The "MatCreateShell" function only accepts one communicator. If I give the WORLD_COMM, the local/global sizes won't match since PETSc will try to multiply local_size * total_processors instead of local_size * processors_per_row (or col). I have gotten around this temporarily by giving ROW_COMM here instead. What I think happens is a different MatShell is created on each row, but when computing the matvec, they all work together. However, if I try to use KSP (CG) with this setup (giving ROW_COMM as the communicator), the process hangs. I believe this is due to the partitioning of the input/output vectors. The matvec itself is fine, but the inner products and other steps of CG fail. In fact, if I restrict to the case where I only have one row of processors, I am able to successfully use KSP. Is there a way to use KSP with this 2D partitioning setup when there are multiple rows of processors? I'd also prefer to work with one global MatShell object instead of this one object per row thing that I'm doing right now. Thanks for your help, Sreeram -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Tue Sep 19 18:22:54 2023 From: bsmith at petsc.dev (Barry Smith) Date: Tue, 19 Sep 2023 19:22:54 -0400 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP In-Reply-To: References: Message-ID: ( a ) ( A B C D ) ( w ) ( b ) = ( E F G H ) ( x ) ( c ) ( I J K L ) ( y ) ( z ) I have no idea what "The input vector is partitioned across each row, and the output vector is partitioned across each column" means. Anyways the shell matrix needs to live on MPI_COMM_WORLD, as do both the (a,b,c) and (w,x,y,z) vector. Now how many MPI ranks do you want to do the compution on? 12? Do you want one matrix A .. Z on each rank? Do you want the (a,b,c) vector spread over all ranks? What about the (w,x,y,z) vector? Barry > On Sep 19, 2023, at 4:42 PM, Sreeram R Venkat wrote: > > I have a custom implementation of a matrix-vector product that inherently relies on a 2D processor partitioning of the matrix. That is, if the matrix looks like: > > A B C D > E F G H > I J K L > in block form, we use 12 processors, each having one block. The input vector is partitioned across each row, and the output vector is partitioned across each column. > > Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a COL_COMM. The ROW/COL communicators are used to do reductions over rows/columns of processors. > > With this setup, I am a bit confused about how to set up the matrix shell. The "MatCreateShell" function only accepts one communicator. If I give the WORLD_COMM, the local/global sizes won't match since PETSc will try to multiply local_size * total_processors instead of local_size * processors_per_row (or col). I have gotten around this temporarily by giving ROW_COMM here instead. What I think happens is a different MatShell is created on each row, but when computing the matvec, they all work together. > > However, if I try to use KSP (CG) with this setup (giving ROW_COMM as the communicator), the process hangs. I believe this is due to the partitioning of the input/output vectors. The matvec itself is fine, but the inner products and other steps of CG fail. In fact, if I restrict to the case where I only have one row of processors, I am able to successfully use KSP. > > Is there a way to use KSP with this 2D partitioning setup when there are multiple rows of processors? I'd also prefer to work with one global MatShell object instead of this one object per row thing that I'm doing right now. > > Thanks for your help, > Sreeram -------------- next part -------------- An HTML attachment was scrubbed... URL: From srvenkat at utexas.edu Tue Sep 19 18:44:30 2023 From: srvenkat at utexas.edu (Sreeram R Venkat) Date: Tue, 19 Sep 2023 18:44:30 -0500 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP In-Reply-To: References: Message-ID: With the example you have given, here is what I would like to do: - 12 MPI ranks - Each rank has one block (rank 0 has A, rank 1 has B, ..., rank 11 has L) - to make the rest of this easier I'll refer to the rank containing block A as "rank A", and so on - rank A, rank B, rank C, and rank D have w, x, y, z respectively - the first step of the custom matvec implementation broadcasts w to rank E and rank I (similarly x is broadcast to rank F and rank J ...) - at the end of the matvec computation, ranks D, H, and L have a, b, and c respectively Thanks, Sreeram On Tue, Sep 19, 2023 at 6:23?PM Barry Smith wrote: > > ( a ) ( A B C D ) ( w ) > ( b ) = ( E F G H ) ( x ) > ( c ) ( I J K L ) ( y ) > ( z ) > > I have no idea what "The input vector is partitioned across each row, and > the output vector is partitioned across each column" means. > > Anyways the shell matrix needs to live on MPI_COMM_WORLD, as do both the > (a,b,c) and (w,x,y,z) vector. > > Now how many MPI ranks do you want to do the compution on? 12? > Do you want one matrix A .. Z on each rank? > > Do you want the (a,b,c) vector spread over all ranks? What about the (w,x,y,z) > vector? > > Barry > > > > On Sep 19, 2023, at 4:42 PM, Sreeram R Venkat wrote: > > I have a custom implementation of a matrix-vector product that inherently > relies on a 2D processor partitioning of the matrix. That is, if the matrix > looks like: > > A B C D > E F G H > I J K L > > in block form, we use 12 processors, each having one block. The input > vector is partitioned across each row, and the output vector is partitioned > across each column. > > Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a > COL_COMM. The ROW/COL communicators are used to do reductions over > rows/columns of processors. > > With this setup, I am a bit confused about how to set up the matrix shell. > The "MatCreateShell" function only accepts one communicator. If I give the > WORLD_COMM, the local/global sizes won't match since PETSc will try to > multiply local_size * total_processors instead of local_size * > processors_per_row (or col). I have gotten around this temporarily by > giving ROW_COMM here instead. What I think happens is a different MatShell > is created on each row, but when computing the matvec, they all work > together. > > However, if I try to use KSP (CG) with this setup (giving ROW_COMM as the > communicator), the process hangs. I believe this is due to the partitioning > of the input/output vectors. The matvec itself is fine, but the inner > products and other steps of CG fail. In fact, if I restrict to the case > where I only have one row of processors, I am able to successfully use KSP. > > Is there a way to use KSP with this 2D partitioning setup when there are > multiple rows of processors? I'd also prefer to work with one global > MatShell object instead of this one object per row thing that I'm doing > right now. > > Thanks for your help, > Sreeram > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Tue Sep 19 19:13:03 2023 From: bsmith at petsc.dev (Barry Smith) Date: Tue, 19 Sep 2023 20:13:03 -0400 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP In-Reply-To: References: Message-ID: The PetscLayout local sizes for PETSc (a,b,c) vector (0,0,0,number of rows of D, 0,0,0, number of rows of H, 0,0,0,number of rows of L) The PetscLayout local sizes for PETSc (w,x,y,z) vector (number of columns of A, number of columns of B, number of columns of C, number of columns of D,0,0,0,0,0,0,0,0,0) The left and right layouts of the shell matrix need to match the two above. There is a huge problem. KSP is written assuming that the left vector layout is the same as the right vector layout. So it can do dot products MPI rank by MPI rank without needing to send individual vector values around. I don't it makes sense to use PETSc with such vector decompositions as you would like. Barry > On Sep 19, 2023, at 7:44 PM, Sreeram R Venkat wrote: > > With the example you have given, here is what I would like to do: > 12 MPI ranks > Each rank has one block (rank 0 has A, rank 1 has B, ..., rank 11 has L) - to make the rest of this easier I'll refer to the rank containing block A as "rank A", and so on > rank A, rank B, rank C, and rank D have w, x, y, z respectively - the first step of the custom matvec implementation broadcasts w to rank E and rank I (similarly x is broadcast to rank F and rank J ...) > at the end of the matvec computation, ranks D, H, and L have a, b, and c respectively > Thanks, > Sreeram > > > On Tue, Sep 19, 2023 at 6:23?PM Barry Smith > wrote: >> >> ( a ) ( A B C D ) ( w ) >> ( b ) = ( E F G H ) ( x ) >> ( c ) ( I J K L ) ( y ) >> ( z ) >> >> I have no idea what "The input vector is partitioned across each row, and the output vector is partitioned across each column" means. >> >> Anyways the shell matrix needs to live on MPI_COMM_WORLD, as do both the (a,b,c) and (w,x,y,z) vector. >> >> Now how many MPI ranks do you want to do the compution on? 12? >> Do you want one matrix A .. Z on each rank? >> >> Do you want the (a,b,c) vector spread over all ranks? What about the (w,x,y,z) vector? >> >> Barry >> >> >> >>> On Sep 19, 2023, at 4:42 PM, Sreeram R Venkat > wrote: >>> >>> I have a custom implementation of a matrix-vector product that inherently relies on a 2D processor partitioning of the matrix. That is, if the matrix looks like: >>> >>> A B C D >>> E F G H >>> I J K L >>> in block form, we use 12 processors, each having one block. The input vector is partitioned across each row, and the output vector is partitioned across each column. >>> >>> Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a COL_COMM. The ROW/COL communicators are used to do reductions over rows/columns of processors. >>> >>> With this setup, I am a bit confused about how to set up the matrix shell. The "MatCreateShell" function only accepts one communicator. If I give the WORLD_COMM, the local/global sizes won't match since PETSc will try to multiply local_size * total_processors instead of local_size * processors_per_row (or col). I have gotten around this temporarily by giving ROW_COMM here instead. What I think happens is a different MatShell is created on each row, but when computing the matvec, they all work together. >>> >>> However, if I try to use KSP (CG) with this setup (giving ROW_COMM as the communicator), the process hangs. I believe this is due to the partitioning of the input/output vectors. The matvec itself is fine, but the inner products and other steps of CG fail. In fact, if I restrict to the case where I only have one row of processors, I am able to successfully use KSP. >>> >>> Is there a way to use KSP with this 2D partitioning setup when there are multiple rows of processors? I'd also prefer to work with one global MatShell object instead of this one object per row thing that I'm doing right now. >>> >>> Thanks for your help, >>> Sreeram >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From srvenkat at utexas.edu Tue Sep 19 19:44:46 2023 From: srvenkat at utexas.edu (Sreeram R Venkat) Date: Tue, 19 Sep 2023 19:44:46 -0500 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP In-Reply-To: References: Message-ID: Thank you for your reply. Let's call this matrix *M*: (A B C D) (E F G H) (I J K L) Now, instead of doing KSP with just *M*, what if I want *M^TM*? In this case, the matvec implementation would be as follows: - same partitioning of blocks A, B, ..., L among the 12 MPI ranks - matvec looks like: (a) (w) (b) = (*M^TM* ) (x) (c) (y) (d) (z) - w, x, y, z stored on ranks A, B, C, D (as before) - a, b, c, d now also stored on ranks A, B, C, D Based on your message, I believe using a PetscLayout for both the (a,b,c,d) and (w,x,y,z) vector of (number of columns of A, number of columns of B, number of columns of C, number of columns of D,0,0,0,0,0,0,0,0,0) should work. I see there are functions "VecSetLayout" and "MatSetLayouts" to set the PetscLayouts of the matrix and vectors. When I create the vectors (I need VecCreateMPICUDA) or matrix shell (with MatCreateShell), I need to pass the local and global sizes. I'm not sure what to do there. Thanks, Sreeram On Tue, Sep 19, 2023, 7:13 PM Barry Smith wrote: > > The PetscLayout local sizes for PETSc (a,b,c) vector (0,0,0,number of > rows of D, 0,0,0, number of rows of H, 0,0,0,number of rows of L) > > > The PetscLayout local sizes for PETSc (w,x,y,z) vector (number of > columns of A, number of columns of B, number of columns of C, number of > columns of D,0,0,0,0,0,0,0,0,0) > > The left and right layouts of the shell matrix need to match the two > above. > > There is a huge problem. KSP is written assuming that the left vector > layout is the same as the right vector layout. So it can do dot products > MPI rank by MPI rank without needing to send individual vector values > around. > > I don't it makes sense to use PETSc with such vector decompositions as > you would like. > > Barry > > > > On Sep 19, 2023, at 7:44 PM, Sreeram R Venkat wrote: > > With the example you have given, here is what I would like to do: > > - 12 MPI ranks > - Each rank has one block (rank 0 has A, rank 1 has B, ..., rank 11 > has L) - to make the rest of this easier I'll refer to the rank containing > block A as "rank A", and so on > - rank A, rank B, rank C, and rank D have w, x, y, z respectively - > the first step of the custom matvec implementation broadcasts w to rank E > and rank I (similarly x is broadcast to rank F and rank J ...) > - at the end of the matvec computation, ranks D, H, and L have a, b, > and c respectively > > Thanks, > Sreeram > > > On Tue, Sep 19, 2023 at 6:23?PM Barry Smith wrote: > >> >> ( a ) ( A B C D ) ( w ) >> ( b ) = ( E F G H ) ( x ) >> ( c ) ( I J K L ) ( y ) >> ( z ) >> >> I have no idea what "The input vector is partitioned across each row, >> and the output vector is partitioned across each column" means. >> >> Anyways the shell matrix needs to live on MPI_COMM_WORLD, as do both the >> (a,b,c) and (w,x,y,z) vector. >> >> Now how many MPI ranks do you want to do the compution on? 12? >> Do you want one matrix A .. Z on each rank? >> >> Do you want the (a,b,c) vector spread over all ranks? What about the (w,x,y,z) >> vector? >> >> Barry >> >> >> >> On Sep 19, 2023, at 4:42 PM, Sreeram R Venkat >> wrote: >> >> I have a custom implementation of a matrix-vector product that inherently >> relies on a 2D processor partitioning of the matrix. That is, if the matrix >> looks like: >> >> A B C D >> E F G H >> I J K L >> >> in block form, we use 12 processors, each having one block. The input >> vector is partitioned across each row, and the output vector is partitioned >> across each column. >> >> Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a >> COL_COMM. The ROW/COL communicators are used to do reductions over >> rows/columns of processors. >> >> With this setup, I am a bit confused about how to set up the matrix >> shell. The "MatCreateShell" function only accepts one communicator. If I >> give the WORLD_COMM, the local/global sizes won't match since PETSc will >> try to multiply local_size * total_processors instead of local_size * >> processors_per_row (or col). I have gotten around this temporarily by >> giving ROW_COMM here instead. What I think happens is a different MatShell >> is created on each row, but when computing the matvec, they all work >> together. >> >> However, if I try to use KSP (CG) with this setup (giving ROW_COMM as the >> communicator), the process hangs. I believe this is due to the partitioning >> of the input/output vectors. The matvec itself is fine, but the inner >> products and other steps of CG fail. In fact, if I restrict to the case >> where I only have one row of processors, I am able to successfully use KSP. >> >> Is there a way to use KSP with this 2D partitioning setup when there are >> multiple rows of processors? I'd also prefer to work with one global >> MatShell object instead of this one object per row thing that I'm doing >> right now. >> >> Thanks for your help, >> Sreeram >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bui at calcreek.com Wed Sep 20 01:10:19 2023 From: bui at calcreek.com (Thuc Bui) Date: Tue, 19 Sep 2023 23:10:19 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <9aac59cc-e175-0a7a-6193-53c0f5443cd8@mcs.anl.gov> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> <013201d9eb19$d55d94d0$8018be70$@calcreek.com> <9aac59cc-e175-0a7a-6193-53c0f5443cd8@mcs.anl.gov> Message-ID: <003601d9eb89$22950a20$67bf1e60$@calcreek.com> Hi Satish and Barry, Thank you very for getting back to me with the suggestion of the OMP_NUM_THREADS environmental variable and how to set the option no_signal_handler per Barry's suggestion. Yes, I am using threaded Intel MKL. So, I first set the environmental variable OMP_NUM_THREADS=1, and run the Visual Studio debugger. It still crashes at the same place with the same errors. I then set the PETSC_OPTIONS=-no_signal_handler, the debugger refuses to pass through the access exception, and I have to stop the debugger; consequently no PETSc errors were reported. I know there is an option somewhere in the VS debugger to bypass this access exception, but I didn't pursue further. Finally, I removed Intel MKL 2000 (to uninstall it requires a 3rd party software!), and use Intel oneAPI MKL (2023) with PETSc 3.18.6 and Visual Studio 2022. Now my code with 1, 2 or 4 cores work! I will try 3.19.4 next and will keep you posted. Thank you again for your help, Thuc Bui ////////////////////////////////////////////////////////////////////////////////////////////////////////////////// ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx='win32fe cl' --with-openmp \ --with-mpi-include='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include:/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include/x64' \ --with-mpi-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpi.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpifec.lib] \ --with-blas-lapack-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_lp64.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_core.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_thread.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_rt.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/libiomp5md.lib] \ --with-mpiexec='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/bin/x64/mpiexec' \ --with-shared-libraries=0 /////////////////////////////////////////////////////////////////////////////////////////////////////////////////// -----Original Message----- From: Satish Balay [mailto:balay at mcs.anl.gov] Sent: Tuesday, September 19, 2023 10:01 AM To: Thuc Bui Cc: 'Barry Smith'; 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing under the VS debugger. To use the option ?no_signal_handler, I believe I will need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsmith at petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > From: petsc-users [ mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui > Sent: Monday, September 18, 2023 4:24 PM > To: 'Barry Smith' > Cc: 'PETSc users list' > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [ mailto:bsmith at petsc.dev] > Sent: Monday, September 18, 2023 3:43 PM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? > > > > Barry > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui < bui at calcreek.com> wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > Many thanks in advance for your help, > > Thuc Bui > > Senior R&D Engineer > > Calabazas Creek Research, Inc > > (650) 948-5361 > > > > > > ############################################### > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > From bui at calcreek.com Wed Sep 20 01:24:15 2023 From: bui at calcreek.com (Thuc Bui) Date: Tue, 19 Sep 2023 23:24:15 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <003601d9eb89$22950a20$67bf1e60$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> <013201d9eb19$d55d94d0$8018be70$@calcreek.com> <9aac59cc-e175-0a7a-6193-53c0f5443cd8@mcs.anl.gov> <003601d9eb89$22950a20$67bf1e60$@calcreek.com> Message-ID: <003701d9eb8b$1469a670$3d3cf350$@calcreek.com> Correction! The MKL library mkl_rt.lib was mistakenly included in the configure below. It is not needed to build PETSc, but the app requires to link to it and petsc.lib. Thuc -----Original Message----- From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui Sent: Tuesday, September 19, 2023 11:10 PM To: 'petsc-users' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Hi Satish and Barry, Thank you very for getting back to me with the suggestion of the OMP_NUM_THREADS environmental variable and how to set the option no_signal_handler per Barry's suggestion. Yes, I am using threaded Intel MKL. So, I first set the environmental variable OMP_NUM_THREADS=1, and run the Visual Studio debugger. It still crashes at the same place with the same errors. I then set the PETSC_OPTIONS=-no_signal_handler, the debugger refuses to pass through the access exception, and I have to stop the debugger; consequently no PETSc errors were reported. I know there is an option somewhere in the VS debugger to bypass this access exception, but I didn't pursue further. Finally, I removed Intel MKL 2000 (to uninstall it requires a 3rd party software!), and use Intel oneAPI MKL (2023) with PETSc 3.18.6 and Visual Studio 2022. Now my code with 1, 2 or 4 cores work! I will try 3.19.4 next and will keep you posted. Thank you again for your help, Thuc Bui ////////////////////////////////////////////////////////////////////////////////////////////////////////////////// ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx='win32fe cl' --with-openmp \ --with-mpi-include='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include:/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include/x64' \ --with-mpi-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpi.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpifec.lib] \ --with-blas-lapack-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_lp64.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_core.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_thread.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_rt.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/libiomp5md.lib] \ --with-mpiexec='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/bin/x64/mpiexec' \ --with-shared-libraries=0 /////////////////////////////////////////////////////////////////////////////////////////////////////////////////// -----Original Message----- From: Satish Balay [mailto:balay at mcs.anl.gov] Sent: Tuesday, September 19, 2023 10:01 AM To: Thuc Bui Cc: 'Barry Smith'; 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing under the VS debugger. To use the option ?no_signal_handler, I believe I will need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsmith at petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > From: petsc-users [ mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui > Sent: Monday, September 18, 2023 4:24 PM > To: 'Barry Smith' > Cc: 'PETSc users list' > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [ mailto:bsmith at petsc.dev] > Sent: Monday, September 18, 2023 3:43 PM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? > > > > Barry > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui < bui at calcreek.com> wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > Many thanks in advance for your help, > > Thuc Bui > > Senior R&D Engineer > > Calabazas Creek Research, Inc > > (650) 948-5361 > > > > > > ############################################### > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > From qince168 at gmail.com Wed Sep 20 06:16:40 2023 From: qince168 at gmail.com (Ce Qin) Date: Wed, 20 Sep 2023 19:16:40 +0800 Subject: [petsc-users] Questions about PCPATCH Message-ID: Dear all, I am currently implementing a multigrid solver for Maxwell's equations in 3D. The AFW smoother has excellent convergence properties for Maxwell's equations. I noticed that PCPATCH provides such types of smoothers. However, I am using the deal.II library to build the patches. PCPATCH seems only to support the PETSc DMPlex data structure. Is there a way to use PCPATCH with user defined patches? Besides, I found that we can also use PCASM with user defined subdomains. Is there any performance difference between PCPATCH and PCASM? Thanks in advance. Best regards, Ce -------------- next part -------------- An HTML attachment was scrubbed... URL: From anna.dalklint at solid.lth.se Wed Sep 20 07:16:32 2023 From: anna.dalklint at solid.lth.se (Anna Dalklint) Date: Wed, 20 Sep 2023 12:16:32 +0000 Subject: [petsc-users] Face Set not appearing when loading GMSH mesh to DMPlex Message-ID: <576f28bb730c467680de36abfbf5b463@solid.lth.se> Hello, I am trying to load a mesh, created via the gmsh api, into a DMPlex. The code is seen below: 6 gmsh::initialize(); 7 elsize0 = 1.0; 8 double a = 20.0; 9 double b = 20.0; 10 double c = 10.0; 11 double d = 30.0; 12 double e = 70.0; 13 14 gmsh::model::geo::addPoint(0.0, 0.0, 0.0, elsize0, 1); 15 gmsh::model::geo::addPoint(a, 0.0, 0.0, elsize0, 2); 16 gmsh::model::geo::addPoint(0.0, d, 0.0, elsize0, 3); 17 gmsh::model::geo::addPoint(a, c, 0.0, elsize0, 4); 18 gmsh::model::geo::addPoint(e, d, 0.0, elsize0, 5); 19 gmsh::model::geo::addPoint(e, c, 0.0, elsize0, 6); 20 gmsh::model::geo::addPoint(a, 0.0, b, elsize0, 7); 21 gmsh::model::geo::addPoint(0.0, 0.0, b, elsize0, 8); 22 gmsh::model::geo::addPoint(0.0, d, b, elsize0, 9); 23 gmsh::model::geo::addPoint(e, d, b, elsize0, 10); 24 gmsh::model::geo::addPoint(e, c, b, elsize0, 11); 25 gmsh::model::geo::addPoint(a, c, b, elsize0, 12); 26 27 // Define lines connecting points 28 gmsh::model::geo::addLine(2, 1, 1); 29 gmsh::model::geo::addLine(1, 3, 2); 30 gmsh::model::geo::addLine(3, 5, 3); 31 gmsh::model::geo::addLine(5, 6, 4); 32 gmsh::model::geo::addLine(6, 4, 5); 33 gmsh::model::geo::addLine(4, 2, 6); 34 gmsh::model::geo::addLine(2, 7, 7); 35 gmsh::model::geo::addLine(7, 8, 8); 36 gmsh::model::geo::addLine(8, 1, 9); 37 gmsh::model::geo::addLine(8, 9, 10); 38 gmsh::model::geo::addLine(9, 3, 11); 39 gmsh::model::geo::addLine(9, 10, 12); 40 gmsh::model::geo::addLine(10, 11, 13); 41 gmsh::model::geo::addLine(11, 12, 14); 42 gmsh::model::geo::addLine(12, 7, 15); 43 gmsh::model::geo::addLine(12, 4, 16); 44 gmsh::model::geo::addLine(11, 6, 17); 45 gmsh::model::geo::addLine(10, 5, 18); 46 47 // Define surfaces through their boundaries 48 gmsh::model::geo::addCurveLoop({3, 4, 5, 6, 1, 2}, 1); 49 gmsh::model::geo::addPlaneSurface({1}, 1); 50 gmsh::model::geo::addCurveLoop({18, 4, -17, -13}, 2); 51 gmsh::model::geo::addPlaneSurface({2}, 2); 52 gmsh::model::geo::addCurveLoop({5, -16, -14, 17}, 3); 53 gmsh::model::geo::addPlaneSurface({3}, 3); 54 gmsh::model::geo::addCurveLoop({16, 6, 7, -15}, 4); 55 gmsh::model::geo::addPlaneSurface({4}, 4); 56 gmsh::model::geo::addCurveLoop({12, 13, 14, 15, 8, 10}, 5); 57 gmsh::model::geo::addPlaneSurface({5}, 5); 58 gmsh::model::geo::addCurveLoop({11, -2, -9, 10}, 6); 59 gmsh::model::geo::addPlaneSurface({6}, 6); 60 gmsh::model::geo::addCurveLoop({1, -9, -8, -7}, 7); 61 gmsh::model::geo::addPlaneSurface({7}, 7); 62 gmsh::model::geo::addCurveLoop({11, 3, -18, -12}, 8); 63 gmsh::model::geo::addPlaneSurface({8}, 8); 64 65 gmsh::model::geo::addSurfaceLoop({8, 1, 2, 3, 4, 7, 6, 5}, 1); 66 gmsh::model::geo::addVolume({1}, 1); 67 68 gmsh::model::geo::synchronize(); 70 72 gmsh::model::addPhysicalGroup(3, {1}, 1); 74 gmsh::model::addPhysicalGroup(2, {7}, 101, "dir_y"); 98 gmsh::option::setNumber("Mesh.Algorithm", 6); 99 gmsh::option::setNumber("Mesh.ElementOrder", 1); 100 gmsh::model::mesh::generate(3); 101 gmsh::write("filename.msh"); The mesh is generated, but the Physical Group is not correctly loaded into the DMPlex. If I run a DMView on my dm, I get: 171 DM Object: Parallel Mesh 4 MPI processes 172 type: plex 173 Parallel Mesh in 3 dimensions: 174 Number of 0-cells per rank: 7138 7192 7328 7171 175 Number of 1-cells per rank: 45825 45992 46817 45824 176 Number of 2-cells per rank: 74791 74901 76203 74568 177 Number of 3-cells per rank: 36103 36100 36713 35914 178 Labels: 179 depth: 4 strata with value/size (0 (7138), 1 (45825), 2 (74791), 3 (36103)) 180 celltype: 4 strata with value/size (0 (7138), 1 (45825), 3 (74791), 6 (36103)) 181 Cell Sets: 1 strata with value/size (1 (36103)) 182 Face Sets: 0 strata with value/size () 183 Vertex Sets: 1 strata with value/size (1 (5200)) Why are the elements of the physicalGroup "dir_y" (Plane Surface 7) not loaded as a face set? If I change the Plane Surface to another surface, e.g. 8, it marks the elements as the correct face set. Another weird thing is that the number of vertices in the above Vertex set is not correct. I have tried changing the numbering of Plane Surface 7 (to e.g. 70) but the issue remains. I run the code with the -dm_plex_gmsh_mark_vertices and -dm_plex_gmsh_multiple_tags flags. Thank you, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From harry-arthur at hotmail.fr Wed Sep 20 08:34:55 2023 From: harry-arthur at hotmail.fr (Harry-Arthur Cousin) Date: Wed, 20 Sep 2023 13:34:55 +0000 Subject: [petsc-users] Problem with snes: petsc 3.4.5 Message-ID: Hello, I'm on petsc version 3.4.5. My program has a time loop where I have to solve a non-linear system of the form F(X) = D*L*J + I + kappa(X) where X is an unknown vector, D and L are diagonal square matrices, J is a vector that can be calculated by solving a linear system with X and kappa is a non-linear application. I use the "-snes_mf" option to, as I understand it, approximate the Jacobian using finite differences. A first version of my problem could be solved, so I made it more complex by changing the values of the matrix L, which used to have the same value on the whole diagonal and now has values of the same order of magnitude but different. This second version takes longer and doesn't converge after a while. I get the message: Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE. However, when I look at the faq (https://petsc.org/release/faq/#why-is-newton-s-method-snes-not-converging-or-converges-slowly), it indicates that it's probably a Jacobian problem. What should I do? Do I have to calculate the explicit Jacobian? The explicit Jacobian requires the inversion of a matrix (due to the linear system for solving J). Kind regards, Harry Cousin -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Wed Sep 20 09:23:50 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 20 Sep 2023 10:23:50 -0400 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP In-Reply-To: References: Message-ID: Use VecCreate(), VecSetSizes(), VecSetType() and MatCreate(), MatSetSizes(), and MatSetType() instead of the convience functions VecCreateMPICUDA() and MatCreateShell(). > On Sep 19, 2023, at 8:44 PM, Sreeram R Venkat wrote: > > Thank you for your reply. > > Let's call this matrix M: > (A B C D) > (E F G H) > (I J K L) > > Now, instead of doing KSP with just M, what if I want M^TM? In this case, the matvec implementation would be as follows: > > same partitioning of blocks A, B, ..., L among the 12 MPI ranks > matvec looks like: > (a) (w) > (b) = (M^TM ) (x) > (c) (y) > (d) (z) > w, x, y, z stored on ranks A, B, C, D (as before) > a, b, c, d now also stored on ranks A, B, C, D > Based on your message, I believe using a PetscLayout for both the (a,b,c,d) and (w,x,y,z) vector of (number of columns of A, number of columns of B, number of columns of C, number of columns of D,0,0,0,0,0,0,0,0,0) should work. > > > I see there are functions "VecSetLayout" and "MatSetLayouts" to set the PetscLayouts of the matrix and vectors. When I create the vectors (I need VecCreateMPICUDA) or matrix shell (with MatCreateShell), I need to pass the local and global sizes. I'm not sure what to do there. > > > Thanks, > Sreeram > > On Tue, Sep 19, 2023, 7:13 PM Barry Smith > wrote: >> >> The PetscLayout local sizes for PETSc (a,b,c) vector (0,0,0,number of rows of D, 0,0,0, number of rows of H, 0,0,0,number of rows of L) >> >> >> The PetscLayout local sizes for PETSc (w,x,y,z) vector (number of columns of A, number of columns of B, number of columns of C, number of columns of D,0,0,0,0,0,0,0,0,0) >> >> The left and right layouts of the shell matrix need to match the two above. >> >> There is a huge problem. KSP is written assuming that the left vector layout is the same as the right vector layout. So it can do dot products MPI rank by MPI rank without needing to send individual vector values around. >> >> I don't it makes sense to use PETSc with such vector decompositions as you would like. >> >> Barry >> >> >> >>> On Sep 19, 2023, at 7:44 PM, Sreeram R Venkat > wrote: >>> >>> With the example you have given, here is what I would like to do: >>> 12 MPI ranks >>> Each rank has one block (rank 0 has A, rank 1 has B, ..., rank 11 has L) - to make the rest of this easier I'll refer to the rank containing block A as "rank A", and so on >>> rank A, rank B, rank C, and rank D have w, x, y, z respectively - the first step of the custom matvec implementation broadcasts w to rank E and rank I (similarly x is broadcast to rank F and rank J ...) >>> at the end of the matvec computation, ranks D, H, and L have a, b, and c respectively >>> Thanks, >>> Sreeram >>> >>> >>> On Tue, Sep 19, 2023 at 6:23?PM Barry Smith > wrote: >>>> >>>> ( a ) ( A B C D ) ( w ) >>>> ( b ) = ( E F G H ) ( x ) >>>> ( c ) ( I J K L ) ( y ) >>>> ( z ) >>>> >>>> I have no idea what "The input vector is partitioned across each row, and the output vector is partitioned across each column" means. >>>> >>>> Anyways the shell matrix needs to live on MPI_COMM_WORLD, as do both the (a,b,c) and (w,x,y,z) vector. >>>> >>>> Now how many MPI ranks do you want to do the compution on? 12? >>>> Do you want one matrix A .. Z on each rank? >>>> >>>> Do you want the (a,b,c) vector spread over all ranks? What about the (w,x,y,z) vector? >>>> >>>> Barry >>>> >>>> >>>> >>>>> On Sep 19, 2023, at 4:42 PM, Sreeram R Venkat > wrote: >>>>> >>>>> I have a custom implementation of a matrix-vector product that inherently relies on a 2D processor partitioning of the matrix. That is, if the matrix looks like: >>>>> >>>>> A B C D >>>>> E F G H >>>>> I J K L >>>>> in block form, we use 12 processors, each having one block. The input vector is partitioned across each row, and the output vector is partitioned across each column. >>>>> >>>>> Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a COL_COMM. The ROW/COL communicators are used to do reductions over rows/columns of processors. >>>>> >>>>> With this setup, I am a bit confused about how to set up the matrix shell. The "MatCreateShell" function only accepts one communicator. If I give the WORLD_COMM, the local/global sizes won't match since PETSc will try to multiply local_size * total_processors instead of local_size * processors_per_row (or col). I have gotten around this temporarily by giving ROW_COMM here instead. What I think happens is a different MatShell is created on each row, but when computing the matvec, they all work together. >>>>> >>>>> However, if I try to use KSP (CG) with this setup (giving ROW_COMM as the communicator), the process hangs. I believe this is due to the partitioning of the input/output vectors. The matvec itself is fine, but the inner products and other steps of CG fail. In fact, if I restrict to the case where I only have one row of processors, I am able to successfully use KSP. >>>>> >>>>> Is there a way to use KSP with this 2D partitioning setup when there are multiple rows of processors? I'd also prefer to work with one global MatShell object instead of this one object per row thing that I'm doing right now. >>>>> >>>>> Thanks for your help, >>>>> Sreeram >>>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Wed Sep 20 09:26:41 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 20 Sep 2023 10:26:41 -0400 Subject: [petsc-users] Problem with snes: petsc 3.4.5 In-Reply-To: References: Message-ID: Run with -snes_monitor and -ksp_monitor_true_residual and send the output > On Sep 20, 2023, at 9:34 AM, Harry-Arthur Cousin wrote: > > Hello, > > I'm on petsc version 3.4.5. > > My program has a time loop where I have to solve a non-linear system of the form F(X) = D*L*J + I + kappa(X) where X is an unknown vector, D and L are diagonal square matrices, J is a vector that can be calculated by solving a linear system with X and kappa is a non-linear application. I use the "-snes_mf" option to, as I understand it, approximate the Jacobian using finite differences. > > A first version of my problem could be solved, so I made it more complex by changing the values of the matrix L, which used to have the same value on the whole diagonal and now has values of the same order of magnitude but different. This second version takes longer and doesn't converge after a while. I get the message: Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE. However, when I look at the faq (https://petsc.org/release/faq/#why-is-newton-s-method-snes-not-converging-or-converges-slowly), it indicates that it's probably a Jacobian problem. What should I do? Do I have to calculate the explicit Jacobian? The explicit Jacobian requires the inversion of a matrix (due to the linear system for solving J). > > > Kind regards, > > Harry Cousin -------------- next part -------------- An HTML attachment was scrubbed... URL: From harry-arthur at hotmail.fr Wed Sep 20 09:36:00 2023 From: harry-arthur at hotmail.fr (Harry-Arthur Cousin) Date: Wed, 20 Sep 2023 14:36:00 +0000 Subject: [petsc-users] Problem with snes: petsc 3.4.5 In-Reply-To: References: Message-ID: Will do. The output is very long, I'm sending you the last 20 iteration of KSP when the nonlinear solver did not converge. That's what i have: Linear solve converged due to CONVERGED_ITS iterations 1 9980 KSP preconditioned resid norm 7.911586848688e-14 true resid norm 3.571299151668e-13 ||r(i)||/||b|| 1.088933920648e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9981 KSP preconditioned resid norm 7.773677194223e-14 true resid norm 3.519061016604e-13 ||r(i)||/||b|| 1.073005857832e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9982 KSP preconditioned resid norm 7.142532169111e-14 true resid norm 3.536747918236e-13 ||r(i)||/||b|| 1.078398816059e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9983 KSP preconditioned resid norm 6.325819556307e-14 true resid norm 3.698647905235e-13 ||r(i)||/||b|| 1.127764153463e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9984 KSP preconditioned resid norm 6.119227152008e-14 true resid norm 3.563406240582e-13 ||r(i)||/||b|| 1.086527273025e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9985 KSP preconditioned resid norm 6.075666963630e-14 true resid norm 3.710895872549e-13 ||r(i)||/||b|| 1.131498712373e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9986 KSP preconditioned resid norm 5.985095889340e-14 true resid norm 3.509409502428e-13 ||r(i)||/||b|| 1.070062990062e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9987 KSP preconditioned resid norm 5.243339292054e-14 true resid norm 3.627159951643e-13 ||r(i)||/||b|| 1.105966579450e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9988 KSP preconditioned resid norm 4.491198445126e-14 true resid norm 4.006851442317e-13 ||r(i)||/||b|| 1.221739278968e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9989 KSP preconditioned resid norm 4.410245117574e-14 true resid norm 4.031793308619e-13 ||r(i)||/||b|| 1.229344366950e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9990 KSP preconditioned resid norm 4.072064997637e-13 true resid norm 4.072064997637e-13 ||r(i)||/||b|| 1.241623710224e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9991 KSP preconditioned resid norm 2.614566817566e-13 true resid norm 3.327810250174e-13 ||r(i)||/||b|| 1.014691099513e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9992 KSP preconditioned resid norm 2.214885215262e-13 true resid norm 3.122694737130e-13 ||r(i)||/||b|| 9.521488059891e-04 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9993 KSP preconditioned resid norm 1.937414464538e-13 true resid norm 2.949371229399e-13 ||r(i)||/||b|| 8.993002937814e-04 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9994 KSP preconditioned resid norm 1.683143904883e-13 true resid norm 3.116491153488e-13 ||r(i)||/||b|| 9.502572555001e-04 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9995 KSP preconditioned resid norm 1.455417378095e-13 true resid norm 3.848207009730e-13 ||r(i)||/||b|| 1.173366600951e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9996 KSP preconditioned resid norm 1.254552363609e-13 true resid norm 3.494786173247e-13 ||r(i)||/||b|| 1.065604153515e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9997 KSP preconditioned resid norm 1.187610795222e-13 true resid norm 3.364834320451e-13 ||r(i)||/||b|| 1.025980203084e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9998 KSP preconditioned resid norm 1.126887893465e-13 true resid norm 4.347573700680e-13 ||r(i)||/||b|| 1.325629770605e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 9999 KSP preconditioned resid norm 1.067379754742e-13 true resid norm 3.907245052617e-13 ||r(i)||/||b|| 1.191368040981e-03 Linear solve converged due to CONVERGED_ITS iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 10000 KSP preconditioned resid norm 1.027326121286e-13 true resid norm 4.122100161195e-13 ||r(i)||/||b|| 1.256880059386e-03 Linear solve did not converge due to DIVERGED_ITS iterations 10000 Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 1 Linear solve converged due to CONVERGED_ITS iterations 1 ________________________________ De : Barry Smith Envoy? : mercredi 20 septembre 2023 16:26 ? : Harry-Arthur Cousin Cc : petsc-users at mcs.anl.gov Objet : Re: [petsc-users] Problem with snes: petsc 3.4.5 Run with -snes_monitor and -ksp_monitor_true_residual and send the output On Sep 20, 2023, at 9:34 AM, Harry-Arthur Cousin wrote: Hello, I'm on petsc version 3.4.5. My program has a time loop where I have to solve a non-linear system of the form F(X) = D*L*J + I + kappa(X) where X is an unknown vector, D and L are diagonal square matrices, J is a vector that can be calculated by solving a linear system with X and kappa is a non-linear application. I use the "-snes_mf" option to, as I understand it, approximate the Jacobian using finite differences. A first version of my problem could be solved, so I made it more complex by changing the values of the matrix L, which used to have the same value on the whole diagonal and now has values of the same order of magnitude but different. This second version takes longer and doesn't converge after a while. I get the message: Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE. However, when I look at the faq (https://petsc.org/release/faq/#why-is-newton-s-method-snes-not-converging-or-converges-slowly), it indicates that it's probably a Jacobian problem. What should I do? Do I have to calculate the explicit Jacobian? The explicit Jacobian requires the inversion of a matrix (due to the linear system for solving J). Kind regards, Harry Cousin -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Wed Sep 20 09:59:20 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 20 Sep 2023 10:59:20 -0400 Subject: [petsc-users] Problem with snes: petsc 3.4.5 In-Reply-To: References: Message-ID: <080FC684-2871-4109-A296-F0728356DC2B@petsc.dev> 10000 KSP preconditioned resid norm 1.027326121286e-13 true resid norm 4.122100161195e-13 ||r(i)||/||b|| 1.256880059386e-03 The residual norms are very small. From the final column we see that the relative decrease in the residual norm was only 1.e-3 meaning the initial linear system residual norm was already very small at the beginning of the linear solve. I suspect you have a very small SNES tolerance? When using matrix-free SNES with complex systems you cannot expect to get really tight convergence. I suggest -snes_rtol 1.e-8 -ksp_atol 1.e-11 But you can try out various values > On Sep 20, 2023, at 10:36 AM, Harry-Arthur Cousin wrote: > > Will do. The output is very long, I'm sending you the last 20 iteration of KSP when the nonlinear solver did not converge. That's what i have: > > Linear solve converged due to CONVERGED_ITS iterations 1 > 9980 KSP preconditioned resid norm 7.911586848688e-14 true resid norm 3.571299151668e-13 ||r(i)||/||b|| 1.088933920648e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9981 KSP preconditioned resid norm 7.773677194223e-14 true resid norm 3.519061016604e-13 ||r(i)||/||b|| 1.073005857832e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9982 KSP preconditioned resid norm 7.142532169111e-14 true resid norm 3.536747918236e-13 ||r(i)||/||b|| 1.078398816059e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9983 KSP preconditioned resid norm 6.325819556307e-14 true resid norm 3.698647905235e-13 ||r(i)||/||b|| 1.127764153463e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9984 KSP preconditioned resid norm 6.119227152008e-14 true resid norm 3.563406240582e-13 ||r(i)||/||b|| 1.086527273025e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9985 KSP preconditioned resid norm 6.075666963630e-14 true resid norm 3.710895872549e-13 ||r(i)||/||b|| 1.131498712373e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9986 KSP preconditioned resid norm 5.985095889340e-14 true resid norm 3.509409502428e-13 ||r(i)||/||b|| 1.070062990062e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9987 KSP preconditioned resid norm 5.243339292054e-14 true resid norm 3.627159951643e-13 ||r(i)||/||b|| 1.105966579450e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9988 KSP preconditioned resid norm 4.491198445126e-14 true resid norm 4.006851442317e-13 ||r(i)||/||b|| 1.221739278968e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9989 KSP preconditioned resid norm 4.410245117574e-14 true resid norm 4.031793308619e-13 ||r(i)||/||b|| 1.229344366950e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9990 KSP preconditioned resid norm 4.072064997637e-13 true resid norm 4.072064997637e-13 ||r(i)||/||b|| 1.241623710224e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9991 KSP preconditioned resid norm 2.614566817566e-13 true resid norm 3.327810250174e-13 ||r(i)||/||b|| 1.014691099513e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9992 KSP preconditioned resid norm 2.214885215262e-13 true resid norm 3.122694737130e-13 ||r(i)||/||b|| 9.521488059891e-04 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9993 KSP preconditioned resid norm 1.937414464538e-13 true resid norm 2.949371229399e-13 ||r(i)||/||b|| 8.993002937814e-04 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9994 KSP preconditioned resid norm 1.683143904883e-13 true resid norm 3.116491153488e-13 ||r(i)||/||b|| 9.502572555001e-04 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9995 KSP preconditioned resid norm 1.455417378095e-13 true resid norm 3.848207009730e-13 ||r(i)||/||b|| 1.173366600951e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9996 KSP preconditioned resid norm 1.254552363609e-13 true resid norm 3.494786173247e-13 ||r(i)||/||b|| 1.065604153515e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9997 KSP preconditioned resid norm 1.187610795222e-13 true resid norm 3.364834320451e-13 ||r(i)||/||b|| 1.025980203084e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9998 KSP preconditioned resid norm 1.126887893465e-13 true resid norm 4.347573700680e-13 ||r(i)||/||b|| 1.325629770605e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 9999 KSP preconditioned resid norm 1.067379754742e-13 true resid norm 3.907245052617e-13 ||r(i)||/||b|| 1.191368040981e-03 > Linear solve converged due to CONVERGED_ITS iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > 10000 KSP preconditioned resid norm 1.027326121286e-13 true resid norm 4.122100161195e-13 ||r(i)||/||b|| 1.256880059386e-03 > Linear solve did not converge due to DIVERGED_ITS iterations 10000 > Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 1 > Linear solve converged due to CONVERGED_ITS iterations 1 > > De : Barry Smith > > Envoy? : mercredi 20 septembre 2023 16:26 > ? : Harry-Arthur Cousin > > Cc : petsc-users at mcs.anl.gov > > Objet : Re: [petsc-users] Problem with snes: petsc 3.4.5 > > > Run with -snes_monitor and -ksp_monitor_true_residual and send the output > >> On Sep 20, 2023, at 9:34 AM, Harry-Arthur Cousin > wrote: >> >> Hello, >> >> I'm on petsc version 3.4.5. >> >> My program has a time loop where I have to solve a non-linear system of the form F(X) = D*L*J + I + kappa(X) where X is an unknown vector, D and L are diagonal square matrices, J is a vector that can be calculated by solving a linear system with X and kappa is a non-linear application. I use the "-snes_mf" option to, as I understand it, approximate the Jacobian using finite differences. >> >> A first version of my problem could be solved, so I made it more complex by changing the values of the matrix L, which used to have the same value on the whole diagonal and now has values of the same order of magnitude but different. This second version takes longer and doesn't converge after a while. I get the message: Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE. However, when I look at the faq (https://petsc.org/release/faq/#why-is-newton-s-method-snes-not-converging-or-converges-slowly), it indicates that it's probably a Jacobian problem. What should I do? Do I have to calculate the explicit Jacobian? The explicit Jacobian requires the inversion of a matrix (due to the linear system for solving J). >> >> >> Kind regards, >> >> Harry Cousin -------------- next part -------------- An HTML attachment was scrubbed... URL: From ramoni.zsedano at gmail.com Wed Sep 20 10:21:12 2023 From: ramoni.zsedano at gmail.com (Ramoni Z. Sedano Azevedo) Date: Wed, 20 Sep 2023 12:21:12 -0300 Subject: [petsc-users] Problem with matrix and vector using GPU Message-ID: Hey! I am using PETSc in a Fortran code and we use MPI parallelization. We would like to use GPU parallelization, but we are encountering an error. PETSc is configured as follows: #!/bin/bash ./configure \ --prefix=${PWD}/installdir \ --with-fortran \ --with-fortran-kernels=true \ --with-cuda \ --download-fblaslapack \ --with-scalar-type=complex \ --with-precision=double \ --with-debugging=yes \ --with-x=0 \ --with-gnu-compilers=1 \ --with-cc=mpicc \ --with-cxx=mpicxx \ --with-fc=mpif90 \ --with-make-exec=make Within my code, matrices and vectors are allocated with the following commands: PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) PetscCallA( DMSetUp(da,ierr) ) PetscCallA( DMCreateGlobalVector(da,b,ierr) ) PetscCallA( VecDuplicate(b,xsol,ierr) ) PetscCallA( VecDuplicate(b,src,ierr) ) PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) PetscCallA( DMCreateLocalVector(da,localx,ierr) ) PetscCallA( VecDuplicate(localx,localb,ierr) ) PetscCallA( VecDuplicate(localx,localsrc,ierr) ) PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) ngrow=3*(l+1)*(m+1)*nzn PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) PetscCallA( MatSetFromOptions(A,ierr) ) PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) PetscCallA( MatSetFromOptions(P, ierr) ) PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) ) PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, ierr) ) PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) When calling the solver function PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) the following error occurs: [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Invalid argument[0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc![0]PETSC ERROR: Option left: name:-vec_type value: cuda[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.[0]PETSC ERROR: Petsc Release Version 3.18.4, unknown The code is executed with the following flags: ./${executable} \ -A_mat_type aijcusparse \ -P_mat_type aijcusparse \ -vec_type cuda \ -use_gpu_aware_mpi 0 \ -em_ksp_monitor_true_residual \ -em_ksp_type bcgs \ -em_pc_type bjacobi \ -em_sub_pc_type ilu \ -em_sub_pc_factor_levels 3 \ -em_sub_pc_factor_fill 6 \ < ./Parameters.inp \ I've already tested using mpiaijcusparse for matrix and mpicuda for vector and the error continues. Would anyone have an idea what I might be doing wrong? Sincerely, Ramoni Z. S. Azevedo -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Wed Sep 20 10:28:07 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 20 Sep 2023 11:28:07 -0400 Subject: [petsc-users] Problem with matrix and vector using GPU In-Reply-To: References: Message-ID: <2DAEC809-C14F-4668-A83B-D301642A3221@petsc.dev> Since you are creating some vectors from the DM you need also the options database option -dm_vec_type cuda Barry > On Sep 20, 2023, at 11:21 AM, Ramoni Z. Sedano Azevedo wrote: > > > Hey! > > I am using PETSc in a Fortran code and we use MPI parallelization. We would like to use GPU parallelization, but we are encountering an error. > > PETSc is configured as follows: > #!/bin/bash > ./configure \ > --prefix=${PWD}/installdir \ > --with-fortran \ > --with-fortran-kernels=true \ > --with-cuda \ > --download-fblaslapack \ > --with-scalar-type=complex \ > --with-precision=double \ > --with-debugging=yes \ > --with-x=0 \ > --with-gnu-compilers=1 \ > --with-cc=mpicc \ > --with-cxx=mpicxx \ > --with-fc=mpif90 \ > --with-make-exec=make > > Within my code, matrices and vectors are allocated with the following commands: > PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) > > PetscCallA( DMSetUp(da,ierr) ) > > PetscCallA( DMCreateGlobalVector(da,b,ierr) ) > PetscCallA( VecDuplicate(b,xsol,ierr) ) > PetscCallA( VecDuplicate(b,src,ierr) ) > PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) > > PetscCallA( DMCreateLocalVector(da,localx,ierr) ) > PetscCallA( VecDuplicate(localx,localb,ierr) ) > PetscCallA( VecDuplicate(localx,localsrc,ierr) ) > PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) > > PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) > > ngrow=3*(l+1)*(m+1)*nzn > > PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) > PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) > PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) > PetscCallA( MatSetFromOptions(A,ierr) ) > PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) > PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) > PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) > PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) > PetscCallA( MatSetFromOptions(P, ierr) ) > PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) ) > PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) > PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) ) > PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) > PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) > > PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) > PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, ierr) ) > PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) > PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) > > When calling the solver function > PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) > the following error occurs: > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: Invalid argument > [0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda > [0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc! > [0]PETSC ERROR: Option left: name:-vec_type value: cuda > [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.18.4, unknown > The code is executed with the following flags: > ./${executable} \ > -A_mat_type aijcusparse \ > -P_mat_type aijcusparse \ > -vec_type cuda \ > -use_gpu_aware_mpi 0 \ > -em_ksp_monitor_true_residual \ > -em_ksp_type bcgs \ > -em_pc_type bjacobi \ > -em_sub_pc_type ilu \ > -em_sub_pc_factor_levels 3 \ > -em_sub_pc_factor_fill 6 \ > < ./Parameters.inp \ > > I've already tested using mpiaijcusparse for matrix and mpicuda for vector and the error continues. > > Would anyone have an idea what I might be doing wrong? > > Sincerely, > Ramoni Z. S. Azevedo > -------------- next part -------------- An HTML attachment was scrubbed... URL: From junchao.zhang at gmail.com Wed Sep 20 10:31:41 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Wed, 20 Sep 2023 10:31:41 -0500 Subject: [petsc-users] Problem with matrix and vector using GPU In-Reply-To: References: Message-ID: Try to also add *-dm_mat_type aijcusparse -dm_vec_type cuda* --Junchao Zhang On Wed, Sep 20, 2023 at 10:21?AM Ramoni Z. Sedano Azevedo < ramoni.zsedano at gmail.com> wrote: > > Hey! > > I am using PETSc in a Fortran code and we use MPI parallelization. We > would like to use GPU parallelization, but we are encountering an error. > > PETSc is configured as follows: > #!/bin/bash > ./configure \ > --prefix=${PWD}/installdir \ > --with-fortran \ > --with-fortran-kernels=true \ > --with-cuda \ > --download-fblaslapack \ > --with-scalar-type=complex \ > --with-precision=double \ > --with-debugging=yes \ > --with-x=0 \ > --with-gnu-compilers=1 \ > --with-cc=mpicc \ > --with-cxx=mpicxx \ > --with-fc=mpif90 \ > --with-make-exec=make > > Within my code, matrices and vectors are allocated with the following > commands: > PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, > DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, > PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, > PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) > > PetscCallA( DMSetUp(da,ierr) ) > > PetscCallA( DMCreateGlobalVector(da,b,ierr) ) > PetscCallA( VecDuplicate(b,xsol,ierr) ) > PetscCallA( VecDuplicate(b,src,ierr) ) > PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) > > PetscCallA( DMCreateLocalVector(da,localx,ierr) ) > PetscCallA( VecDuplicate(localx,localb,ierr) ) > PetscCallA( VecDuplicate(localx,localsrc,ierr) ) > PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) > > PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) > > ngrow=3*(l+1)*(m+1)*nzn > > PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) > PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) > PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) > PetscCallA( MatSetFromOptions(A,ierr) ) > PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) > PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, > ierr) ) > > PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, > PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, > i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) > PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) > PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) > PetscCallA( MatSetFromOptions(P, ierr) ) > PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) ) > PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, > ierr) ) > > PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, > PETSC_NULL_INTEGER, ierr) ) > PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, > i15, PETSC_NULL_INTEGER, ierr) ) > > PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, > PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, > PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, > PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) > ) > PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) > PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) > > PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) > PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, ierr) ) > PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) > PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) > > When calling the solver function > PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) > the following error occurs: > > [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Invalid argument[0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc![0]PETSC ERROR: Option left: name:-vec_type value: cuda[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.[0]PETSC ERROR: Petsc Release Version 3.18.4, unknown > > The code is executed with the following flags: > ./${executable} \ > -A_mat_type aijcusparse \ > -P_mat_type aijcusparse \ > -vec_type cuda \ > -use_gpu_aware_mpi 0 \ > -em_ksp_monitor_true_residual \ > -em_ksp_type bcgs \ > -em_pc_type bjacobi \ > -em_sub_pc_type ilu \ > -em_sub_pc_factor_levels 3 \ > -em_sub_pc_factor_fill 6 \ > < ./Parameters.inp \ > > I've already tested using mpiaijcusparse for matrix and mpicuda for vector > and the error continues. > > Would anyone have an idea what I might be doing wrong? > > Sincerely, > Ramoni Z. S. Azevedo > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrsd at gmail.com Wed Sep 20 12:08:45 2023 From: andrsd at gmail.com (David Andrs) Date: Wed, 20 Sep 2023 11:08:45 -0600 Subject: [petsc-users] Face Set not appearing when loading GMSH mesh to DMPlex In-Reply-To: <576f28bb730c467680de36abfbf5b463@solid.lth.se> References: <576f28bb730c467680de36abfbf5b463@solid.lth.se> Message-ID: Hi Anna, I think you are looking at an output from a processor that does not have the face set loaded. If I load your mesh with a single MPI, I see: DM Object: DM_0x84000000_0 1 MPI processes type: plex DM_0x84000000_0 in 3 dimensions: Number of 0-cells per rank: 27499 Number of 1-cells per rank: 180922 Number of 2-cells per rank: 298443 Number of 3-cells per rank: 145019 Labels: celltype: 4 strata with value/size (0 (27499), 6 (145019), 3 (298443), 1 (180922)) depth: 4 strata with value/size (0 (27499), 1 (180922), 2 (298443), 3 (145019)) Cell Sets: 1 strata with value/size (1 (145019)) Face Sets: 1 strata with value/size (101 (934)) Vertex Sets: 2 strata with value/size (101 (428), 1 (19092)) Which seems to match the gmsh script. If I load your mesh with more MPIs, and print the DM via `DMView(dm, PETSC_VIEWER_STDOUT_SELF);` then I can see that some MPI ranks do not have it. I think this is expected behavior - only ranks that own the elements attached to the face set will have the face set (or part of it) defined. Similarly for vertex sets. At least that's how I understand it. Are you after having the face sets and vertex sets on all ranks? -- David On Wed, Sep 20, 2023 at 6:17?AM Anna Dalklint via petsc-users < petsc-users at mcs.anl.gov> wrote: > Hello, > > > I am trying to load a mesh, created via the gmsh api, into a DMPlex. The > code is seen below: > > 6 gmsh::initialize(); > 7 elsize0 = 1.0; > 8 double a = 20.0; > 9 double b = 20.0; > 10 double c = 10.0; > 11 double d = 30.0; > 12 double e = 70.0; > 13 > 14 gmsh::model::geo::addPoint(0.0, 0.0, 0.0, elsize0, 1); > 15 gmsh::model::geo::addPoint(a, 0.0, 0.0, elsize0, 2); > 16 gmsh::model::geo::addPoint(0.0, d, 0.0, elsize0, 3); > 17 gmsh::model::geo::addPoint(a, c, 0.0, elsize0, 4); > 18 gmsh::model::geo::addPoint(e, d, 0.0, elsize0, 5); > 19 gmsh::model::geo::addPoint(e, c, 0.0, elsize0, 6); > 20 gmsh::model::geo::addPoint(a, 0.0, b, elsize0, 7); > 21 gmsh::model::geo::addPoint(0.0, 0.0, b, elsize0, 8); > 22 gmsh::model::geo::addPoint(0.0, d, b, elsize0, 9); > 23 gmsh::model::geo::addPoint(e, d, b, elsize0, 10); > 24 gmsh::model::geo::addPoint(e, c, b, elsize0, 11); > 25 gmsh::model::geo::addPoint(a, c, b, elsize0, 12); > 26 > 27 // Define lines connecting points > 28 gmsh::model::geo::addLine(2, 1, 1); > 29 gmsh::model::geo::addLine(1, 3, 2); > 30 gmsh::model::geo::addLine(3, 5, 3); > 31 gmsh::model::geo::addLine(5, 6, 4); > 32 gmsh::model::geo::addLine(6, 4, 5); > 33 gmsh::model::geo::addLine(4, 2, 6); > 34 gmsh::model::geo::addLine(2, 7, 7); > 35 gmsh::model::geo::addLine(7, 8, 8); > 36 gmsh::model::geo::addLine(8, 1, 9); > 37 gmsh::model::geo::addLine(8, 9, 10); > 38 gmsh::model::geo::addLine(9, 3, 11); > 39 gmsh::model::geo::addLine(9, 10, 12); > 40 gmsh::model::geo::addLine(10, 11, 13); > 41 gmsh::model::geo::addLine(11, 12, 14); > 42 gmsh::model::geo::addLine(12, 7, 15); > 43 gmsh::model::geo::addLine(12, 4, 16); > 44 gmsh::model::geo::addLine(11, 6, 17); > 45 gmsh::model::geo::addLine(10, 5, 18); > 46 > 47 // Define surfaces through their boundaries > 48 gmsh::model::geo::addCurveLoop({3, 4, 5, 6, 1, 2}, 1); > 49 gmsh::model::geo::addPlaneSurface({1}, 1); > 50 gmsh::model::geo::addCurveLoop({18, 4, -17, -13}, 2); > 51 gmsh::model::geo::addPlaneSurface({2}, 2); > 52 gmsh::model::geo::addCurveLoop({5, -16, -14, 17}, 3); > 53 gmsh::model::geo::addPlaneSurface({3}, 3); > 54 gmsh::model::geo::addCurveLoop({16, 6, 7, -15}, 4); > 55 gmsh::model::geo::addPlaneSurface({4}, 4); > 56 gmsh::model::geo::addCurveLoop({12, 13, 14, 15, 8, 10}, 5); > 57 gmsh::model::geo::addPlaneSurface({5}, 5); > 58 gmsh::model::geo::addCurveLoop({11, -2, -9, 10}, 6); > 59 gmsh::model::geo::addPlaneSurface({6}, 6); > 60 gmsh::model::geo::addCurveLoop({1, -9, -8, -7}, 7); > 61 gmsh::model::geo::addPlaneSurface({7}, 7); > 62 gmsh::model::geo::addCurveLoop({11, 3, -18, -12}, 8); > 63 gmsh::model::geo::addPlaneSurface({8}, 8); > 64 > 65 gmsh::model::geo::addSurfaceLoop({8, 1, 2, 3, 4, 7, 6, 5}, 1); > 66 gmsh::model::geo::addVolume({1}, 1); > 67 > 68 gmsh::model::geo::synchronize(); > 70 > 72 gmsh::model::addPhysicalGroup(3, {1}, 1); > 74 gmsh::model::addPhysicalGroup(2, {7}, 101, "dir_y"); > > 98 gmsh::option::setNumber("Mesh.Algorithm", 6); > 99 gmsh::option::setNumber("Mesh.ElementOrder", 1); > 100 gmsh::model::mesh::generate(3); > 101 gmsh::write("filename.msh"); > > > The mesh is generated, but the Physical Group is not correctly loaded into > the DMPlex. If I run a DMView on my dm, I get: > > > 171 DM Object: Parallel Mesh 4 MPI processes > 172 type: plex > 173 Parallel Mesh in 3 dimensions: > 174 Number of 0-cells per rank: 7138 7192 7328 7171 > 175 Number of 1-cells per rank: 45825 45992 46817 45824 > 176 Number of 2-cells per rank: 74791 74901 76203 74568 > 177 Number of 3-cells per rank: 36103 36100 36713 35914 > 178 Labels: > 179 depth: 4 strata with value/size (0 (7138), 1 (45825), 2 (74791), 3 > (36103)) > 180 celltype: 4 strata with value/size (0 (7138), 1 (45825), 3 (74791), > 6 (36103)) > 181 Cell Sets: 1 strata with value/size (1 (36103)) > 182 Face Sets: 0 strata with value/size () > 183 Vertex Sets: 1 strata with value/size (1 (5200)) > > > Why are the elements of the physicalGroup "dir_y" (Plane Surface 7) not > loaded as a face set? If I change the Plane Surface to another surface, > e.g. 8, it marks the elements as the correct face set. Another weird thing > is that the number of vertices in the above Vertex set is not correct. > > > I have tried changing the numbering of Plane Surface 7 (to e.g. 70) but > the issue remains. > > > I run the code with the -dm_plex_gmsh_mark_vertices and > -dm_plex_gmsh_multiple_tags flags. > > > Thank you, > Anna > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ramoni.zsedano at gmail.com Wed Sep 20 12:12:44 2023 From: ramoni.zsedano at gmail.com (Ramoni Z. Sedano Azevedo) Date: Wed, 20 Sep 2023 14:12:44 -0300 Subject: [petsc-users] Problem with matrix and vector using GPU In-Reply-To: References: Message-ID: Thanks for the tip. Using dm_mat_type and dm_vec_type the code runs. ./${executable} \ -A_dm_mat_type aijcusparse \ -P_dm_mat_type aijcusparse \ -dm_vec_type cuda \ -use_gpu_aware_mpi 0 \ -em_ksp_monitor_true_residual \ -em_ksp_type bcgs \ -em_pc_type bjacobi \ -em_sub_pc_type ilu \ -em_sub_pc_factor_levels 3 \ -em_sub_pc_factor_fill 6 \ < ./Parameters.inp \ But at the end the message appears: WARNING! There are options you set that were not used! WARNING! could be spelling mistake, etc! There are 3 unused database options. They are: Option left: name:-A_dm_mat_type value: aijcusparse Option left: name:-dm_vec_type value: cuda Option left: name:-P_dm_mat_type value: aijcusparse Using nvprof does not include kernels, only API use. Ramoni Z. S. Azevedo Em qua., 20 de set. de 2023 ?s 12:31, Junchao Zhang escreveu: > Try to also add *-dm_mat_type aijcusparse -dm_vec_type cuda* > > --Junchao Zhang > > > On Wed, Sep 20, 2023 at 10:21?AM Ramoni Z. Sedano Azevedo < > ramoni.zsedano at gmail.com> wrote: > >> >> Hey! >> >> I am using PETSc in a Fortran code and we use MPI parallelization. We >> would like to use GPU parallelization, but we are encountering an error. >> >> PETSc is configured as follows: >> #!/bin/bash >> ./configure \ >> --prefix=${PWD}/installdir \ >> --with-fortran \ >> --with-fortran-kernels=true \ >> --with-cuda \ >> --download-fblaslapack \ >> --with-scalar-type=complex \ >> --with-precision=double \ >> --with-debugging=yes \ >> --with-x=0 \ >> --with-gnu-compilers=1 \ >> --with-cc=mpicc \ >> --with-cxx=mpicxx \ >> --with-fc=mpif90 \ >> --with-make-exec=make >> >> Within my code, matrices and vectors are allocated with the following >> commands: >> PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, >> DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, >> PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, >> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) >> >> PetscCallA( DMSetUp(da,ierr) ) >> >> PetscCallA( DMCreateGlobalVector(da,b,ierr) ) >> PetscCallA( VecDuplicate(b,xsol,ierr) ) >> PetscCallA( VecDuplicate(b,src,ierr) ) >> PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) >> >> PetscCallA( DMCreateLocalVector(da,localx,ierr) ) >> PetscCallA( VecDuplicate(localx,localb,ierr) ) >> PetscCallA( VecDuplicate(localx,localsrc,ierr) ) >> PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) >> >> PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) >> >> ngrow=3*(l+1)*(m+1)*nzn >> >> PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) >> PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) >> PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) >> PetscCallA( MatSetFromOptions(A,ierr) ) >> PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) >> PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >> ierr) ) >> >> PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, >> PETSC_NULL_INTEGER, ierr) ) >> >> PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >> i15, PETSC_NULL_INTEGER, ierr) ) >> >> PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) >> PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) >> PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) >> PetscCallA( MatSetFromOptions(P, ierr) ) >> PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) ) >> PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >> ierr) ) >> >> PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, >> PETSC_NULL_INTEGER, ierr) ) >> PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >> i15, PETSC_NULL_INTEGER, ierr) ) >> >> PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, >> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >> PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) >> ) >> PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) >> PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) >> >> PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) >> PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, ierr) ) >> PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) >> PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) >> >> When calling the solver function >> PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) >> the following error occurs: >> >> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Invalid argument[0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc![0]PETSC ERROR: Option left: name:-vec_type value: cuda[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.[0]PETSC ERROR: Petsc Release Version 3.18.4, unknown >> >> The code is executed with the following flags: >> ./${executable} \ >> -A_mat_type aijcusparse \ >> -P_mat_type aijcusparse \ >> -vec_type cuda \ >> -use_gpu_aware_mpi 0 \ >> -em_ksp_monitor_true_residual \ >> -em_ksp_type bcgs \ >> -em_pc_type bjacobi \ >> -em_sub_pc_type ilu \ >> -em_sub_pc_factor_levels 3 \ >> -em_sub_pc_factor_fill 6 \ >> < ./Parameters.inp \ >> >> I've already tested using mpiaijcusparse for matrix and mpicuda for >> vector and the error continues. >> >> Would anyone have an idea what I might be doing wrong? >> >> Sincerely, >> Ramoni Z. S. Azevedo >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefano.zampini at gmail.com Wed Sep 20 12:26:17 2023 From: stefano.zampini at gmail.com (Stefano Zampini) Date: Wed, 20 Sep 2023 19:26:17 +0200 Subject: [petsc-users] Problem with matrix and vector using GPU In-Reply-To: References: Message-ID: You are missing a call to DMSetFromOptions On Wed, Sep 20, 2023, 19:20 Ramoni Z. Sedano Azevedo < ramoni.zsedano at gmail.com> wrote: > Thanks for the tip. Using dm_mat_type and dm_vec_type the code runs. > ./${executable} \ > -A_dm_mat_type aijcusparse \ > -P_dm_mat_type aijcusparse \ > -dm_vec_type cuda \ > -use_gpu_aware_mpi 0 \ > -em_ksp_monitor_true_residual \ > -em_ksp_type bcgs \ > -em_pc_type bjacobi \ > -em_sub_pc_type ilu \ > -em_sub_pc_factor_levels 3 \ > -em_sub_pc_factor_fill 6 \ > < ./Parameters.inp \ > > But at the end the message appears: > WARNING! There are options you set that were not used! > WARNING! could be spelling mistake, etc! > There are 3 unused database options. They are: > Option left: name:-A_dm_mat_type value: aijcusparse > Option left: name:-dm_vec_type value: cuda > Option left: name:-P_dm_mat_type value: aijcusparse > > Using nvprof does not include kernels, only API use. > > Ramoni Z. S. Azevedo > > Em qua., 20 de set. de 2023 ?s 12:31, Junchao Zhang < > junchao.zhang at gmail.com> escreveu: > >> Try to also add *-dm_mat_type aijcusparse -dm_vec_type cuda* >> >> --Junchao Zhang >> >> >> On Wed, Sep 20, 2023 at 10:21?AM Ramoni Z. Sedano Azevedo < >> ramoni.zsedano at gmail.com> wrote: >> >>> >>> Hey! >>> >>> I am using PETSc in a Fortran code and we use MPI parallelization. We >>> would like to use GPU parallelization, but we are encountering an error. >>> >>> PETSc is configured as follows: >>> #!/bin/bash >>> ./configure \ >>> --prefix=${PWD}/installdir \ >>> --with-fortran \ >>> --with-fortran-kernels=true \ >>> --with-cuda \ >>> --download-fblaslapack \ >>> --with-scalar-type=complex \ >>> --with-precision=double \ >>> --with-debugging=yes \ >>> --with-x=0 \ >>> --with-gnu-compilers=1 \ >>> --with-cc=mpicc \ >>> --with-cxx=mpicxx \ >>> --with-fc=mpif90 \ >>> --with-make-exec=make >>> >>> Within my code, matrices and vectors are allocated with the following >>> commands: >>> PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, >>> DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, >>> PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, >>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) >>> >>> PetscCallA( DMSetUp(da,ierr) ) >>> >>> PetscCallA( DMCreateGlobalVector(da,b,ierr) ) >>> PetscCallA( VecDuplicate(b,xsol,ierr) ) >>> PetscCallA( VecDuplicate(b,src,ierr) ) >>> PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) >>> >>> PetscCallA( DMCreateLocalVector(da,localx,ierr) ) >>> PetscCallA( VecDuplicate(localx,localb,ierr) ) >>> PetscCallA( VecDuplicate(localx,localsrc,ierr) ) >>> PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) >>> >>> PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) >>> >>> ngrow=3*(l+1)*(m+1)*nzn >>> >>> PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) >>> PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) >>> PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) >>> PetscCallA( MatSetFromOptions(A,ierr) ) >>> PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) >>> PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >>> ierr) ) >>> >>> PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, >>> PETSC_NULL_INTEGER, ierr) ) >>> >>> PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >>> i15, PETSC_NULL_INTEGER, ierr) ) >>> >>> PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) >>> PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) >>> PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) >>> PetscCallA( MatSetFromOptions(P, ierr) ) >>> PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) ) >>> PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >>> ierr) ) >>> >>> PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, >>> PETSC_NULL_INTEGER, ierr) ) >>> PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >>> i15, PETSC_NULL_INTEGER, ierr) ) >>> >>> PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, >>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >>> PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) >>> ) >>> PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) >>> PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) >>> >>> PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) >>> PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, ierr) >>> ) >>> PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) >>> PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) >>> >>> When calling the solver function >>> PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) >>> the following error occurs: >>> >>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Invalid argument[0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc![0]PETSC ERROR: Option left: name:-vec_type value: cuda[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.[0]PETSC ERROR: Petsc Release Version 3.18.4, unknown >>> >>> The code is executed with the following flags: >>> ./${executable} \ >>> -A_mat_type aijcusparse \ >>> -P_mat_type aijcusparse \ >>> -vec_type cuda \ >>> -use_gpu_aware_mpi 0 \ >>> -em_ksp_monitor_true_residual \ >>> -em_ksp_type bcgs \ >>> -em_pc_type bjacobi \ >>> -em_sub_pc_type ilu \ >>> -em_sub_pc_factor_levels 3 \ >>> -em_sub_pc_factor_fill 6 \ >>> < ./Parameters.inp \ >>> >>> I've already tested using mpiaijcusparse for matrix and mpicuda for >>> vector and the error continues. >>> >>> Would anyone have an idea what I might be doing wrong? >>> >>> Sincerely, >>> Ramoni Z. S. Azevedo >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From junchao.zhang at gmail.com Wed Sep 20 12:47:39 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Wed, 20 Sep 2023 12:47:39 -0500 Subject: [petsc-users] Problem with matrix and vector using GPU In-Reply-To: References: Message-ID: Since you create the matrices alone, I think you should use -A_mat_type aijcusparse \ -P_mat_type aijcusparse \ instead of -A_dm_mat_type aijcusparse \ -P_dm_mat_type aijcusparse \ Perhaps you can remove "-dm_vec_type cuda" as dm mat type already determines dm vector type --Junchao Zhang On Wed, Sep 20, 2023 at 12:12?PM Ramoni Z. Sedano Azevedo < ramoni.zsedano at gmail.com> wrote: > Thanks for the tip. Using dm_mat_type and dm_vec_type the code runs. > ./${executable} \ > -A_dm_mat_type aijcusparse \ > -P_dm_mat_type aijcusparse \ > -dm_vec_type cuda \ > -use_gpu_aware_mpi 0 \ > -em_ksp_monitor_true_residual \ > -em_ksp_type bcgs \ > -em_pc_type bjacobi \ > -em_sub_pc_type ilu \ > -em_sub_pc_factor_levels 3 \ > -em_sub_pc_factor_fill 6 \ > < ./Parameters.inp \ > > But at the end the message appears: > WARNING! There are options you set that were not used! > WARNING! could be spelling mistake, etc! > There are 3 unused database options. They are: > Option left: name:-A_dm_mat_type value: aijcusparse > Option left: name:-dm_vec_type value: cuda > Option left: name:-P_dm_mat_type value: aijcusparse > > Using nvprof does not include kernels, only API use. > > Ramoni Z. S. Azevedo > > Em qua., 20 de set. de 2023 ?s 12:31, Junchao Zhang < > junchao.zhang at gmail.com> escreveu: > >> Try to also add *-dm_mat_type aijcusparse -dm_vec_type cuda* >> >> --Junchao Zhang >> >> >> On Wed, Sep 20, 2023 at 10:21?AM Ramoni Z. Sedano Azevedo < >> ramoni.zsedano at gmail.com> wrote: >> >>> >>> Hey! >>> >>> I am using PETSc in a Fortran code and we use MPI parallelization. We >>> would like to use GPU parallelization, but we are encountering an error. >>> >>> PETSc is configured as follows: >>> #!/bin/bash >>> ./configure \ >>> --prefix=${PWD}/installdir \ >>> --with-fortran \ >>> --with-fortran-kernels=true \ >>> --with-cuda \ >>> --download-fblaslapack \ >>> --with-scalar-type=complex \ >>> --with-precision=double \ >>> --with-debugging=yes \ >>> --with-x=0 \ >>> --with-gnu-compilers=1 \ >>> --with-cc=mpicc \ >>> --with-cxx=mpicxx \ >>> --with-fc=mpif90 \ >>> --with-make-exec=make >>> >>> Within my code, matrices and vectors are allocated with the following >>> commands: >>> PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, >>> DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, >>> PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, >>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) >>> >>> PetscCallA( DMSetUp(da,ierr) ) >>> >>> PetscCallA( DMCreateGlobalVector(da,b,ierr) ) >>> PetscCallA( VecDuplicate(b,xsol,ierr) ) >>> PetscCallA( VecDuplicate(b,src,ierr) ) >>> PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) >>> >>> PetscCallA( DMCreateLocalVector(da,localx,ierr) ) >>> PetscCallA( VecDuplicate(localx,localb,ierr) ) >>> PetscCallA( VecDuplicate(localx,localsrc,ierr) ) >>> PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) >>> >>> PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) >>> >>> ngrow=3*(l+1)*(m+1)*nzn >>> >>> PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) >>> PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) >>> PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) >>> PetscCallA( MatSetFromOptions(A,ierr) ) >>> PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) >>> PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >>> ierr) ) >>> >>> PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, >>> PETSC_NULL_INTEGER, ierr) ) >>> >>> PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >>> i15, PETSC_NULL_INTEGER, ierr) ) >>> >>> PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) >>> PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) >>> PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) >>> PetscCallA( MatSetFromOptions(P, ierr) ) >>> PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) ) >>> PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >>> ierr) ) >>> >>> PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, >>> PETSC_NULL_INTEGER, ierr) ) >>> PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >>> i15, PETSC_NULL_INTEGER, ierr) ) >>> >>> PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, >>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >>> PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) >>> ) >>> PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) >>> PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) >>> >>> PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) >>> PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, ierr) >>> ) >>> PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) >>> PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) >>> >>> When calling the solver function >>> PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) >>> the following error occurs: >>> >>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Invalid argument[0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc![0]PETSC ERROR: Option left: name:-vec_type value: cuda[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.[0]PETSC ERROR: Petsc Release Version 3.18.4, unknown >>> >>> The code is executed with the following flags: >>> ./${executable} \ >>> -A_mat_type aijcusparse \ >>> -P_mat_type aijcusparse \ >>> -vec_type cuda \ >>> -use_gpu_aware_mpi 0 \ >>> -em_ksp_monitor_true_residual \ >>> -em_ksp_type bcgs \ >>> -em_pc_type bjacobi \ >>> -em_sub_pc_type ilu \ >>> -em_sub_pc_factor_levels 3 \ >>> -em_sub_pc_factor_fill 6 \ >>> < ./Parameters.inp \ >>> >>> I've already tested using mpiaijcusparse for matrix and mpicuda for >>> vector and the error continues. >>> >>> Would anyone have an idea what I might be doing wrong? >>> >>> Sincerely, >>> Ramoni Z. S. Azevedo >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bui at calcreek.com Wed Sep 20 12:48:46 2023 From: bui at calcreek.com (Thuc Bui) Date: Wed, 20 Sep 2023 10:48:46 -0700 Subject: [petsc-users] Problem with BLASdot in 3.19.4 In-Reply-To: <003701d9eb8b$1469a670$3d3cf350$@calcreek.com> References: <004801d9ea7f$3807ed10$a817c730$@calcreek.com> <555871F7-F625-42D4-A56C-BF566319589C@petsc.dev> <006201d9ea87$43cd68c0$cb683a40$@calcreek.com> <009501d9eabf$1fac77f0$5f0567d0$@calcreek.com> <9C51D3C4-647E-4960-B313-190FF9FF3FDC@petsc.dev> <013201d9eb19$d55d94d0$8018be70$@calcreek.com> <9aac59cc-e175-0a7a-6193-53c0f5443cd8@mcs.anl.gov> <003601d9eb89$22950a20$67bf1e60$@calcreek.com> <003701d9eb8b$1469a670$3d3cf350$@calcreek.com> Message-ID: <00f701d9ebea$b4f85af0$1ee910d0$@calcreek.com> Just FYI, with the configuration below, PETSc 3.19.5 works fine with Visual Studio 2022, statically linked to MS MPI and Intel MKL 2023. Thuc -----Original Message----- From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui Sent: Tuesday, September 19, 2023 11:24 PM To: 'petsc-users' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Correction! The MKL library mkl_rt.lib was mistakenly included in the configure below. It is not needed to build PETSc, but the app requires to link to it and petsc.lib. Thuc -----Original Message----- From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui Sent: Tuesday, September 19, 2023 11:10 PM To: 'petsc-users' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Hi Satish and Barry, Thank you very for getting back to me with the suggestion of the OMP_NUM_THREADS environmental variable and how to set the option no_signal_handler per Barry's suggestion. Yes, I am using threaded Intel MKL. So, I first set the environmental variable OMP_NUM_THREADS=1, and run the Visual Studio debugger. It still crashes at the same place with the same errors. I then set the PETSC_OPTIONS=-no_signal_handler, the debugger refuses to pass through the access exception, and I have to stop the debugger; consequently no PETSc errors were reported. I know there is an option somewhere in the VS debugger to bypass this access exception, but I didn't pursue further. Finally, I removed Intel MKL 2000 (to uninstall it requires a 3rd party software!), and use Intel oneAPI MKL (2023) with PETSc 3.18.6 and Visual Studio 2022. Now my code with 1, 2 or 4 cores work! I will try 3.19.4 next and will keep you posted. Thank you again for your help, Thuc Bui ////////////////////////////////////////////////////////////////////////////////////////////////////////////////// ./configure --with-cc='win32fe cl' --with-fc=0 --with-cxx='win32fe cl' --with-openmp \ --with-mpi-include='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include:/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/include/x64' \ --with-mpi-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpi.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/Lib/x64/msmpifec.lib] \ --with-blas-lapack-lib=[/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_lp64.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_core.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_intel_thread.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/mkl_rt.lib,/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/IntelMKL/latest/lib64/libiomp5md.lib] \ --with-mpiexec='/cygdrive/d/Users/bbwannabe/Documents/Petsc/externalpackages/MSMPI/latest/bin/x64/mpiexec' \ --with-shared-libraries=0 /////////////////////////////////////////////////////////////////////////////////////////////////////////////////// -----Original Message----- From: Satish Balay [mailto:balay at mcs.anl.gov] Sent: Tuesday, September 19, 2023 10:01 AM To: Thuc Bui Cc: 'Barry Smith'; 'PETSc users list' Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 Its a run time option to petsc (application) binary. So you can either specify it via command line - at run time - or add it to env variable "PETSC_OPTIONS" - or add it to $HOME/.petscrc file Satish On Tue, 19 Sep 2023, Thuc Bui wrote: > Hi Barry, > > > > Thanks for getting back to me. The diagnostics were generated when tracing under the VS debugger. To use the option ?no_signal_handler, I believe I will need to reconfigure PETSc with this additional option. I will try it now. > > > > Thuc > > > > > > From: Barry Smith [mailto:bsmith at petsc.dev] > Sent: Tuesday, September 19, 2023 8:24 AM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Can you run in the Microsoft Visual Studio debugger? Use the additional PETSc option -no_signal_handler > > > > > > It won't show exactly where the SEGV happens but might focus in a bit on it. For example it may be ddot() or ddot_(). > > > > Barry > > > > > > > > > > On Sep 19, 2023, at 2:04 AM, Thuc Bui wrote: > > > > Hi Barry, > > > > Visual Studio 2022 is the problem! The code linked to Petsc 3.18.6 built with VS 2022 also crashes at the same place. The same errors are shown below. I don?t remember for sure, but I don?t think I was able to configure Petsc 3.19.4 with VS 2019. However, I will still try that next. > > > > Thanks for your help, > > Thuc > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\impls\seq\bvec2.c:216 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:111 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\impls\gmres\gmres.c:228 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:899 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\petsc-3.18.6\src\ksp\ksp\interface\itfunc.c:1071 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > > > > > From: petsc-users [ mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Thuc Bui > Sent: Monday, September 18, 2023 4:24 PM > To: 'Barry Smith' > Cc: 'PETSc users list' > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > Thanks a lot Barry, for getting back to me. Will do what you have suggested, and get back with the results. > > > > Best regards, > > Thuc > > > > From: Barry Smith [ mailto:bsmith at petsc.dev] > Sent: Monday, September 18, 2023 3:43 PM > To: Thuc Bui > Cc: PETSc users list > Subject: Re: [petsc-users] Problem with BLASdot in 3.19.4 > > > > > > Ok, two things are being changed at the same time: the version of PETSc and the version of Visual Studio. > > > > Could you please try with the new Visual Studio version but the same older PETSc version? If that works could you try with the old Visual Studio version but the new PETSc version? > > > > Barry > > > > > > > > On Sep 18, 2023, at 6:26 PM, Thuc Bui < bui at calcreek.com> wrote: > > > > Dear Petsc users and experts, > > > > If someone can direct me how to track this bug, I would really appreciate it. > > > > The Petsc DLL library version 3.19.4 was built on Windows 10 with Visual Studio 2022, and with Microsoft MPI 10.1.2 and Intel MKL 2020.3.279. The same code works fine with Petsc 3.18.6 using the same versions of MS MPI and Intel MKL, and built with Visual Studio 2019. > > > > When my code calls PetscCall(KSPSolve(...)), it gets to PetscCall(KSPGMRESCycle(...)), PetscCall(VecNormalize(VEC_VV(0), &res)), PetscCall(VecNorm(x, NORM_2, &norm)) and then crashes in VecNorm_Seq() at: > > > > PetscCallBLAS("BLASdot", ztmp[type == NORM_1_AND_2] = PetscSqrtReal(PetscRealPart(BLASdot_(&bn, xx, &one, xx, &one)))); > > > > I tried to step into BLASdot_, but was unable to. I assume BLASdot_ belong to Intel MKL, and its library does not contain debug information. After the code exits, the errors are shown below the hash line. > > > > Should I install the latest Intel MKL to work with Petsc 3.19.4? > > > > Many thanks in advance for your help, > > Thuc Bui > > Senior R&D Engineer > > Calabazas Creek Research, Inc > > (650) 948-5361 > > > > > > ############################################### > > > > [0]PETSC ERROR: ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > > [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------ > > [0]PETSC ERROR: The line numbers in the error traceback are not always exact. > > [0]PETSC ERROR: #1 BLASdot() > > [0]PETSC ERROR: #2 VecNorm_Seq() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\impls\seq\bvec2.c:213 > > [0]PETSC ERROR: #3 VecNorm() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:237 > > [0]PETSC ERROR: #4 VecNormalize() at D:\Users\bbwannabe\Documents\Petsc\latest\src\vec\vec\interface\rvector.c:318 > > [0]PETSC ERROR: #5 KSPGMRESCycle() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:110 > > [0]PETSC ERROR: #6 KSPSolve_GMRES() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\impls\gmres\gmres.c:227 > > [0]PETSC ERROR: #7 KSPSolve_Private() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:898 > > [0]PETSC ERROR: #8 KSPSolve() at D:\Users\bbwannabe\Documents\Petsc\latest\src\ksp\ksp\interface\itfunc.c:1070 > > > > job aborted: > > [ranks] message > > > > [0] application aborted > > aborting MPI_COMM_WORLD (comm=0x44000000), error 59, comm rank 0 > > > > From srvenkat at utexas.edu Wed Sep 20 13:34:58 2023 From: srvenkat at utexas.edu (Sreeram R Venkat) Date: Wed, 20 Sep 2023 13:34:58 -0500 Subject: [petsc-users] 2D Partitioning matrix-shell and KSP In-Reply-To: References: Message-ID: Thank you for your help. I will try this solution. Sreeram On Wed, Sep 20, 2023 at 9:24?AM Barry Smith wrote: > > Use VecCreate(), VecSetSizes(), VecSetType() and MatCreate(), > MatSetSizes(), and MatSetType() instead of the convience functions > VecCreateMPICUDA() and MatCreateShell(). > > > On Sep 19, 2023, at 8:44 PM, Sreeram R Venkat wrote: > > Thank you for your reply. > > Let's call this matrix *M*: > (A B C D) > (E F G H) > (I J K L) > > Now, instead of doing KSP with just *M*, what if I want *M^TM*? In this > case, the matvec implementation would be as follows: > > > - same partitioning of blocks A, B, ..., L among the 12 MPI ranks > - matvec looks like: > > (a) (w) > (b) = (*M^TM* ) (x) > (c) (y) > (d) (z) > > - w, x, y, z stored on ranks A, B, C, D (as before) > - a, b, c, d now also stored on ranks A, B, C, D > > Based on your message, I believe using a PetscLayout for both the > (a,b,c,d) and (w,x,y,z) vector of (number of columns of A, number of > columns of B, number of columns of C, number of columns of > D,0,0,0,0,0,0,0,0,0) should work. > > > I see there are functions "VecSetLayout" and "MatSetLayouts" to set the > PetscLayouts of the matrix and vectors. When I create the vectors (I need > VecCreateMPICUDA) or matrix shell (with MatCreateShell), I need to pass the > local and global sizes. I'm not sure what to do there. > > > Thanks, > Sreeram > > On Tue, Sep 19, 2023, 7:13 PM Barry Smith wrote: > >> >> The PetscLayout local sizes for PETSc (a,b,c) vector (0,0,0,number of >> rows of D, 0,0,0, number of rows of H, 0,0,0,number of rows of L) >> >> >> The PetscLayout local sizes for PETSc (w,x,y,z) vector (number of >> columns of A, number of columns of B, number of columns of C, number of >> columns of D,0,0,0,0,0,0,0,0,0) >> >> The left and right layouts of the shell matrix need to match the two >> above. >> >> There is a huge problem. KSP is written assuming that the left vector >> layout is the same as the right vector layout. So it can do dot products >> MPI rank by MPI rank without needing to send individual vector values >> around. >> >> I don't it makes sense to use PETSc with such vector decompositions as >> you would like. >> >> Barry >> >> >> >> On Sep 19, 2023, at 7:44 PM, Sreeram R Venkat >> wrote: >> >> With the example you have given, here is what I would like to do: >> >> - 12 MPI ranks >> - Each rank has one block (rank 0 has A, rank 1 has B, ..., rank 11 >> has L) - to make the rest of this easier I'll refer to the rank containing >> block A as "rank A", and so on >> - rank A, rank B, rank C, and rank D have w, x, y, z respectively - >> the first step of the custom matvec implementation broadcasts w to rank E >> and rank I (similarly x is broadcast to rank F and rank J ...) >> - at the end of the matvec computation, ranks D, H, and L have a, b, >> and c respectively >> >> Thanks, >> Sreeram >> >> >> On Tue, Sep 19, 2023 at 6:23?PM Barry Smith wrote: >> >>> >>> ( a ) ( A B C D ) ( w ) >>> ( b ) = ( E F G H ) ( x ) >>> ( c ) ( I J K L ) ( y ) >>> ( z ) >>> >>> I have no idea what "The input vector is partitioned across each row, >>> and the output vector is partitioned across each column" means. >>> >>> Anyways the shell matrix needs to live on MPI_COMM_WORLD, as do both the >>> (a,b,c) and (w,x,y,z) vector. >>> >>> Now how many MPI ranks do you want to do the compution on? 12? >>> Do you want one matrix A .. Z on each rank? >>> >>> Do you want the (a,b,c) vector spread over all ranks? What about the (w,x,y,z) >>> vector? >>> >>> Barry >>> >>> >>> >>> On Sep 19, 2023, at 4:42 PM, Sreeram R Venkat >>> wrote: >>> >>> I have a custom implementation of a matrix-vector product that >>> inherently relies on a 2D processor partitioning of the matrix. That is, if >>> the matrix looks like: >>> >>> A B C D >>> E F G H >>> I J K L >>> >>> in block form, we use 12 processors, each having one block. The input >>> vector is partitioned across each row, and the output vector is partitioned >>> across each column. >>> >>> Each processor has 3 communicators: the WORLD_COMM, a ROW_COMM, and a >>> COL_COMM. The ROW/COL communicators are used to do reductions over >>> rows/columns of processors. >>> >>> With this setup, I am a bit confused about how to set up the matrix >>> shell. The "MatCreateShell" function only accepts one communicator. If I >>> give the WORLD_COMM, the local/global sizes won't match since PETSc will >>> try to multiply local_size * total_processors instead of local_size * >>> processors_per_row (or col). I have gotten around this temporarily by >>> giving ROW_COMM here instead. What I think happens is a different MatShell >>> is created on each row, but when computing the matvec, they all work >>> together. >>> >>> However, if I try to use KSP (CG) with this setup (giving ROW_COMM as >>> the communicator), the process hangs. I believe this is due to the >>> partitioning of the input/output vectors. The matvec itself is fine, but >>> the inner products and other steps of CG fail. In fact, if I restrict to >>> the case where I only have one row of processors, I am able to successfully >>> use KSP. >>> >>> Is there a way to use KSP with this 2D partitioning setup when there are >>> multiple rows of processors? I'd also prefer to work with one global >>> MatShell object instead of this one object per row thing that I'm doing >>> right now. >>> >>> Thanks for your help, >>> Sreeram >>> >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wence at gmx.li Wed Sep 20 15:14:10 2023 From: wence at gmx.li (Lawrence Mitchell) Date: Wed, 20 Sep 2023 21:14:10 +0100 Subject: [petsc-users] Questions about PCPATCH In-Reply-To: References: Message-ID: On Wed, 20 Sept 2023 at 12:17, Ce Qin wrote: > > Dear all, > > I am currently implementing a multigrid solver for Maxwell's equations in 3D. > The AFW smoother has excellent convergence properties for Maxwell's equations. I > noticed that PCPATCH provides such types of smoothers. However, I am using the > deal.II library to build the patches. PCPATCH seems only to support the PETSc > DMPlex data structure. Is there a way to use PCPATCH with user defined patches? When we implemented, we didn't have a better idea about the callback structure. If you can shoe-horn into the API PCPatch provides, then it can work, but I guess deal.II doesn't use DMPlex for its mesh management, so I don't think PCPatch is going to give you that much. > Besides, I found that we can also use PCASM with user defined subdomains. > Is there any performance difference between PCPATCH and PCASM? For PCASM you have to assemble the global matrix and then extract the subdomains, which might be expensive (in theory, pcpatch has a low memory mode where you only assemble and factor one patch at a time, but in most cases where you're using it, it's slower). There are some other small optimisations in pcpatch that could be ported to PCASM for small patches (for example, there's a mode where the patch solver is just the application of an already factored matrix, so you don't go through the KSP/PC/MatSolve callstack), but we didn't do it. But it likely depends a bit on your problem too (with pcpatch you effectively assemble the operator twice if you're using sparse matrices, rather than matrix-free, so that can be a bit more expensive). In summary: give it a go with PCASM. Lawrence From bsmith at petsc.dev Wed Sep 20 22:30:14 2023 From: bsmith at petsc.dev (Barry Smith) Date: Wed, 20 Sep 2023 23:30:14 -0400 Subject: [petsc-users] [petsc-maint] PETSc with Xcode 15 In-Reply-To: References: Message-ID: Possible the Xcode command line tools need updating. Take a look at https://stackoverflow.com/questions/42538171/how-to-update-xcode-command-line-tools > On Sep 20, 2023, at 10:43 PM, Ju Liu wrote: > > Hi PETSc team: > > I recently got my Xcode command line tools upgraded to version 15. When installing PETSc, the configure command returns an error. My configure command is > > ./configure --with-cc=gcc --with-fc=0 --with-cxx=0 --download-f2cblaslapack --download-mpich > > and the message is "Cannot locate all the standard C header files needed by PETSc". > > The configure.log file is attached. > > How shall I fix this? > > Thanks, > > Ju > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ramoni.zsedano at gmail.com Thu Sep 21 08:22:02 2023 From: ramoni.zsedano at gmail.com (Ramoni Z. Sedano Azevedo) Date: Thu, 21 Sep 2023 10:22:02 -0300 Subject: [petsc-users] Problem with matrix and vector using GPU In-Reply-To: References: Message-ID: Using the following flags when calling the code -A_mat_type aijcusparse\ -P_mat_type aijcusparse \ -dm_vec_type cuda\ -use_gpu_aware_mpi 0 \ and adding the function PetscCallA(DMSetFromOptions(da, ierr)) between functions PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1,m+1,nzn, PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3,i1, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) PetscCallA( DMSetUp(da,ierr) ) It finally worked. Thanks! Ramoni Em qua., 20 de set. de 2023 ?s 14:47, Junchao Zhang escreveu: > Since you create the matrices alone, I think you should use > -A_mat_type aijcusparse \ > -P_mat_type aijcusparse \ > instead of > -A_dm_mat_type aijcusparse \ > -P_dm_mat_type aijcusparse \ > > Perhaps you can remove "-dm_vec_type cuda" as dm mat type already > determines dm vector type > > --Junchao Zhang > > > On Wed, Sep 20, 2023 at 12:12?PM Ramoni Z. Sedano Azevedo < > ramoni.zsedano at gmail.com> wrote: > >> Thanks for the tip. Using dm_mat_type and dm_vec_type the code runs. >> ./${executable} \ >> -A_dm_mat_type aijcusparse \ >> -P_dm_mat_type aijcusparse \ >> -dm_vec_type cuda \ >> -use_gpu_aware_mpi 0 \ >> -em_ksp_monitor_true_residual \ >> -em_ksp_type bcgs \ >> -em_pc_type bjacobi \ >> -em_sub_pc_type ilu \ >> -em_sub_pc_factor_levels 3 \ >> -em_sub_pc_factor_fill 6 \ >> < ./Parameters.inp \ >> >> But at the end the message appears: >> WARNING! There are options you set that were not used! >> WARNING! could be spelling mistake, etc! >> There are 3 unused database options. They are: >> Option left: name:-A_dm_mat_type value: aijcusparse >> Option left: name:-dm_vec_type value: cuda >> Option left: name:-P_dm_mat_type value: aijcusparse >> >> Using nvprof does not include kernels, only API use. >> >> Ramoni Z. S. Azevedo >> >> Em qua., 20 de set. de 2023 ?s 12:31, Junchao Zhang < >> junchao.zhang at gmail.com> escreveu: >> >>> Try to also add *-dm_mat_type aijcusparse -dm_vec_type cuda* >>> >>> --Junchao Zhang >>> >>> >>> On Wed, Sep 20, 2023 at 10:21?AM Ramoni Z. Sedano Azevedo < >>> ramoni.zsedano at gmail.com> wrote: >>> >>>> >>>> Hey! >>>> >>>> I am using PETSc in a Fortran code and we use MPI parallelization. We >>>> would like to use GPU parallelization, but we are encountering an error. >>>> >>>> PETSc is configured as follows: >>>> #!/bin/bash >>>> ./configure \ >>>> --prefix=${PWD}/installdir \ >>>> --with-fortran \ >>>> --with-fortran-kernels=true \ >>>> --with-cuda \ >>>> --download-fblaslapack \ >>>> --with-scalar-type=complex \ >>>> --with-precision=double \ >>>> --with-debugging=yes \ >>>> --with-x=0 \ >>>> --with-gnu-compilers=1 \ >>>> --with-cc=mpicc \ >>>> --with-cxx=mpicxx \ >>>> --with-fc=mpif90 \ >>>> --with-make-exec=make >>>> >>>> Within my code, matrices and vectors are allocated with the following >>>> commands: >>>> PetscCallA( DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, >>>> DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DMDA_STENCIL_BOX, l+1, m+1, nzn, >>>> PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, i3, i1, PETSC_NULL_INTEGER, >>>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, da, ierr) ) >>>> >>>> PetscCallA( DMSetUp(da,ierr) ) >>>> >>>> PetscCallA( DMCreateGlobalVector(da,b,ierr) ) >>>> PetscCallA( VecDuplicate(b,xsol,ierr) ) >>>> PetscCallA( VecDuplicate(b,src,ierr) ) >>>> PetscCallA( VecDuplicate(b,rhoxyz,ierr) ) >>>> >>>> PetscCallA( DMCreateLocalVector(da,localx,ierr) ) >>>> PetscCallA( VecDuplicate(localx,localb,ierr) ) >>>> PetscCallA( VecDuplicate(localx,localsrc,ierr) ) >>>> PetscCallA( VecDuplicate(localx,lrhoxyz,ierr) ) >>>> >>>> PetscCallA( VecGetLocalSize(xsol,mloc,ierr) ) >>>> >>>> ngrow=3*(l+1)*(m+1)*nzn >>>> >>>> PetscCallA( MatCreate(PETSC_COMM_WORLD,A,ierr) ) >>>> PetscCallA( MatSetOptionsPrefix(A,'A_',ierr) ) >>>> PetscCallA( MatSetSizes(A,mloc,mloc,ngrow,ngrow,ierr) ) >>>> PetscCallA( MatSetFromOptions(A,ierr) ) >>>> PetscCallA( MatSeqAIJSetPreallocation(A,i15,PETSC_NULL_INTEGER,ierr) ) >>>> PetscCallA( MatSeqBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >>>> ierr) ) >>>> >>>> PetscCallA( MatMPIAIJSetPreallocation(A, i15, PETSC_NULL_INTEGER, i15, >>>> PETSC_NULL_INTEGER, ierr) ) >>>> >>>> PetscCallA( MatMPIBAIJSetPreallocation(A, i3, i15, PETSC_NULL_INTEGER, >>>> i15, PETSC_NULL_INTEGER, ierr) ) >>>> >>>> PetscCallA( MatCreate(PETSC_COMM_WORLD, P, ierr) ) >>>> PetscCallA( MatSetOptionsPrefix(P, 'P_', ierr) ) >>>> PetscCallA( MatSetSizes(P, mloc, mloc, ngrow, ngrow, ierr) ) >>>> PetscCallA( MatSetFromOptions(P, ierr) ) >>>> PetscCallA( MatSeqAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, ierr) >>>> ) >>>> PetscCallA( MatSeqBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >>>> ierr) ) >>>> >>>> PetscCallA( MatMPIAIJSetPreallocation(P, i15, PETSC_NULL_INTEGER, i15, >>>> PETSC_NULL_INTEGER, ierr) ) >>>> PetscCallA( MatMPIBAIJSetPreallocation(P, i3, i15, PETSC_NULL_INTEGER, >>>> i15, PETSC_NULL_INTEGER, ierr) ) >>>> >>>> PetscCallA( DMDAGetInfo(da, PETSC_NULL_INTEGER, mx, my, mz, >>>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >>>> PETSC_NULL_INTEGER, PETSC_NULL_INTEGER, >>>> PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr) >>>> ) >>>> PetscCallA( DMDAGetCorners(da,xs,ys,zs,xm,ym,zm,ierr) ) >>>> PetscCallA( DMDAGetGhostCorners(da,gxs,gys,gzs,gxm,gym,gzm,ierr) ) >>>> >>>> PetscCallA( DMLocalToGlobal(da,localsrc,INSERT_VALUES,src,ierr) ) >>>> PetscCallA( DMGlobalToLocalBegin(da, src, INSERT_VALUES, localsrc, >>>> ierr) ) >>>> PetscCallA( DMGlobalToLocalEnd(da,src,INSERT_VALUES,localsrc,ierr) ) >>>> PetscCallA( DMLocalToGlobal(da,localb,INSERT_VALUES,b,ierr) ) >>>> >>>> When calling the solver function >>>> PetscCallA( KSPSolve(ksp,b,xsol,ierr) ) >>>> the following error occurs: >>>> >>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------[0]PETSC ERROR: Invalid argument[0]PETSC ERROR: Object (seq) is not seqcuda or mpicuda[0]PETSC ERROR: WARNING! There are option(s) set that were not used! Could be the program crashed before they were used or a spelling mistake, etc![0]PETSC ERROR: Option left: name:-vec_type value: cuda[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.[0]PETSC ERROR: Petsc Release Version 3.18.4, unknown >>>> >>>> The code is executed with the following flags: >>>> ./${executable} \ >>>> -A_mat_type aijcusparse \ >>>> -P_mat_type aijcusparse \ >>>> -vec_type cuda \ >>>> -use_gpu_aware_mpi 0 \ >>>> -em_ksp_monitor_true_residual \ >>>> -em_ksp_type bcgs \ >>>> -em_pc_type bjacobi \ >>>> -em_sub_pc_type ilu \ >>>> -em_sub_pc_factor_levels 3 \ >>>> -em_sub_pc_factor_fill 6 \ >>>> < ./Parameters.inp \ >>>> >>>> I've already tested using mpiaijcusparse for matrix and mpicuda for >>>> vector and the error continues. >>>> >>>> Would anyone have an idea what I might be doing wrong? >>>> >>>> Sincerely, >>>> Ramoni Z. S. Azevedo >>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From Di.Miao at synopsys.com Wed Sep 20 15:32:57 2023 From: Di.Miao at synopsys.com (Di Miao) Date: Wed, 20 Sep 2023 20:32:57 +0000 Subject: [petsc-users] PETSc openMP Message-ID: To whom it may concern, I would like to run PETSc in a multi-threaded way (KSP per thread). I checked PETSc's manual and it says: There is an OpenMP thread-safe subset of PETSc that may be configured for using --with-threadsafety [--with-openmp or --download-concurrencykit]. I am confused about the square bracket here. Does this mean I need to --with-threadsafety +( --with-openmp/--download-concurrencykit) or this mean I can add --with-threadsafety or --with-openmp or --download-concurrencykit? Looking for your explanation on these flags! Thank you Di -------------- next part -------------- An HTML attachment was scrubbed... URL: From liujuy at gmail.com Wed Sep 20 21:43:29 2023 From: liujuy at gmail.com (Ju Liu) Date: Thu, 21 Sep 2023 10:43:29 +0800 Subject: [petsc-users] PETSc with Xcode 15 Message-ID: Hi PETSc team: I recently got my Xcode command line tools upgraded to version 15. When installing PETSc, the configure command returns an error. My configure command is ./configure --with-cc=gcc --with-fc=0 --with-cxx=0 --download-f2cblaslapack --download-mpich and the message is "Cannot locate all the standard C header files needed by PETSc". The configure.log file is attached. How shall I fix this? Thanks, Ju -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 920004 bytes Desc: not available URL: From bourdin at mcmaster.ca Thu Sep 21 10:02:33 2023 From: bourdin at mcmaster.ca (Blaise Bourdin) Date: Thu, 21 Sep 2023 15:02:33 +0000 Subject: [petsc-users] PETSc with Xcode 15 In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From bourdin at mcmaster.ca Thu Sep 21 10:05:35 2023 From: bourdin at mcmaster.ca (Blaise Bourdin) Date: Thu, 21 Sep 2023 15:05:35 +0000 Subject: [petsc-users] Face Set not appearing when loading GMSH mesh to DMPlex In-Reply-To: <576f28bb730c467680de36abfbf5b463@solid.lth.se> References: <576f28bb730c467680de36abfbf5b463@solid.lth.se> Message-ID: <6693E735-6BDE-4014-B5A7-2B5C7A7FF560@mcmaster.ca> An HTML attachment was scrubbed... URL: From junchao.zhang at gmail.com Thu Sep 21 10:10:09 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Thu, 21 Sep 2023 10:10:09 -0500 Subject: [petsc-users] PETSc openMP In-Reply-To: References: Message-ID: include/petsc/private/petscimpl.h has #if defined(__cplusplus) #error "Thread safety requires either --download-concurrencykit, std::atomic, or --with-openmp" #else #error "Thread safety requires either --download-concurrencykit, stdatomic.h, or --with-openmp" #endif So it means when you require --with-threadsafety, your system needs to have std atomic; otherwise you need to add --download-concurrencykit or --with-openmp --Junchao Zhang On Thu, Sep 21, 2023 at 9:39?AM Di Miao via petsc-users < petsc-users at mcs.anl.gov> wrote: > To whom it may concern, > > > > I would like to run PETSc in a multi-threaded way (KSP per thread). I > checked PETSc?s manual and it says: > > > > There is an OpenMP thread-safe subset of PETSc that may be configured for > using --with-threadsafety [--with-openmp or --download-concurrencykit]. > > > > I am confused about the square bracket here. Does this mean I need to > --with-threadsafety +( --with-openmp/--download-concurrencykit) or this > mean I can add --with-threadsafety or --with-openmp or > --download-concurrencykit? > > > > Looking for your explanation on these flags! > > > > Thank you > > Di > -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Thu Sep 21 10:27:46 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 21 Sep 2023 10:27:46 -0500 (CDT) Subject: [petsc-users] PETSc with Xcode 15 In-Reply-To: References: Message-ID: <43c7f867-c758-df9b-ea2e-12f09b3a1dfc@mcs.anl.gov> Do you get this failure with petsc main branch as well? Satish On Thu, 21 Sep 2023, Blaise Bourdin wrote: > FWIW, CLT 15.0 also seems to include changes to the linker, with incompatible options etc? I was able to rebuild mpich and petsc but I get many linker warnings and have not fully tested my build > > Before CLT 15.0 update > > SiMini:mef90-dmplex (dmplex)$ ld -v > > @(#)PROGRAM:ld? PROJECT:ld64-857.1 > > BUILD 23:13:29 May? 7 2023 > > configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em > > LTO support using: LLVM version 14.0.3, (clang-1403.0.22.14.1) (static support for 29, runtime is 29) > > TAPI support using: Apple TAPI version 14.0.3 (tapi-1403.0.5.1) > > > vs after: > > bblaptop:mef90-dmplex (dmplex)$ ld -v > > @(#)PROGRAM:ld? PROJECT:dyld-1015.7 > > BUILD 18:48:48 Aug 22 2023 > > configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em > > will use ld-classic for: armv6 armv7 armv7s arm64_32 i386 armv6m armv7k armv7m armv7em > > LTO support using: LLVM version 15.0.0 (static support for 29, runtime is 29) > > TAPI support using: Apple TAPI version 15.0.0 (tapi-1500.0.12.3) > > Library search paths: > > Framework search paths: > > > > bblaptop:tutorials (main)$ pwd > > /opt/HPC/petsc-main/src/vec/vec/tutorials > > bblaptop:tutorials (main)$ make ex1 > > mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-search_paths_first -Wl,-no_compact_unwind -Wimplicit-function-declaration -Wunused -Wuninitialized -fPIC -g3 -O0? > -I/opt/HPC/petsc-main/include -I/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/include -I/opt/X11/include? ? ? ex1.c? -Wl,-rpath,/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -L/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib > -Wl,-rpath,/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -L/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -Wl,-rpath,/opt/homebrew/Cellar/mpich/4.1.2/lib -L/opt/homebrew/Cellar/mpich/4.1.2/lib > -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc > -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current -lpetsc -lHYPRE -ldmumps -lmumps_common -lpord -lpthread -lscalapack > -lsuperlu -lml -llapack -lblas -lparmetis -lmetis -lexoIIv2for32 -lexodus -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lchaco -ltriangle -lz -lctetgen -lX11 -lmpifort -lmpi -lpmpi -lgfortran -lemutls_w -lquadmath -lc++ -o ex1 > > ld: warning: -multiply_defined is obsolete > > ld: warning: -multiply_defined is obsolete > > ld: warning: duplicate -rpath '/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib' ignored > > ld: warning: -bind_at_load is deprecated on macOS > > ld: warning: ignoring duplicate libraries: '-lmpi', '-lpmpi' > > > > > That?s quite a curveball a week ahead of a major software update. > > Blaise > > On Sep 20, 2023, at 10:43 PM, Ju Liu wrote: > > Caution: External email. > > Hi PETSc team: > I recently got my Xcode command line tools upgraded to version 15. When installing PETSc, the configure command returns an error.?My configure command is? > > ./configure --with-cc=gcc --with-fc=0 --with-cxx=0 --download-f2cblaslapack --download-mpich > > and the message is "Cannot locate all the standard C header files needed by PETSc". > > The configure.log file is attached. > > How shall I fix this?? > > Thanks, > > Ju > > > > ?? > Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1) > Professor, Department of Mathematics &?Statistics > Hamilton Hall room 409A, McMaster?University > 1280 Main Street West, Hamilton,?Ontario L8S 4K1, Canada? > https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243 > > > From bsmith at petsc.dev Thu Sep 21 11:26:39 2023 From: bsmith at petsc.dev (Barry Smith) Date: Thu, 21 Sep 2023 12:26:39 -0400 Subject: [petsc-users] PETSc openMP In-Reply-To: References: Message-ID: If you plan to use OpenMP for threading then use --with-threadsafety --with-openmp > On Sep 21, 2023, at 11:10 AM, Junchao Zhang wrote: > > include/petsc/private/petscimpl.h has > > #if defined(__cplusplus) > #error "Thread safety requires either --download-concurrencykit, std::atomic, or --with-openmp" > #else > #error "Thread safety requires either --download-concurrencykit, stdatomic.h, or --with-openmp" > #endif > > So it means when you require --with-threadsafety, your system needs to have std atomic; otherwise you need to add --download-concurrencykit or --with-openmp > > --Junchao Zhang > > > On Thu, Sep 21, 2023 at 9:39?AM Di Miao via petsc-users > wrote: >> To whom it may concern, >> >> >> >> I would like to run PETSc in a multi-threaded way (KSP per thread). I checked PETSc?s manual and it says: >> >> >> >> There is an OpenMP thread-safe subset of PETSc that may be configured for using --with-threadsafety [--with-openmp or --download-concurrencykit]. >> >> >> >> I am confused about the square bracket here. Does this mean I need to --with-threadsafety +( --with-openmp/--download-concurrencykit) or this mean I can add --with-threadsafety or --with-openmp or --download-concurrencykit? >> >> >> >> Looking for your explanation on these flags! >> >> >> >> Thank you >> >> Di >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Thu Sep 21 11:35:01 2023 From: bsmith at petsc.dev (Barry Smith) Date: Thu, 21 Sep 2023 12:35:01 -0400 Subject: [petsc-users] [petsc-maint] PETSc with Xcode 15 In-Reply-To: References: Message-ID: <565B6989-DCA6-4FE6-90A0-1B09F27D2E64@petsc.dev> Where are the flags such as -multiply_defined being added? PETSc configure is suppose to check each flag before it adds it to the list of flags it uses. So normally I would expect these flags would just not exist in the link lines etc. > On Sep 21, 2023, at 11:02 AM, Blaise Bourdin wrote: > > FWIW, CLT 15.0 also seems to include changes to the linker, with incompatible options etc? I was able to rebuild mpich and petsc but I get many linker warnings and have not fully tested my build > > Before CLT 15.0 update > SiMini:mef90-dmplex (dmplex)$ ld -v > @(#)PROGRAM:ld PROJECT:ld64-857.1 > BUILD 23:13:29 May 7 2023 > configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em > LTO support using: LLVM version 14.0.3, (clang-1403.0.22.14.1) (static support for 29, runtime is 29) > TAPI support using: Apple TAPI version 14.0.3 (tapi-1403.0.5.1) > > vs after: > bblaptop:mef90-dmplex (dmplex)$ ld -v > @(#)PROGRAM:ld PROJECT:dyld-1015.7 > BUILD 18:48:48 Aug 22 2023 > configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em > will use ld-classic for: armv6 armv7 armv7s arm64_32 i386 armv6m armv7k armv7m armv7em > LTO support using: LLVM version 15.0.0 (static support for 29, runtime is 29) > TAPI support using: Apple TAPI version 15.0.0 (tapi-1500.0.12.3) > Library search paths: > Framework search paths: > > > bblaptop:tutorials (main)$ pwd > /opt/HPC/petsc-main/src/vec/vec/tutorials > bblaptop:tutorials (main)$ make ex1 > mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-search_paths_first -Wl,-no_compact_unwind -Wimplicit-function-declaration -Wunused -Wuninitialized -fPIC -g3 -O0 -I/opt/HPC/petsc-main/include -I/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/include -I/opt/X11/include ex1.c -Wl,-rpath,/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -L/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -Wl,-rpath,/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -L/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -Wl,-rpath,/opt/homebrew/Cellar/mpich/4.1.2/lib -L/opt/homebrew/Cellar/mpich/4.1.2/lib -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current -lpetsc -lHYPRE -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu -lml -llapack -lblas -lparmetis -lmetis -lexoIIv2for32 -lexodus -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lchaco -ltriangle -lz -lctetgen -lX11 -lmpifort -lmpi -lpmpi -lgfortran -lemutls_w -lquadmath -lc++ -o ex1 > ld: warning: -multiply_defined is obsolete > ld: warning: -multiply_defined is obsolete > ld: warning: duplicate -rpath '/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib' ignored > ld: warning: -bind_at_load is deprecated on macOS > ld: warning: ignoring duplicate libraries: '-lmpi', '-lpmpi' > > > > That?s quite a curveball a week ahead of a major software update. > > Blaise > >> On Sep 20, 2023, at 10:43 PM, Ju Liu wrote: >> >> Caution: External email. >> >> Hi PETSc team: >> >> I recently got my Xcode command line tools upgraded to version 15. When installing PETSc, the configure command returns an error. My configure command is >> >> ./configure --with-cc=gcc --with-fc=0 --with-cxx=0 --download-f2cblaslapack --download-mpich >> >> and the message is "Cannot locate all the standard C header files needed by PETSc". >> >> The configure.log file is attached. >> >> How shall I fix this? >> >> Thanks, >> >> Ju >> > > ? > Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1) > Professor, Department of Mathematics & Statistics > Hamilton Hall room 409A, McMaster University > 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada > https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pierre.jolivet at lip6.fr Thu Sep 21 11:49:53 2023 From: pierre.jolivet at lip6.fr (Pierre Jolivet) Date: Thu, 21 Sep 2023 18:49:53 +0200 Subject: [petsc-users] [petsc-maint] PETSc with Xcode 15 In-Reply-To: <565B6989-DCA6-4FE6-90A0-1B09F27D2E64@petsc.dev> References: <565B6989-DCA6-4FE6-90A0-1B09F27D2E64@petsc.dev> Message-ID: <5D8CCD4B-59F4-4C80-AA28-7B7255605B38@lip6.fr> This is enough to bypass most of the warnings. There is still the "ld: warning: ignoring duplicate libraries:", but I think these should be filtered (unlike the other warnings which should be fixed). Thanks, Pierre ? diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py index 152272a9709..2d73fb20660 100644 --- a/config/BuildSystem/config/setCompilers.py +++ b/config/BuildSystem/config/setCompilers.py @@ -2316,6 +2316,6 @@ class Configure(config.base.Configure): if 'with-shared-ld' in self.argDB: - yield (self.argDB['with-shared-ld'], ['-dynamiclib -single_module', '-undefined dynamic_lookup', '-multiply_defined suppress', '-no_compact_unwind'], 'dylib') + yield (self.argDB['with-shared-ld'], ['-dynamiclib', '-undefined dynamic_lookup', '-no_compact_unwind'], 'dylib') if hasattr(self, 'CXX') and self.mainLanguage == 'Cxx': - yield (self.CXX, ['-dynamiclib -single_module', '-undefined dynamic_lookup', '-multiply_defined suppress', '-no_compact_unwind'], 'dylib') - yield (self.CC, ['-dynamiclib -single_module', '-undefined dynamic_lookup', '-multiply_defined suppress', '-no_compact_unwind'], 'dylib') + yield (self.CXX, ['-dynamiclib', '-undefined dynamic_lookup', '-no_compact_unwind'], 'dylib') + yield (self.CC, ['-dynamiclib', '-undefined dynamic_lookup', '-no_compact_unwind'], 'dylib') if hasattr(self, 'CXX') and self.mainLanguage == 'Cxx': @@ -2437,3 +2437,3 @@ class Configure(config.base.Configure): self.pushLanguage(language) - for testFlag in ['-Wl,-bind_at_load','-Wl,-multiply_defined,suppress', '-Wl,-multiply_defined -Wl,suppress', '-Wl,-commons,use_dylibs', '-Wl,-search_paths_first', '-Wl,-no_compact_unwind']: + for testFlag in ['-Wl,-search_paths_first', '-Wl,-no_compact_unwind']: if self.checkLinkerFlag(testFlag): @@ -2536,6 +2536,6 @@ class Configure(config.base.Configure): if 'with-dynamic-ld' in self.argDB: - yield (self.argDB['with-dynamic-ld'], ['-dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress'], 'dylib') + yield (self.argDB['with-dynamic-ld'], ['-dynamiclib'], 'dylib') if hasattr(self, 'CXX') and self.mainLanguage == 'Cxx': - yield (self.CXX, ['-dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress'], 'dylib') - yield (self.CC, ['-dynamiclib -single_module -undefined dynamic_lookup -multiply_defined suppress'], 'dylib') + yield (self.CXX, ['-dynamiclib'], 'dylib') + yield (self.CC, ['-dynamiclib'], 'dylib') # Shared default diff --git a/config/PETSc/options/sharedLibraries.py b/config/PETSc/options/sharedLibraries.py index fae390456e8..c1e7861c290 100755 --- a/config/PETSc/options/sharedLibraries.py +++ b/config/PETSc/options/sharedLibraries.py @@ -68,3 +68,3 @@ class Configure(config.base.Configure): self.addMakeMacro('SONAME_FUNCTION', '$(1).$(2).dylib') - self.addMakeMacro('SL_LINKER_FUNCTION', '-dynamiclib -install_name $(call SONAME_FUNCTION,$(1),$(2)) -compatibility_version $(2) -current_version $(3) -single_module -multiply_defined suppress -undefined dynamic_lookup') + self.addMakeMacro('SL_LINKER_FUNCTION', '-dynamiclib -install_name $(call SONAME_FUNCTION,$(1),$(2)) -compatibility_version $(2) -current_version $(3) -undefined dynamic_lookup') elif self.setCompilers.CC.find('win32fe') >=0: > On 21 Sep 2023, at 6:35 PM, Barry Smith wrote: > > > Where are the flags such as -multiply_defined being added? PETSc configure is suppose to check each flag before it adds it to the list of flags it uses. So normally I would expect these flags would just not exist in the link lines etc. > >> On Sep 21, 2023, at 11:02 AM, Blaise Bourdin wrote: >> >> FWIW, CLT 15.0 also seems to include changes to the linker, with incompatible options etc? I was able to rebuild mpich and petsc but I get many linker warnings and have not fully tested my build >> >> Before CLT 15.0 update >> SiMini:mef90-dmplex (dmplex)$ ld -v >> @(#)PROGRAM:ld PROJECT:ld64-857.1 >> BUILD 23:13:29 May 7 2023 >> configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em >> LTO support using: LLVM version 14.0.3, (clang-1403.0.22.14.1) (static support for 29, runtime is 29) >> TAPI support using: Apple TAPI version 14.0.3 (tapi-1403.0.5.1) >> >> vs after: >> bblaptop:mef90-dmplex (dmplex)$ ld -v >> @(#)PROGRAM:ld PROJECT:dyld-1015.7 >> BUILD 18:48:48 Aug 22 2023 >> configured to support archs: armv6 armv7 armv7s arm64 arm64e arm64_32 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em >> will use ld-classic for: armv6 armv7 armv7s arm64_32 i386 armv6m armv7k armv7m armv7em >> LTO support using: LLVM version 15.0.0 (static support for 29, runtime is 29) >> TAPI support using: Apple TAPI version 15.0.0 (tapi-1500.0.12.3) >> Library search paths: >> Framework search paths: >> >> >> bblaptop:tutorials (main)$ pwd >> /opt/HPC/petsc-main/src/vec/vec/tutorials >> bblaptop:tutorials (main)$ make ex1 >> mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-search_paths_first -Wl,-no_compact_unwind -Wimplicit-function-declaration -Wunused -Wuninitialized -fPIC -g3 -O0 -I/opt/HPC/petsc-main/include -I/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/include -I/opt/X11/include ex1.c -Wl,-rpath,/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -L/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -Wl,-rpath,/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -L/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -Wl,-rpath,/opt/homebrew/Cellar/mpich/4.1.2/lib -L/opt/homebrew/Cellar/mpich/4.1.2/lib -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc/aarch64-apple-darwin22/13 -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current/gcc -Wl,-rpath,/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current -L/opt/homebrew/Cellar/gcc/13.2.0/lib/gcc/current -lpetsc -lHYPRE -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu -lml -llapack -lblas -lparmetis -lmetis -lexoIIv2for32 -lexodus -lnetcdf -lpnetcdf -lhdf5_hl -lhdf5 -lchaco -ltriangle -lz -lctetgen -lX11 -lmpifort -lmpi -lpmpi -lgfortran -lemutls_w -lquadmath -lc++ -o ex1 >> ld: warning: -multiply_defined is obsolete >> ld: warning: -multiply_defined is obsolete >> ld: warning: duplicate -rpath '/opt/HPC/petsc-main/ventura-gcc13.2-arm64-g/lib' ignored >> ld: warning: -bind_at_load is deprecated on macOS >> ld: warning: ignoring duplicate libraries: '-lmpi', '-lpmpi' >> >> >> >> That?s quite a curveball a week ahead of a major software update. >> >> Blaise >> >>> On Sep 20, 2023, at 10:43 PM, Ju Liu wrote: >>> >>> Caution: External email. >>> >>> Hi PETSc team: >>> >>> I recently got my Xcode command line tools upgraded to version 15. When installing PETSc, the configure command returns an error. My configure command is >>> >>> ./configure --with-cc=gcc --with-fc=0 --with-cxx=0 --download-f2cblaslapack --download-mpich >>> >>> and the message is "Cannot locate all the standard C header files needed by PETSc". >>> >>> The configure.log file is attached. >>> >>> How shall I fix this? >>> >>> Thanks, >>> >>> Ju >>> >> >> ? >> Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1) >> Professor, Department of Mathematics & Statistics >> Hamilton Hall room 409A, McMaster University >> 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada >> https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243 >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: patch.txt URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From Di.Miao at synopsys.com Thu Sep 21 16:07:07 2023 From: Di.Miao at synopsys.com (Di Miao) Date: Thu, 21 Sep 2023 21:07:07 +0000 Subject: [petsc-users] 'Unable to locate PETSc dynamic library' error Message-ID: To whom it may concern, In our build system, PETSc/SLEPc is compiled in one place and the *.so lib are then moved to another place for future use. Before we add the '-with-thread-safety' flag, this works well. Now, we would like to run PETSc on multiple threads. As suggested by the manual, we added '-with-thread-safety' flag. The udpated libpetsc.so leads to the following error message: Unable to locate PETSc dynamic library You cannot move the dynamic libraries! My question is other than compile PETSc as a static library, is there any other solutions that can let us compile libpetsc.so in one place and distribute it to other folders without causing this error? Thank you, Di [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Unable to open file [0]PETSC ERROR: Unable to locate PETSc dynamic library You cannot move the dynamic libraries! [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.19.2, Jun 01, 2023 [0]PETSC ERROR: Unknown Name on a arch-linux-c-opt named tcadprod39.synopsys.com by tcad Wed Sep 20 02:37:04 2023 [0]PETSC ERROR: Configure options --with-mpi-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../tcad_mpi_mpich --with-64-bit-indices=true --with-blaslapack-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl --with-shared-libraries --with-clean=true --with-debugging=0 --with-mkl_pardiso-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --download-mumps=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/MUMPS_5.6.0.tar.gz --download-scalapack=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/v2.2.0.tar.gz --with-ssl-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../libressl --with-openmp=true --with-threadsafety=true --with-log=0 [0]PETSC ERROR: #1 PetscInitialize_DynamicLibraries() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/dll/reg.c:88 [0]PETSC ERROR: #2 PetscInitialize_Common() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1030 [0]PETSC ERROR: #3 PetscInitialize() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1276 [0]PETSC ERROR: #4 SlepcInitialize() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/sys/slepcinit.c:264 [0]PETSC ERROR: #5 EPSCreate() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 [0]PETSC ERROR: #6 EPSCreate() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 Start calculating extreme eigenvalues.. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash. application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59 : system msg for write_line failure : Bad file descriptor -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Thu Sep 21 16:43:30 2023 From: bsmith at petsc.dev (Barry Smith) Date: Thu, 21 Sep 2023 17:43:30 -0400 Subject: [petsc-users] 'Unable to locate PETSc dynamic library' error In-Reply-To: References: Message-ID: <16F6597E-65AD-43E1-A21E-5A16CFFE9403@petsc.dev> The recommended approach is to use --with-prefix=directory where you want PETSc installed instead of copying files manually after configure and make I don't see why ?with-thread-safety would affect this but > On Sep 21, 2023, at 5:07 PM, Di Miao via petsc-users wrote: > > To whom it may concern, > > In our build system, PETSc/SLEPc is compiled in one place and the *.so lib are then moved to another place for future use. Before we add the ??with-thread-safety? flag, this works well. Now, we would like to run PETSc on multiple threads. As suggested by the manual, we added ??with-thread-safety? flag. The udpated libpetsc.so leads to the following error message: > > Unable to locate PETSc dynamic library > You cannot move the dynamic libraries! > > My question is other than compile PETSc as a static library, is there any other solutions that can let us compile libpetsc.so in one place and distribute it to other folders without causing this error? > > Thank you, > Di > > [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- > [0]PETSC ERROR: Unable to open file > [0]PETSC ERROR: Unable to locate PETSc dynamic library > You cannot move the dynamic libraries! > [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.19.2, Jun 01, 2023 > [0]PETSC ERROR: Unknown Name on a arch-linux-c-opt named tcadprod39.synopsys.com by tcad Wed Sep 20 02:37:04 2023 > [0]PETSC ERROR: Configure options --with-mpi-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../tcad_mpi_mpich --with-64-bit-indices=true --with-blaslapack-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl --with-shared-libraries --with-clean=true --with-debugging=0 --with-mkl_pardiso-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --download-mumps=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/MUMPS_5.6.0.tar.gz --download-scalapack=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/v2.2.0.tar.gz --with-ssl-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../libressl --with-openmp=true --with-threadsafety=true --with-log=0 > [0]PETSC ERROR: #1 PetscInitialize_DynamicLibraries() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/dll/reg.c:88 > [0]PETSC ERROR: #2 PetscInitialize_Common() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1030 > [0]PETSC ERROR: #3 PetscInitialize() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1276 > [0]PETSC ERROR: #4 SlepcInitialize() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/sys/slepcinit.c:264 > [0]PETSC ERROR: #5 EPSCreate() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 > [0]PETSC ERROR: #6 EPSCreate() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 > Start calculating extreme eigenvalues.. > [0]PETSC ERROR: ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run > [0]PETSC ERROR: to get more information on the crash. > [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash. > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59 > : > system msg for write_line failure : Bad file descriptor -------------- next part -------------- An HTML attachment was scrubbed... URL: From Di.Miao at synopsys.com Thu Sep 21 16:59:07 2023 From: Di.Miao at synopsys.com (Di Miao) Date: Thu, 21 Sep 2023 21:59:07 +0000 Subject: [petsc-users] 'Unable to locate PETSc dynamic library' error In-Reply-To: <16F6597E-65AD-43E1-A21E-5A16CFFE9403@petsc.dev> References: <16F6597E-65AD-43E1-A21E-5A16CFFE9403@petsc.dev> Message-ID: Hi Barry, I found the following snippet in PetscInitialize_DynamicLibraries: #if defined(PETSC_HAVE_THREADSAFETY) /* These must be all initialized here because it is not safe for individual threads to call these initialize routines */ preload = PETSC_TRUE; #endif and ?PetscLoadDynamicLibrary("", &found)? is called only if preload==true and petsc is built as a shared lib. We have not faced this issue before we add ??with-thread-safety?. What we are doing is: Compile petsc/slepc as shared libraries, ship both executable and libpetsc.so libslepc.so to other users. Does this error message indicate that what we are doing is not robust and it is better to use static libraries instead? Thank you Di From: Barry Smith Sent: Thursday, September 21, 2023 2:44 PM To: Di Miao Cc: petsc-users at mcs.anl.gov; Udit Pillai Subject: Re: [petsc-users] 'Unable to locate PETSc dynamic library' error The recommended approach is to use --with-prefix=directory where you want PETSc installed instead of copying files manually after configure and make I don't see why ?with-thread-safety would affect this but On Sep 21, 2023, at 5:07 PM, Di Miao via petsc-users > wrote: To whom it may concern, In our build system, PETSc/SLEPc is compiled in one place and the *.so lib are then moved to another place for future use. Before we add the ??with-thread-safety? flag, this works well. Now, we would like to run PETSc on multiple threads. As suggested by the manual, we added ??with-thread-safety? flag. The udpated libpetsc.so leads to the following error message: Unable to locate PETSc dynamic library You cannot move the dynamic libraries! My question is other than compile PETSc as a static library, is there any other solutions that can let us compile libpetsc.so in one place and distribute it to other folders without causing this error? Thank you, Di [0]PETSC ERROR: --------------------- Error Message -------------------------------------------------------------- [0]PETSC ERROR: Unable to open file [0]PETSC ERROR: Unable to locate PETSc dynamic library You cannot move the dynamic libraries! [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting. [0]PETSC ERROR: Petsc Release Version 3.19.2, Jun 01, 2023 [0]PETSC ERROR: Unknown Name on a arch-linux-c-opt named tcadprod39.synopsys.com by tcad Wed Sep 20 02:37:04 2023 [0]PETSC ERROR: Configure options --with-mpi-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../tcad_mpi_mpich --with-64-bit-indices=true --with-blaslapack-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl --with-shared-libraries --with-clean=true --with-debugging=0 --with-mkl_pardiso-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 --download-mumps=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/MUMPS_5.6.0.tar.gz --download-scalapack=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/v2.2.0.tar.gz --with-ssl-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../libressl --with-openmp=true --with-threadsafety=true --with-log=0 [0]PETSC ERROR: #1 PetscInitialize_DynamicLibraries() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/dll/reg.c:88 [0]PETSC ERROR: #2 PetscInitialize_Common() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1030 [0]PETSC ERROR: #3 PetscInitialize() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1276 [0]PETSC ERROR: #4 SlepcInitialize() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/sys/slepcinit.c:264 [0]PETSC ERROR: #5 EPSCreate() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 [0]PETSC ERROR: #6 EPSCreate() at /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 Start calculating extreme eigenvalues.. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/ [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is causing the crash. application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59 : system msg for write_line failure : Bad file descriptor -------------- next part -------------- An HTML attachment was scrubbed... URL: From junchao.zhang at gmail.com Thu Sep 21 17:57:49 2023 From: junchao.zhang at gmail.com (Junchao Zhang) Date: Thu, 21 Sep 2023 17:57:49 -0500 Subject: [petsc-users] 'Unable to locate PETSc dynamic library' error In-Reply-To: References: <16F6597E-65AD-43E1-A21E-5A16CFFE9403@petsc.dev> Message-ID: >From the code, it seems you need to let your users set env var PETSC_LIB_DIR to the library location, or PETSC_DIR to the prefix path and PETSC_ARCH to "" static PetscErrorCode PetscLoadDynamicLibrary(const char *name, PetscBool *found) { char libs[PETSC_MAX_PATH_LEN], dlib[PETSC_MAX_PATH_LEN]; PetscFunctionBegin; PetscCall(PetscStrncpy(libs, "${PETSC_LIB_DIR}/libpetsc", sizeof(libs))); PetscCall(PetscStrlcat(libs, name, sizeof(libs))); PetscCall(PetscDLLibraryRetrieve(PETSC_COMM_WORLD, libs, dlib, 1024, found)); if (*found) { PetscCall(PetscDLLibraryAppend(PETSC_COMM_WORLD, &PetscDLLibrariesLoaded, dlib)); } else { PetscCall(PetscStrncpy(libs, "${PETSC_DIR}/${PETSC_ARCH}/lib/libpetsc", sizeof(libs))); PetscCall(PetscStrlcat(libs, name, sizeof(libs))); PetscCall(PetscDLLibraryRetrieve(PETSC_COMM_WORLD, libs, dlib, 1024, found)); if (*found) PetscCall(PetscDLLibraryAppend(PETSC_COMM_WORLD, &PetscDLLibrariesLoaded, dlib)); } PetscFunctionReturn(PETSC_SUCCESS); } --Junchao Zhang On Thu, Sep 21, 2023 at 4:59?PM Di Miao via petsc-users < petsc-users at mcs.anl.gov> wrote: > Hi Barry, > > > > I found the following snippet in PetscInitialize_DynamicLibraries: > > > > #if defined(PETSC_HAVE_THREADSAFETY) > > /* These must be all initialized here because it is not safe for > individual threads to call these initialize routines */ > > preload = PETSC_TRUE; > > #endif > > > > and ?PetscLoadDynamicLibrary("", &found)? is called only if preload==true > and petsc is built as a shared lib. We have not faced this issue before we > add ??with-thread-safety?. > > > > What we are doing is: > > Compile petsc/slepc as shared libraries, ship both executable and > libpetsc.so libslepc.so to other users. > > > > Does this error message indicate that what we are doing is not robust and > it is better to use static libraries instead? > > > > Thank you > > Di > > > > *From:* Barry Smith > *Sent:* Thursday, September 21, 2023 2:44 PM > *To:* Di Miao > *Cc:* petsc-users at mcs.anl.gov; Udit Pillai > *Subject:* Re: [petsc-users] 'Unable to locate PETSc dynamic library' > error > > > > > > The recommended approach is to use --with-prefix=directory where you > want PETSc installed instead of copying files manually after configure and > make > > > > I don't see why ?with-thread-safety would affect this but > > > > > > On Sep 21, 2023, at 5:07 PM, Di Miao via petsc-users < > petsc-users at mcs.anl.gov> wrote: > > > > To whom it may concern, > > > > In our build system, PETSc/SLEPc is compiled in one place and the *.so lib > are then moved to another place for future use. Before we add the > ??with-thread-safety? flag, this works well. Now, we would like to run > PETSc on multiple threads. As suggested by the manual, we added > ??with-thread-safety? flag. The udpated libpetsc.so leads to the following > error message: > > > > Unable to locate PETSc dynamic library > > You cannot move the dynamic libraries! > > > > My question is other than compile PETSc as a static library, is there any > other solutions that can let us compile libpetsc.so in one place and > distribute it to other folders without causing this error? > > > > Thank you, > > Di > > > > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > > [0]PETSC ERROR: Unable to open file > > [0]PETSC ERROR: Unable to locate PETSc dynamic library > > You cannot move the dynamic libraries! > > [0]PETSC ERROR: See https://petsc.org/release/faq/ > > for trouble shooting. > > [0]PETSC ERROR: Petsc Release Version 3.19.2, Jun 01, 2023 > > [0]PETSC ERROR: Unknown Name on a arch-linux-c-opt named > tcadprod39.synopsys.com by tcad Wed Sep 20 02:37:04 2023 > > [0]PETSC ERROR: Configure options > --with-mpi-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../tcad_mpi_mpich > --with-64-bit-indices=true > --with-blaslapack-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl > --with-shared-libraries --with-clean=true --with-debugging=0 > --with-mkl_pardiso-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../mkl > COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > --download-mumps=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/MUMPS_5.6.0.tar.gz > --download-scalapack=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/v2.2.0.tar.gz > --with-ssl-dir=/SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/../libressl > --with-openmp=true --with-threadsafety=true --with-log=0 > > [0]PETSC ERROR: #1 PetscInitialize_DynamicLibraries() at > /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/dll/reg.c:88 > > [0]PETSC ERROR: #2 PetscInitialize_Common() at > /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1030 > > [0]PETSC ERROR: #3 PetscInitialize() at > /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/petsc/petsc-3.19.2/src/sys/objects/pinit.c:1276 > > [0]PETSC ERROR: #4 SlepcInitialize() at > /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/sys/slepcinit.c:264 > > [0]PETSC ERROR: #5 EPSCreate() at > /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 > > [0]PETSC ERROR: #6 EPSCreate() at > /SCRATCH/tcad/ci_2_0/workspace/incremental_build_main at 2/slepc/slepc-3.19.2/src/eps/interface/epsbasic.c:56 > > Start calculating extreme eigenvalues.. > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > > [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind > > and https://petsc.org/release/faq/ > > > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and > run > > [0]PETSC ERROR: to get more information on the crash. > > [0]PETSC ERROR: Run with -malloc_debug to check if memory corruption is > causing the crash. > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59 > > : > > system msg for write_line failure : Bad file descriptor > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From anna.dalklint at solid.lth.se Thu Sep 21 23:39:49 2023 From: anna.dalklint at solid.lth.se (Anna Dalklint) Date: Fri, 22 Sep 2023 04:39:49 +0000 Subject: [petsc-users] Face Set not appearing when loading GMSH mesh to DMPlex In-Reply-To: <6693E735-6BDE-4014-B5A7-2B5C7A7FF560@mcmaster.ca> References: <576f28bb730c467680de36abfbf5b463@solid.lth.se>, <6693E735-6BDE-4014-B5A7-2B5C7A7FF560@mcmaster.ca> Message-ID: Hi again, David was right, the DMView call only printed the sets on the master rank (which I wasn't aware of). So there was no issue! Thank you, Anna ________________________________ From: Blaise Bourdin Sent: Thursday, September 21, 2023 5:05:35 PM To: Anna Dalklint Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Face Set not appearing when loading GMSH mesh to DMPlex Can you send me the geo or msh file, or instruction on how to build your example? I am not familiar with the gmsh API Blaise On Sep 20, 2023, at 8:16 AM, Anna Dalklint via petsc-users wrote: Caution: External email. Hello, I am trying to load a mesh, created via the gmsh api, into a DMPlex. The code is seen below: 6 gmsh::initialize(); 7 elsize0 = 1.0; 8 double a = 20.0; 9 double b = 20.0; 10 double c = 10.0; 11 double d = 30.0; 12 double e = 70.0; 13 14 gmsh::model::geo::addPoint(0.0, 0.0, 0.0, elsize0, 1); 15 gmsh::model::geo::addPoint(a, 0.0, 0.0, elsize0, 2); 16 gmsh::model::geo::addPoint(0.0, d, 0.0, elsize0, 3); 17 gmsh::model::geo::addPoint(a, c, 0.0, elsize0, 4); 18 gmsh::model::geo::addPoint(e, d, 0.0, elsize0, 5); 19 gmsh::model::geo::addPoint(e, c, 0.0, elsize0, 6); 20 gmsh::model::geo::addPoint(a, 0.0, b, elsize0, 7); 21 gmsh::model::geo::addPoint(0.0, 0.0, b, elsize0, 8); 22 gmsh::model::geo::addPoint(0.0, d, b, elsize0, 9); 23 gmsh::model::geo::addPoint(e, d, b, elsize0, 10); 24 gmsh::model::geo::addPoint(e, c, b, elsize0, 11); 25 gmsh::model::geo::addPoint(a, c, b, elsize0, 12); 26 27 // Define lines connecting points 28 gmsh::model::geo::addLine(2, 1, 1); 29 gmsh::model::geo::addLine(1, 3, 2); 30 gmsh::model::geo::addLine(3, 5, 3); 31 gmsh::model::geo::addLine(5, 6, 4); 32 gmsh::model::geo::addLine(6, 4, 5); 33 gmsh::model::geo::addLine(4, 2, 6); 34 gmsh::model::geo::addLine(2, 7, 7); 35 gmsh::model::geo::addLine(7, 8, 8); 36 gmsh::model::geo::addLine(8, 1, 9); 37 gmsh::model::geo::addLine(8, 9, 10); 38 gmsh::model::geo::addLine(9, 3, 11); 39 gmsh::model::geo::addLine(9, 10, 12); 40 gmsh::model::geo::addLine(10, 11, 13); 41 gmsh::model::geo::addLine(11, 12, 14); 42 gmsh::model::geo::addLine(12, 7, 15); 43 gmsh::model::geo::addLine(12, 4, 16); 44 gmsh::model::geo::addLine(11, 6, 17); 45 gmsh::model::geo::addLine(10, 5, 18); 46 47 // Define surfaces through their boundaries 48 gmsh::model::geo::addCurveLoop({3, 4, 5, 6, 1, 2}, 1); 49 gmsh::model::geo::addPlaneSurface({1}, 1); 50 gmsh::model::geo::addCurveLoop({18, 4, -17, -13}, 2); 51 gmsh::model::geo::addPlaneSurface({2}, 2); 52 gmsh::model::geo::addCurveLoop({5, -16, -14, 17}, 3); 53 gmsh::model::geo::addPlaneSurface({3}, 3); 54 gmsh::model::geo::addCurveLoop({16, 6, 7, -15}, 4); 55 gmsh::model::geo::addPlaneSurface({4}, 4); 56 gmsh::model::geo::addCurveLoop({12, 13, 14, 15, 8, 10}, 5); 57 gmsh::model::geo::addPlaneSurface({5}, 5); 58 gmsh::model::geo::addCurveLoop({11, -2, -9, 10}, 6); 59 gmsh::model::geo::addPlaneSurface({6}, 6); 60 gmsh::model::geo::addCurveLoop({1, -9, -8, -7}, 7); 61 gmsh::model::geo::addPlaneSurface({7}, 7); 62 gmsh::model::geo::addCurveLoop({11, 3, -18, -12}, 8); 63 gmsh::model::geo::addPlaneSurface({8}, 8); 64 65 gmsh::model::geo::addSurfaceLoop({8, 1, 2, 3, 4, 7, 6, 5}, 1); 66 gmsh::model::geo::addVolume({1}, 1); 67 68 gmsh::model::geo::synchronize(); 70 72 gmsh::model::addPhysicalGroup(3, {1}, 1); 74 gmsh::model::addPhysicalGroup(2, {7}, 101, "dir_y"); 98 gmsh::option::setNumber("Mesh.Algorithm", 6); 99 gmsh::option::setNumber("Mesh.ElementOrder", 1); 100 gmsh::model::mesh::generate(3); 101 gmsh::write("filename.msh"); The mesh is generated, but the Physical Group is not correctly loaded into the DMPlex. If I run a DMView on my dm, I get: 171 DM Object: Parallel Mesh 4 MPI processes 172 type: plex 173 Parallel Mesh in 3 dimensions: 174 Number of 0-cells per rank: 7138 7192 7328 7171 175 Number of 1-cells per rank: 45825 45992 46817 45824 176 Number of 2-cells per rank: 74791 74901 76203 74568 177 Number of 3-cells per rank: 36103 36100 36713 35914 178 Labels: 179 depth: 4 strata with value/size (0 (7138), 1 (45825), 2 (74791), 3 (36103)) 180 celltype: 4 strata with value/size (0 (7138), 1 (45825), 3 (74791), 6 (36103)) 181 Cell Sets: 1 strata with value/size (1 (36103)) 182 Face Sets: 0 strata with value/size () 183 Vertex Sets: 1 strata with value/size (1 (5200)) Why are the elements of the physicalGroup "dir_y" (Plane Surface 7) not loaded as a face set? If I change the Plane Surface to another surface, e.g. 8, it marks the elements as the correct face set. Another weird thing is that the number of vertices in the above Vertex set is not correct. I have tried changing the numbering of Plane Surface 7 (to e.g. 70) but the issue remains. I run the code with the -dm_plex_gmsh_mark_vertices and -dm_plex_gmsh_multiple_tags flags. Thank you, Anna ? Canada Research Chair in Mathematical and Computational Aspects of Solid Mechanics (Tier 1) Professor, Department of Mathematics & Statistics Hamilton Hall room 409A, McMaster University 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada https://www.math.mcmaster.ca/bourdin | +1 (905) 525 9140 ext. 27243 -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Sat Sep 23 05:00:35 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Sat, 23 Sep 2023 10:00:35 +0000 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: I just would like to clarify a couple of things. 1)The M and N, in MatCreateBIJ, refer to the actual number of global rows/cols or global blocked rows/cols? But d_nz and o_nz only refer to blocked rows. 2) In MatZeroRowsColumnsIS, you mentioned I could use the actual row numbers instead of block rows. Is there any option to SWITCH between the two, when using MatZeroRowsColumnsIS? Thank you, Karthik. From: Matthew Knepley Date: Sunday, 10 September 2023 at 22:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 5:00?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I get it. Q1) In other words when using MatSetValuesBlocked, for bs = 2, I could pass all 64 entrees of the element matrix row-oriented by setting m = n = 4 (along with the respective idxm and idxn)? Yes. Q2) However, at a given node variable u can fixed while v is free. In that case, while using MatZeroRowsColumns I need to know the global index of the variable u (i.e. row/column index in the system matrix A). Here, block size does not come in handy as it did when using MatSetValuesBlocked. You would use the actual row numbers instead of block rows. You can use either. Q3) When assembling the system matrix A in this way, would it allow me to use PCFIELDSPLIT for coupled systems? Yes. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 21:23 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 4:16?PM Karthikeyan Chockalingam - STFC UKRI > wrote: Thank you. I almost got it and have a couple of questions. Let me summarize, I have an element Jacobian matrix of size 8 x 8 for QAUD4 (for variables u and v) ordered such that the degrees of freedom at a node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4]. Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not have an on-diagonal and off-diagonal block structure? Does it not matter? It does have block structure in that each entry in your original matrix is now a 2x2 block entry in the matrix for 2 fields. When assembling the element Jacobian into the system matrix A, I would make use of MatSetValues. For each element, I presume m = 8 and n = 8 along with idxm and idxn, are passed to MatSetValues. Meaning I have to figure out the global index (say idxm) set of size 8 corresponding to the system matrix A. What you can do is call https://petsc.org/main/manualpages/Mat/MatSetValuesBlocked/ and give the same indices that you would have given for the original matrix, but instead of a value at each location, we now have a 2x2 block. Q2) What does setting the block size bs = 2 accomplish? Because the way to assemble the Jacobian into the system matrix A seems to me no different than I did for the single variable scalar problem. This is answered above. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 20:18 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I don?t see an option to give block size. https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ Thanks, Matt Many thanks, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 20:09 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I will solve the coupled problem in a non-linear fashion using SNES, so I will have one residual for each variable R(u1) and R(u2) and the resulting Jacobian matrix J = [J11 J12 J21 J22] for each element. For first-order Lagrange elements (in 2D) will have four nodes, then J would be of size 8 x 8. Let's say the variables are u and v. The order would be [u1 u2 u3 u4 v1 v2 v3 v4]. Or should I rearrange the above entr?es in the element Jacobian so as to have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will not have block ordering I guess. This is the correct order to get block matrices. In my case, the discretization of the u and v are from the same element space. Can you please elaborate when you say, ?Just enlarge the block size of your matrix?? I have never used block size before and not sure what it accomplishes. Do you mean to say, I should use MATBAIJ instead of MATAIJ? You do not need to change the type, just give the AIJ matrix a blocksize of 2. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 19:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: Hello, I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions. Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns, A = [A00 A01 A10 A11] This is usually not a good way to think of it. This division means that all variables of one field come before all those of another. It is much more common to group together all the unknowns at a given point. You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location. Thanks, Matt the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor. Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations? -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide. Kind regards, Karthik. -- Karthik Chockalingam, Ph.D. Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Sep 23 08:22:48 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 23 Sep 2023 09:22:48 -0400 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: On Sat, Sep 23, 2023 at 6:00?AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > I just would like to clarify a couple of things. > > > > 1)The M and N, in MatCreateBIJ, refer to the actual number of global > rows/cols or global blocked rows/cols? > > > > But d_nz and o_nz only refer to blocked rows. > Yes. > 2) In MatZeroRowsColumnsIS, you mentioned I could use the actual row > numbers instead of block rows. Is there any option to SWITCH between the > two, when using MatZeroRowsColumnsIS? > I do not understand the question. When would switching happen? Thanks, Matt > Thank you, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 22:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 5:00?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I get it. > > > > Q1) In other words when using MatSetValuesBlocked, for bs = 2, I could > pass all 64 entrees of the element matrix row-oriented by setting m = n = > 4 (along with the respective idxm and idxn)? > > > > Yes. > > > > Q2) However, at a given node variable u can fixed while v is free. In that > case, while using MatZeroRowsColumns I need to know the global index of the > variable u (i.e. row/column index in the system matrix A). Here, block size > does not come in handy as it did when using MatSetValuesBlocked. > > > > You would use the actual row numbers instead of block rows. You can use > either. > > > > Q3) When assembling the system matrix A in this way, would it allow me to > use PCFIELDSPLIT for coupled systems? > > > > Yes. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 21:23 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 4:16?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > Thank you. I almost got it and have a couple of questions. > > > > Let me summarize, I have an element Jacobian matrix of size 8 x 8 for > QAUD4 (for variables u and v) ordered such that the degrees of freedom at a > node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4]. > > > > Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not > have an on-diagonal and off-diagonal block structure? Does it not matter? > > > > It does have block structure in that each entry in your original matrix is > now a 2x2 block entry in the matrix for 2 fields. > > > > When assembling the element Jacobian into the system matrix A, I would > make use of MatSetValues. For each element, I *presume* m = 8 and n = 8 > along with idxm and idxn, are passed to MatSetValues. Meaning I have to > figure out the global index (say idxm) set of size 8 corresponding to the > system matrix A. > > > > What you can do is call > > > > https://petsc.org/main/manualpages/Mat/MatSetValuesBlocked/ > > > > and give the same indices that you would have given for the original > matrix, but instead of a value at each location, we now have a 2x2 block. > > > > Q2) What does setting the block size bs = 2 accomplish? Because the way to > assemble the Jacobian into the system matrix A seems to me no different > than I did for the single variable scalar problem. > > > > This is answered above. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:18 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I don?t see an option to give block size. > > https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ > > > > https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ > > > > Thanks, > > > > Matt > > > > > > Many thanks, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:09 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I will solve the coupled problem in a non-linear fashion using SNES, so I > will have one residual for each variable R(u1) and R(u2) and the resulting > Jacobian matrix > > > > J = [J11 J12 > > J21 J22] for each element. > > > > For first-order Lagrange elements (in 2D) will have four nodes, then J > would be of size 8 x 8. Let's say the variables are u and v. The order > would be [u1 u2 u3 u4 v1 v2 v3 v4]. > > > > Or should I rearrange the above entr?es in the element Jacobian so as to > have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will > not have block ordering I guess. > > > > This is the correct order to get block matrices. > > > > In my case, the discretization of the u and v are from the same element > space. > > Can you please elaborate when you say, ?Just enlarge the block size of > your matrix?? > > I have never used block size before and not sure what it accomplishes. > > Do you mean to say, I should use MATBAIJ instead of MATAIJ? > > > > You do not need to change the type, just give the AIJ matrix a blocksize > of 2. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 19:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > Hello, > > > > I have so far solved scalar field problems using finite elements on a > given (*unstructured*) mesh. I made use of MATMPIAIJ to create matrixes, > MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to > set boundary conditions. > > > > Now, I would like to solve a coupled system of equations for the > quantities u1 and u2 on the (*unstructured*) mesh. I.e., the matrix > should get the double number of rows and columns, > > > > A = [A00 A01 > > A10 A11] > > > > This is usually not a good way to think of it. This division means that > all variables of one field come before > > all those of another. It is much more common to group together all the > unknowns at a given point. > > > > You could, if the discretizations of u1 and u2 are the same, just enlarge > the blocksize of your matrix. Then you set u1 and u2 for each vec location, > or a 2x2 block for each Jacobian location. > > > > Thanks, > > > > Matt > > > > the vectors contain twice the number of entries (e.g. first all u1s and > then all u2s). I would like to be sure that the entries of u1 and u2, which > are associated with the same element are located on the same processor. > > > > Is a pre-defined structure already available within PETSc to enlarge such > a single equation to store the entries of coupled equations? > > > > -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 > > -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 > > > > Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently > to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); > > > > I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ > and MatSetValues to create and assign values to matrix entries > respectively. I would be grateful if you could provide the stepwise guide. > > > > Kind regards, > > Karthik. > > > > -- > > *Karthik Chockalingam, Ph.D.* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From karthikeyan.chockalingam at stfc.ac.uk Sat Sep 23 08:32:28 2023 From: karthikeyan.chockalingam at stfc.ac.uk (Karthikeyan Chockalingam - STFC UKRI) Date: Sat, 23 Sep 2023 13:32:28 +0000 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: Sorry, you didn?t answer my first equation. 1)The M and N, in MatCreateBIJ, refer to the actual number of global rows/cols or global blocked rows/cols? 2) The row indexes used in MatZeroRowsColumnsIS, would refer to the actual row or the blocked row? Below is your response to my previous email: ?You would use the actual row numbers instead of block rows. You can use either.? How can I use either (or switch)? Thanks, Karthik, From: Matthew Knepley Date: Saturday, 23 September 2023 at 14:23 To: Chockalingam, Karthikeyan (STFC,DL,HC) Cc: petsc-users at mcs.anl.gov Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sat, Sep 23, 2023 at 6:00?AM Karthikeyan Chockalingam - STFC UKRI > wrote: I just would like to clarify a couple of things. 1)The M and N, in MatCreateBIJ, refer to the actual number of global rows/cols or global blocked rows/cols? But d_nz and o_nz only refer to blocked rows. Yes. 2) In MatZeroRowsColumnsIS, you mentioned I could use the actual row numbers instead of block rows. Is there any option to SWITCH between the two, when using MatZeroRowsColumnsIS? I do not understand the question. When would switching happen? Thanks, Matt Thank you, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 22:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 5:00?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I get it. Q1) In other words when using MatSetValuesBlocked, for bs = 2, I could pass all 64 entrees of the element matrix row-oriented by setting m = n = 4 (along with the respective idxm and idxn)? Yes. Q2) However, at a given node variable u can fixed while v is free. In that case, while using MatZeroRowsColumns I need to know the global index of the variable u (i.e. row/column index in the system matrix A). Here, block size does not come in handy as it did when using MatSetValuesBlocked. You would use the actual row numbers instead of block rows. You can use either. Q3) When assembling the system matrix A in this way, would it allow me to use PCFIELDSPLIT for coupled systems? Yes. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 21:23 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 4:16?PM Karthikeyan Chockalingam - STFC UKRI > wrote: Thank you. I almost got it and have a couple of questions. Let me summarize, I have an element Jacobian matrix of size 8 x 8 for QAUD4 (for variables u and v) ordered such that the degrees of freedom at a node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4]. Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not have an on-diagonal and off-diagonal block structure? Does it not matter? It does have block structure in that each entry in your original matrix is now a 2x2 block entry in the matrix for 2 fields. When assembling the element Jacobian into the system matrix A, I would make use of MatSetValues. For each element, I presume m = 8 and n = 8 along with idxm and idxn, are passed to MatSetValues. Meaning I have to figure out the global index (say idxm) set of size 8 corresponding to the system matrix A. What you can do is call https://petsc.org/main/manualpages/Mat/MatSetValuesBlocked/ and give the same indices that you would have given for the original matrix, but instead of a value at each location, we now have a 2x2 block. Q2) What does setting the block size bs = 2 accomplish? Because the way to assemble the Jacobian into the system matrix A seems to me no different than I did for the single variable scalar problem. This is answered above. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 20:18 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I don?t see an option to give block size. https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ Thanks, Matt Many thanks, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 20:09 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI > wrote: I will solve the coupled problem in a non-linear fashion using SNES, so I will have one residual for each variable R(u1) and R(u2) and the resulting Jacobian matrix J = [J11 J12 J21 J22] for each element. For first-order Lagrange elements (in 2D) will have four nodes, then J would be of size 8 x 8. Let's say the variables are u and v. The order would be [u1 u2 u3 u4 v1 v2 v3 v4]. Or should I rearrange the above entr?es in the element Jacobian so as to have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will not have block ordering I guess. This is the correct order to get block matrices. In my case, the discretization of the u and v are from the same element space. Can you please elaborate when you say, ?Just enlarge the block size of your matrix?? I have never used block size before and not sure what it accomplishes. Do you mean to say, I should use MATBAIJ instead of MATAIJ? You do not need to change the type, just give the AIJ matrix a blocksize of 2. Thanks, Matt Kind regards, Karthik. From: Matthew Knepley > Date: Sunday, 10 September 2023 at 19:03 To: Chockalingam, Karthikeyan (STFC,DL,HC) > Cc: petsc-users at mcs.anl.gov > Subject: Re: [petsc-users] Coupled system of equations on unstructured mesh On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via petsc-users > wrote: Hello, I have so far solved scalar field problems using finite elements on a given (unstructured) mesh. I made use of MATMPIAIJ to create matrixes, MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to set boundary conditions. Now, I would like to solve a coupled system of equations for the quantities u1 and u2 on the (unstructured) mesh. I.e., the matrix should get the double number of rows and columns, A = [A00 A01 A10 A11] This is usually not a good way to think of it. This division means that all variables of one field come before all those of another. It is much more common to group together all the unknowns at a given point. You could, if the discretizations of u1 and u2 are the same, just enlarge the blocksize of your matrix. Then you set u1 and u2 for each vec location, or a 2x2 block for each Jacobian location. Thanks, Matt the vectors contain twice the number of entries (e.g. first all u1s and then all u2s). I would like to be sure that the entries of u1 and u2, which are associated with the same element are located on the same processor. Is a pre-defined structure already available within PETSc to enlarge such a single equation to store the entries of coupled equations? -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ and MatSetValues to create and assign values to matrix entries respectively. I would be grateful if you could provide the stepwise guide. Kind regards, Karthik. -- Karthik Chockalingam, Ph.D. Senior Research Software Engineer High Performance Systems Engineering Group Hartree Centre | Science and Technology Facilities Council karthikeyan.chockalingam at stfc.ac.uk Error! Filename not specified. -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Sat Sep 23 09:14:05 2023 From: knepley at gmail.com (Matthew Knepley) Date: Sat, 23 Sep 2023 10:14:05 -0400 Subject: [petsc-users] Coupled system of equations on unstructured mesh In-Reply-To: References: Message-ID: On Sat, Sep 23, 2023 at 9:32?AM Karthikeyan Chockalingam - STFC UKRI < karthikeyan.chockalingam at stfc.ac.uk> wrote: > Sorry, you didn?t answer my first equation. > > 1)The M and N, in MatCreateBIJ, refer to the actual number of *global *rows/cols > or *global blocke*d rows/cols? > I did answer. It is global rows/cols. > 2) The row indexes used in MatZeroRowsColumnsIS, would refer to the > actual row or the blocked row? > Actual rows and cols. > Below is your response to my previous email: > > ?You would use the actual row numbers instead of block rows. You can use > either.? How can I use either (or switch)? > I believe I meant you can use either the array or IS forms. Thanks, Matt > Thanks, > > Karthik, > > > > *From: *Matthew Knepley > *Date: *Saturday, 23 September 2023 at 14:23 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sat, Sep 23, 2023 at 6:00?AM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I just would like to clarify a couple of things. > > > > 1)The M and N, in MatCreateBIJ, refer to the actual number of global > rows/cols or global blocked rows/cols? > > > > But d_nz and o_nz only refer to blocked rows. > > > > Yes. > > > > 2) In MatZeroRowsColumnsIS, you mentioned I could use the actual row > numbers instead of block rows. Is there any option to SWITCH between the > two, when using MatZeroRowsColumnsIS? > > > > I do not understand the question. When would switching happen? > > > > Thanks, > > > > Matt > > > > Thank you, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 22:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 5:00?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I get it. > > > > Q1) In other words when using MatSetValuesBlocked, for bs = 2, I could > pass all 64 entrees of the element matrix row-oriented by setting m = n = > 4 (along with the respective idxm and idxn)? > > > > Yes. > > > > Q2) However, at a given node variable u can fixed while v is free. In that > case, while using MatZeroRowsColumns I need to know the global index of the > variable u (i.e. row/column index in the system matrix A). Here, block size > does not come in handy as it did when using MatSetValuesBlocked. > > > > You would use the actual row numbers instead of block rows. You can use > either. > > > > Q3) When assembling the system matrix A in this way, would it allow me to > use PCFIELDSPLIT for coupled systems? > > > > Yes. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 21:23 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 4:16?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > Thank you. I almost got it and have a couple of questions. > > > > Let me summarize, I have an element Jacobian matrix of size 8 x 8 for > QAUD4 (for variables u and v) ordered such that the degrees of freedom at a > node are grouped together i.e. [u1 v1 u2 v2 u3 v3 u4 v4]. > > > > Q1) But this ordering of element Jacobian matrix of size 8 x 8, does not > have an on-diagonal and off-diagonal block structure? Does it not matter? > > > > It does have block structure in that each entry in your original matrix is > now a 2x2 block entry in the matrix for 2 fields. > > > > When assembling the element Jacobian into the system matrix A, I would > make use of MatSetValues. For each element, I *presume* m = 8 and n = 8 > along with idxm and idxn, are passed to MatSetValues. Meaning I have to > figure out the global index (say idxm) set of size 8 corresponding to the > system matrix A. > > > > What you can do is call > > > > https://petsc.org/main/manualpages/Mat/MatSetValuesBlocked/ > > > > and give the same indices that you would have given for the original > matrix, but instead of a value at each location, we now have a 2x2 block. > > > > Q2) What does setting the block size bs = 2 accomplish? Because the way to > assemble the Jacobian into the system matrix A seems to me no different > than I did for the single variable scalar problem. > > > > This is answered above. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:18 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:15?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I don?t see an option to give block size. > > https://petsc.org/release/manualpages/Mat/MatCreateAIJ/ > > > > https://petsc.org/release/manualpages/Mat/MatSetBlockSize/ > > > > Thanks, > > > > Matt > > > > > > Many thanks, > > Karthik. > > > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 20:09 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 3:01?PM Karthikeyan Chockalingam - STFC UKRI < > karthikeyan.chockalingam at stfc.ac.uk> wrote: > > I will solve the coupled problem in a non-linear fashion using SNES, so I > will have one residual for each variable R(u1) and R(u2) and the resulting > Jacobian matrix > > > > J = [J11 J12 > > J21 J22] for each element. > > > > For first-order Lagrange elements (in 2D) will have four nodes, then J > would be of size 8 x 8. Let's say the variables are u and v. The order > would be [u1 u2 u3 u4 v1 v2 v3 v4]. > > > > Or should I rearrange the above entr?es in the element Jacobian so as to > have [u1 v1 u2 v2 u3 v3 u4 v4] ordering? In that case, the Jacobian will > not have block ordering I guess. > > > > This is the correct order to get block matrices. > > > > In my case, the discretization of the u and v are from the same element > space. > > Can you please elaborate when you say, ?Just enlarge the block size of > your matrix?? > > I have never used block size before and not sure what it accomplishes. > > Do you mean to say, I should use MATBAIJ instead of MATAIJ? > > > > You do not need to change the type, just give the AIJ matrix a blocksize > of 2. > > > > Thanks, > > > > Matt > > > > Kind regards, > > Karthik. > > > > *From: *Matthew Knepley > *Date: *Sunday, 10 September 2023 at 19:03 > *To: *Chockalingam, Karthikeyan (STFC,DL,HC) < > karthikeyan.chockalingam at stfc.ac.uk> > *Cc: *petsc-users at mcs.anl.gov > *Subject: *Re: [petsc-users] Coupled system of equations on unstructured > mesh > > On Sun, Sep 10, 2023 at 1:48?PM Karthikeyan Chockalingam - STFC UKRI via > petsc-users wrote: > > Hello, > > > > I have so far solved scalar field problems using finite elements on a > given (*unstructured*) mesh. I made use of MATMPIAIJ to create matrixes, > MatCreateVecs(A, &b, &x) to create vectors, and MatZeroRowsColumnsIS to > set boundary conditions. > > > > Now, I would like to solve a coupled system of equations for the > quantities u1 and u2 on the (*unstructured*) mesh. I.e., the matrix > should get the double number of rows and columns, > > > > A = [A00 A01 > > A10 A11] > > > > This is usually not a good way to think of it. This division means that > all variables of one field come before > > all those of another. It is much more common to group together all the > unknowns at a given point. > > > > You could, if the discretizations of u1 and u2 are the same, just enlarge > the blocksize of your matrix. Then you set u1 and u2 for each vec location, > or a 2x2 block for each Jacobian location. > > > > Thanks, > > > > Matt > > > > the vectors contain twice the number of entries (e.g. first all u1s and > then all u2s). I would like to be sure that the entries of u1 and u2, which > are associated with the same element are located on the same processor. > > > > Is a pre-defined structure already available within PETSc to enlarge such > a single equation to store the entries of coupled equations? > > > > -\Delta u_1+c_{11} u_1+c_{12} u_2=f_1 > > -\Delta u_2+c_{21} u_1+c_{22} u_2=f_2 > > > > Would I still be able to use MatZeroRowsColumnsIS u1 and u2 independently > to enforce boundary conditions? MatZeroRowsColumnsIS(A, is, 1, x, b); > > > > I don?t know where to begin. I have so far only been exposed to using MATMPIAIJ > and MatSetValues to create and assign values to matrix entries > respectively. I would be grateful if you could provide the stepwise guide. > > > > Kind regards, > > Karthik. > > > > -- > > *Karthik Chockalingam, Ph.D.* > > Senior Research Software Engineer > > High Performance Systems Engineering Group > > Hartree Centre | Science and Technology Facilities Council > > karthikeyan.chockalingam at stfc.ac.uk > > > > *Error! Filename not specified.* > > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > > > > > -- > > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > > > https://www.cse.buffalo.edu/~knepley/ > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From msc.felipe.caro at gmail.com Sun Sep 24 04:59:12 2023 From: msc.felipe.caro at gmail.com (Felipe Caro) Date: Sun, 24 Sep 2023 11:59:12 +0200 Subject: [petsc-users] Issues with PETSc Configuration using gfortran-13 after Updating to Xcode 15 on MacOS Ventura 13.6 Message-ID: Hello PETSc Support Team, I hope this email finds you well. I need help configuring PETSc on my Mac running MacOS Ventura 13.6 with Xcode 15. I have recently updated my operating system and Xcode and am facing issues setting up PETSc with gfortran-13. Thank you for your assistance. System Information - MacOS Version: Ventura 13.6 - Xcode Version: 15 - gfortran Version: 13 (installed via Homebrew) - PETSc Version: [Your PETSc Version] Steps to Reproduce I followed the standard installation steps as outlined in the PETSc documentation. Below is the relevant section of the Bash script I used for configuration: #!/bin/bash # PETSc environment variables export PETSC_DIR=/path/to/petsc export PETSC_ARCH=arch-cmplx-opt # Configuration cd $PETSC_DIR ./configure --with-cc=gcc-13 --with-cxx=g++-13 --with-fc=gfortran-13 --with-f90=gfortran-13 \ --with-debugging=no --with-scalar-type=complex --with-openmp \ --download-mpich --download-fblaslapack --download-scalapack \ --download-mumps --download-metis --download-parmetis --download-hwloc \ COPTFLAGS="-O3" CXXOPTFLAGS="-O3" FOPTFLAGS="-Ofast" $PETSC_ARCH Error Message The configure script throws the following error: UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): Fortran compiler you provided with --with-fc=gfortran-13 cannot be found or does not work. Cannot compile/link FC with gfortran-13. To verify if gfortran-13 is working, I tested it by compiling a simple Fortran program, and it worked despite a linker warning related to duplicate libraries. Additional Information I also ran brew doctor to ensure my Homebrew setup was fine and no issues were found. Can you guide me on how to resolve this issue? I can also provide the configure.log file if that would be helpful for debugging. Thank you for your time and assistance. Best regards, Felipe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bsmith at petsc.dev Sun Sep 24 11:37:52 2023 From: bsmith at petsc.dev (Barry Smith) Date: Sun, 24 Sep 2023 12:37:52 -0400 Subject: [petsc-users] Issues with PETSc Configuration using gfortran-13 after Updating to Xcode 15 on MacOS Ventura 13.6 In-Reply-To: References: Message-ID: <1BB6AC77-A736-4BB4-9D69-D709A7C5A86B@petsc.dev> Please send configure.log to petsc-maint at mcs.anl .gov > On Sep 24, 2023, at 5:59 AM, Felipe Caro wrote: > > Hello PETSc Support Team, > > I hope this email finds you well. I need help configuring PETSc on my Mac running MacOS Ventura 13.6 with Xcode 15. I have recently updated my operating system and Xcode and am facing issues setting up PETSc with gfortran-13. > > Thank you for your assistance. > > System Information > MacOS Version: Ventura 13.6 > Xcode Version: 15 > gfortran Version: 13 (installed via Homebrew) > PETSc Version: [Your PETSc Version] > Steps to Reproduce > I followed the standard installation steps as outlined in the PETSc documentation. Below is the relevant section of the Bash script I used for configuration: > > #!/bin/bash > > # PETSc environment variables > export PETSC_DIR=/path/to/petsc > export PETSC_ARCH=arch-cmplx-opt > > # Configuration > cd $PETSC_DIR > ./configure --with-cc=gcc-13 --with-cxx=g++-13 --with-fc=gfortran-13 --with-f90=gfortran-13 \ > --with-debugging=no --with-scalar-type=complex --with-openmp \ > --download-mpich --download-fblaslapack --download-scalapack \ > --download-mumps --download-metis --download-parmetis --download-hwloc \ > COPTFLAGS="-O3" CXXOPTFLAGS="-O3" FOPTFLAGS="-Ofast" $PETSC_ARCH > > Error Message > The configure script throws the following error: > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > Fortran compiler you provided with --with-fc=gfortran-13 cannot be found or does not work. > Cannot compile/link FC with gfortran-13. > > To verify if gfortran-13 is working, I tested it by compiling a simple Fortran program, and it worked despite a linker warning related to duplicate libraries. > Additional Information > I also ran brew doctor to ensure my Homebrew setup was fine and no issues were found. > Can you guide me on how to resolve this issue? I can also provide the configure.log file if that would be helpful for debugging. > Thank you for your time and assistance. > > Best regards, > Felipe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From qiyuelu1 at gmail.com Sun Sep 24 14:47:45 2023 From: qiyuelu1 at gmail.com (Qiyue Lu) Date: Sun, 24 Sep 2023 14:47:45 -0500 Subject: [petsc-users] VecScale failed because the local size mismatch Message-ID: Hello, I have a vector (petsc_temp2) with size 1182 on my laptop without MPI. However, when I tried to call VecScale(petsc_temp2, 1.0/2.0); It failed with Cannot change/reset vector sizes to -1 local 1182 global after previously setting them to 1182 local 1182 global I wonder how this comes out and how the local size could be -1? Thanks Qiyue Lu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jroman at dsic.upv.es Mon Sep 25 01:25:04 2023 From: jroman at dsic.upv.es (Jose E. Roman) Date: Mon, 25 Sep 2023 08:25:04 +0200 Subject: [petsc-users] Orthogonalization of a (sparse) PETSc matrix In-Reply-To: <987DA5F8-DC3F-4199-828E-17D239DEC442@dsic.upv.es> References: <814F2E55-A62D-4799-B118-7DC706F1A65A@corintis.com> <987DA5F8-DC3F-4199-828E-17D239DEC442@dsic.upv.es> Message-ID: <8853B9D3-E367-4B17-87C3-EFCD4A089BCB@dsic.upv.es> Thanasis: I have finished the change that I mentioned in my previous email, the details are here https://gitlab.com/slepc/slepc/-/merge_requests/586 The change has been already merged into the main branch, and thus will be included in version 3.20, to be released on Friday this week. You should now be able to do bv = SLEPc.BV().createFromMat(A)) instead of bv = SLEPc.BV().createFromMat(A.convert('dense')) without error or cost penalty. Thanks. Jose > El 30 ago 2023, a las 9:17, Jose E. Roman escribi?: > > The conversion from MATAIJ to MATDENSE should be very cheap, see https://gitlab.com/petsc/petsc/-/blob/main/src/mat/impls/dense/seq/dense.c?ref_type=heads#L172 > > The matrix copy hidden inside createFromMat() is likely more expensive. I am currently working on a modification of BV that will be included in version 3.20 if everything goes well - then I think I can allow passing a sparse matrix to createFromMat() and do the conversion internally, avoiding the matrix copy. > > Jose > > >> El 29 ago 2023, a las 22:46, Thanasis Boutsikakis escribi?: >> >> Thanks Jose, >> >> This works indeed. However, I was under the impression that this conversion might be very costly for big matrices with low sparsity and it would scale with the number of non-zero values. >> >> Do you have any idea of the efficiency of this operation? >> >> Thanks >> >>> On 29 Aug 2023, at 19:13, Jose E. Roman wrote: >>> >>> The result of bv.orthogonalize() is most probably a dense matrix, and the result replaces the input matrix, that's why the input matrix is required to be dense. >>> >>> You can simply do this: >>> >>> bv = SLEPc.BV().createFromMat(A.convert('dense')) >>> >>> Jose >>> >>>> El 29 ago 2023, a las 18:50, Thanasis Boutsikakis escribi?: >>>> >>>> Hi all, I have the following code that orthogonalizes a PETSc matrix. The problem is that this implementation requires that the PETSc matrix is dense, otherwise, it fails at bv.SetFromOptions(). Hence the assert in orthogonality(). >>>> >>>> What could I do in order to be able to orthogonalize sparse matrices as well? Could I convert it efficiently? (I tried to no avail) >>>> >>>> Thanks! >>>> >>>> """Experimenting with matrix orthogonalization""" >>>> >>>> import contextlib >>>> import sys >>>> import time >>>> import numpy as np >>>> from firedrake import COMM_WORLD >>>> from firedrake.petsc import PETSc >>>> >>>> import slepc4py >>>> >>>> slepc4py.init(sys.argv) >>>> from slepc4py import SLEPc >>>> >>>> from numpy.testing import assert_array_almost_equal >>>> >>>> EPSILON_USER = 1e-4 >>>> EPS = sys.float_info.epsilon >>>> >>>> >>>> def Print(message: str): >>>> """Print function that prints only on rank 0 with color >>>> >>>> Args: >>>> message (str): message to be printed >>>> """ >>>> PETSc.Sys.Print(message) >>>> >>>> >>>> def create_petsc_matrix(input_array, sparse=True): >>>> """Create a PETSc matrix from an input_array >>>> >>>> Args: >>>> input_array (np array): Input array >>>> partition_like (PETSc mat, optional): Petsc matrix. Defaults to None. >>>> sparse (bool, optional): Toggle for sparese or dense. Defaults to True. >>>> >>>> Returns: >>>> PETSc mat: PETSc matrix >>>> """ >>>> # Check if input_array is 1D and reshape if necessary >>>> assert len(input_array.shape) == 2, "Input array should be 2-dimensional" >>>> global_rows, global_cols = input_array.shape >>>> >>>> size = ((None, global_rows), (global_cols, global_cols)) >>>> >>>> # Create a sparse or dense matrix based on the 'sparse' argument >>>> if sparse: >>>> matrix = PETSc.Mat().createAIJ(size=size, comm=COMM_WORLD) >>>> else: >>>> matrix = PETSc.Mat().createDense(size=size, comm=COMM_WORLD) >>>> matrix.setUp() >>>> >>>> local_rows_start, local_rows_end = matrix.getOwnershipRange() >>>> >>>> for counter, i in enumerate(range(local_rows_start, local_rows_end)): >>>> # Calculate the correct row in the array for the current process >>>> row_in_array = counter + local_rows_start >>>> matrix.setValues( >>>> i, range(global_cols), input_array[row_in_array, :], addv=False >>>> ) >>>> >>>> # Assembly the matrix to compute the final structure >>>> matrix.assemblyBegin() >>>> matrix.assemblyEnd() >>>> >>>> return matrix >>>> >>>> >>>> def orthogonality(A): # sourcery skip: avoid-builtin-shadow >>>> """Checking and correcting orthogonality >>>> >>>> Args: >>>> A (PETSc.Mat): Matrix of size [m x k]. >>>> >>>> Returns: >>>> PETSc.Mat: Matrix of size [m x k]. >>>> """ >>>> # Check if the matrix is dense >>>> mat_type = A.getType() >>>> assert mat_type in ( >>>> "seqdense", >>>> "mpidense", >>>> ), "A must be a dense matrix. SLEPc.BV().createFromMat() requires a dense matrix." >>>> >>>> m, k = A.getSize() >>>> >>>> Phi1 = A.getColumnVector(0) >>>> Phi2 = A.getColumnVector(k - 1) >>>> >>>> # Compute dot product using PETSc function >>>> dot_product = Phi1.dot(Phi2) >>>> >>>> if abs(dot_product) > min(EPSILON_USER, EPS * m): >>>> Print(" Matrix is not orthogonal") >>>> >>>> # Type can be CHOL, GS, mro(), SVQB, TSQR, TSQRCHOL >>>> _type = SLEPc.BV().OrthogBlockType.GS >>>> >>>> bv = SLEPc.BV().createFromMat(A) >>>> bv.setFromOptions() >>>> bv.setOrthogonalization(_type) >>>> bv.orthogonalize() >>>> >>>> A = bv.createMat() >>>> >>>> Print(" Matrix successfully orthogonalized") >>>> >>>> # # Assembly the matrix to compute the final structure >>>> if not A.assembled: >>>> A.assemblyBegin() >>>> A.assemblyEnd() >>>> else: >>>> Print(" Matrix is orthogonal") >>>> >>>> return A >>>> >>>> >>>> # -------------------------------------------- >>>> # EXP: Orthogonalization of an mpi PETSc matrix >>>> # -------------------------------------------- >>>> >>>> m, k = 11, 7 >>>> # Generate the random numpy matrices >>>> np.random.seed(0) # sets the seed to 0 >>>> A_np = np.random.randint(low=0, high=6, size=(m, k)) >>>> >>>> A = create_petsc_matrix(A_np, sparse=False) >>>> >>>> A_orthogonal = orthogonality(A) >>>> >>>> # -------------------------------------------- >>>> # TEST: Orthogonalization of a numpy matrix >>>> # -------------------------------------------- >>>> # Generate A_np_orthogonal >>>> A_np_orthogonal, _ = np.linalg.qr(A_np) >>>> >>>> # Get the local values from A_orthogonal >>>> local_rows_start, local_rows_end = A_orthogonal.getOwnershipRange() >>>> A_orthogonal_local = A_orthogonal.getValues( >>>> range(local_rows_start, local_rows_end), range(k) >>>> ) >>>> >>>> # Assert the correctness of the multiplication for the local subset >>>> assert_array_almost_equal( >>>> np.abs(A_orthogonal_local), >>>> np.abs(A_np_orthogonal[local_rows_start:local_rows_end, :]), >>>> decimal=5, >>>> ) >>> >> > From msc.felipe.caro at gmail.com Mon Sep 25 02:42:37 2023 From: msc.felipe.caro at gmail.com (Felipe Caro) Date: Mon, 25 Sep 2023 09:42:37 +0200 Subject: [petsc-users] Issues with PETSc Configuration using gfortran-13 after Updating to Xcode 15 on MacOS Ventura 13.6 In-Reply-To: <1BB6AC77-A736-4BB4-9D69-D709A7C5A86B@petsc.dev> References: <1BB6AC77-A736-4BB4-9D69-D709A7C5A86B@petsc.dev> Message-ID: Hello PETSc Support Team, I hope this email finds you well. I need help configuring PETSc on my Mac running MacOS Ventura 13.6 with Xcode 15. I have recently updated my operating system and Xcode and am facing issues setting up PETSc with gfortran-13. Thank you for your assistance. System Information - MacOS Version: Ventura 13.6 - Xcode Version: 15 - gfortran Version: 13 (installed via Homebrew) - PETSc Version: [Your PETSc Version] Steps to Reproduce I followed the standard installation steps as outlined in the PETSc documentation. Below is the relevant section of the Bash script I used for configuration: #!/bin/bash # PETSc environment variables export PETSC_DIR=/path/to/petsc export PETSC_ARCH=arch-cmplx-opt # Configuration cd $PETSC_DIR ./configure --with-cc=gcc-13 --with-cxx=g++-13 --with-fc=gfortran-13 --with-f90=gfortran-13 \ --with-debugging=no --with-scalar-type=complex --with-openmp \ --download-mpich --download-fblaslapack --download-scalapack \ --download-mumps --download-metis --download-parmetis --download-hwloc \ COPTFLAGS="-O3" CXXOPTFLAGS="-O3" FOPTFLAGS="-Ofast" $PETSC_ARCH Error Message The configure script throws the following error: UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): Fortran compiler you provided with --with-fc=gfortran-13 cannot be found or does not work. Cannot compile/link FC with gfortran-13. To verify if gfortran-13 is working, I tested it by compiling a simple Fortran program, and it worked despite a linker warning related to duplicate libraries. Additional Information I also ran brew doctor to ensure my Homebrew setup was fine and no issues were found. Can you guide me on how to resolve this issue? I can also provide the configure.log file if that would be helpful for debugging. Thank you for your time and assistance. I am attaching my config.log Best Regards, Felipe. El dom, 24 sept 2023 a la(s) 18:38, Barry Smith (bsmith at petsc.dev) escribi?: > > Please send configure.log to petsc-maint at mcs.anl.gov > > On Sep 24, 2023, at 5:59 AM, Felipe Caro > wrote: > > Hello PETSc Support Team, > > I hope this email finds you well. I need help configuring PETSc on my Mac > running MacOS Ventura 13.6 with Xcode 15. I have recently updated my > operating system and Xcode and am facing issues setting up PETSc with > gfortran-13. > > Thank you for your assistance. > > System Information > > - MacOS Version: Ventura 13.6 > - Xcode Version: 15 > - gfortran Version: 13 (installed via Homebrew) > - PETSc Version: [Your PETSc Version] > > Steps to Reproduce > I followed the standard installation steps as outlined in the PETSc > documentation. Below is the relevant section of the Bash script I used for > configuration: > > #!/bin/bash > > # PETSc environment variables > export PETSC_DIR=/path/to/petsc > export PETSC_ARCH=arch-cmplx-opt > > # Configuration > cd $PETSC_DIR > ./configure --with-cc=gcc-13 --with-cxx=g++-13 --with-fc=gfortran-13 > --with-f90=gfortran-13 \ > --with-debugging=no --with-scalar-type=complex --with-openmp \ > --download-mpich --download-fblaslapack --download-scalapack \ > --download-mumps --download-metis --download-parmetis --download-hwloc \ > COPTFLAGS="-O3" CXXOPTFLAGS="-O3" FOPTFLAGS="-Ofast" $PETSC_ARCH > > Error Message > The configure script throws the following error: > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > Fortran compiler you provided with --with-fc=gfortran-13 cannot be found > or does not work. > Cannot compile/link FC with gfortran-13. > > To verify if gfortran-13 is working, I tested it by compiling a simple > Fortran program, and it worked despite a linker warning related to > duplicate libraries. > Additional Information > I also ran brew doctor to ensure my Homebrew setup was fine and no issues > were found. > Can you guide me on how to resolve this issue? I can also provide the > configure.log file if that would be helpful for debugging. > Thank you for your time and assistance. > > Best regards, > Felipe. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: installopt.sh Type: application/x-sh Size: 1054 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PETSc_opt_25-09-2023_09.41.50.log Type: application/octet-stream Size: 4335 bytes Desc: not available URL: From mfadams at lbl.gov Mon Sep 25 06:15:20 2023 From: mfadams at lbl.gov (Mark Adams) Date: Mon, 25 Sep 2023 07:15:20 -0400 Subject: [petsc-users] VecScale failed because the local size mismatch In-Reply-To: References: Message-ID: That is strange. Do you have the error handling code in VecSet that you are just not showing here? This error comes from VecSetSizes. Mark On Sun, Sep 24, 2023 at 3:49?PM Qiyue Lu wrote: > Hello, > I have a vector (petsc_temp2) with size 1182 on my laptop without MPI. > However, when I tried to call > VecScale(petsc_temp2, 1.0/2.0); > It failed with > Cannot change/reset vector sizes to -1 local 1182 global after previously > setting them to 1182 local 1182 global > > I wonder how this comes out and how the local size could be -1? > > Thanks > Qiyue Lu > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Mon Sep 25 06:48:53 2023 From: knepley at gmail.com (Matthew Knepley) Date: Mon, 25 Sep 2023 07:48:53 -0400 Subject: [petsc-users] VecScale failed because the local size mismatch In-Reply-To: References: Message-ID: On Sun, Sep 24, 2023 at 3:49?PM Qiyue Lu wrote: > Hello, > I have a vector (petsc_temp2) with size 1182 on my laptop without MPI. > However, when I tried to call > VecScale(petsc_temp2, 1.0/2.0); > It failed with > Cannot change/reset vector sizes to -1 local 1182 global after previously > setting them to 1182 local 1182 global > 1) Use PetscCall() to check all PETSc calls 2) Send the entire error output Thanks, Matt > I wonder how this comes out and how the local size could be -1? > > Thanks > Qiyue Lu > > > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From amessikh at yahoo.com Mon Sep 25 03:33:06 2023 From: amessikh at yahoo.com (Azeddine Messikh) Date: Mon, 25 Sep 2023 08:33:06 +0000 (UTC) Subject: [petsc-users] Boundary integral problem References: <1621606128.5024918.1695630786287.ref@mail.yahoo.com> Message-ID: <1621606128.5024918.1695630786287@mail.yahoo.com> Dear developers I tried to run ex24.c https://petsc.org/release/src/snes/tutorials/ex24.c.html using the following command line ./ex24 -sol_type quadratic -dm_plex_simplex 0? -field_petscspace_degree 1 -potential_petscspace_degree 1 -dm_plex_box_faces 2,1 I discovered that at 254: PetscCall(PetscWeakFormSetIndexBdResidual(wf, label, 1, 0, 0, 0, f0_bd_quadratic_q, 0, NULL));?reverses the value of the integrals at the top only. That isThe boundary integral corresponding to node 5 becomes that of 4 and vise-versa. Same thing for nodes 5 and 6. The mesh index is as follows *4---*5---*6 ?|?????? |????? | ?|?????? |????? |*1--- *2---*3 However,? if I use? -dm_plex_simplex 1 there is no problem. The model is in the form Au = b the value of b with? "-dm_plex_simplex 0" is[0.25 0.0104167 0. 0. 0.145833 0. -0.583333 0.177083 0. 0.0833333 -0.28125 0. 0. -0.6875 0. -0.75 -0.364583 0.] and for -dm_plex_simplex 1 [0.0833333 0.0104167 0. 0. 0.145833 0. -0.583333 0.177083 0. 0.25 -0.260417 0. 1.43404e-16 -0.645833 0. -0.75 -0.427083 0.] you can see that the value at node 1 =0.25? and node 4 = 0.0833333 ( simplex 0) which is reversed, that is, ? ?? node 4 =0.25? and node 1 = 0.0833333 (simplex 1) So, my own calculation shows that at node 1 should be 0.083333 not 0.25.The -dm_plex_simplex 1 gives the correct answer but -dm_plex_simplex 0 gives wrong answer. Would you please help me in this matter.?Sincerely yoursAzeddine M? ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From ivanluthfi5 at gmail.com Mon Sep 25 15:11:25 2023 From: ivanluthfi5 at gmail.com (Ivan Luthfi) Date: Tue, 26 Sep 2023 04:11:25 +0800 Subject: [petsc-users] I cannot find my libpetsc.a in my installation pets-3.4.5 Message-ID: Dear developers, I cannot find libpetsc.a in my library. Do you have any suggestion how can I figure this out. From balay at mcs.anl.gov Mon Sep 25 15:20:27 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Mon, 25 Sep 2023 15:20:27 -0500 (CDT) Subject: [petsc-users] I cannot find my libpetsc.a in my installation pets-3.4.5 In-Reply-To: References: Message-ID: What are you looking at? Send 'ls' from PETSC_DIR/PETSC_ARCH/lib Perhaps its a shared library build - and you have libpetsc.so? BTW: the current release is 3.19 - and you are attempting to build a super old version 3.4. We recommend using the latest version to avoid build and other compatibility issues. Satish On Tue, 26 Sep 2023, Ivan Luthfi wrote: > Dear developers, > I cannot find libpetsc.a in my library. > Do you have any suggestion how can I figure this out. > From ivanluthfi5 at gmail.com Mon Sep 25 19:27:18 2023 From: ivanluthfi5 at gmail.com (Ivan Luthfi) Date: Tue, 26 Sep 2023 08:27:18 +0800 Subject: [petsc-users] I cannot find my libpetsc.a in my installation pets-3.4.5 In-Reply-To: References: Message-ID: the reason I install the old version is because i try to run an old code file that was compiled with the same version On Tue, Sep 26, 2023 at 4:20 AM Satish Balay wrote: > > What are you looking at? Send 'ls' from PETSC_DIR/PETSC_ARCH/lib > > Perhaps its a shared library build - and you have libpetsc.so? > > BTW: the current release is 3.19 - and you are attempting to build a super > old version 3.4. > > We recommend using the latest version to avoid build and other > compatibility issues. > > Satish > > On Tue, 26 Sep 2023, Ivan Luthfi wrote: > > > Dear developers, > > I cannot find libpetsc.a in my library. > > Do you have any suggestion how can I figure this out. > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Mon Sep 25 19:44:13 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Mon, 25 Sep 2023 19:44:13 -0500 (CDT) Subject: [petsc-users] I cannot find my libpetsc.a in my installation pets-3.4.5 In-Reply-To: References: Message-ID: <6eb555a7-73b9-9637-d833-4dcb1a7702fa@mcs.anl.gov> We generally recommend getting a basic build going for such use case - and then migrate it to latest version as old versions have more issues [as you might be encountering now] Also - you haven't responded to my follow-up regarding the issue you are encountering. If you are having build issues - you might want to recheck the installation instructions (for petsc-3.4) - and send us relevant logs. Satish On Tue, 26 Sep 2023, Ivan Luthfi wrote: > the reason I install the old version is because i try to run an old code > file that was compiled with the same version > > On Tue, Sep 26, 2023 at 4:20 AM Satish Balay wrote: > > > > > What are you looking at? Send 'ls' from PETSC_DIR/PETSC_ARCH/lib > > > > Perhaps its a shared library build - and you have libpetsc.so? > > > > BTW: the current release is 3.19 - and you are attempting to build a super > > old version 3.4. > > > > We recommend using the latest version to avoid build and other > > compatibility issues. > > > > Satish > > > > On Tue, 26 Sep 2023, Ivan Luthfi wrote: > > > > > Dear developers, > > > I cannot find libpetsc.a in my library. > > > Do you have any suggestion how can I figure this out. > > > > > > > > From ivanluthfi5 at gmail.com Mon Sep 25 19:49:18 2023 From: ivanluthfi5 at gmail.com (Ivan Luthfi) Date: Tue, 26 Sep 2023 08:49:18 +0800 Subject: [petsc-users] I cannot find my libpetsc.a in my installation pets-3.4.5 In-Reply-To: <6eb555a7-73b9-9637-d833-4dcb1a7702fa@mcs.anl.gov> References: <6eb555a7-73b9-9637-d833-4dcb1a7702fa@mcs.anl.gov> Message-ID: Sorry, In the petsc_lib i only found out the libpetsc.so, but not libpetsc.a, are they functionality the same ? thank you for your recommendation, i will try as your recommendation step by step, because the code uses some deprecated function that I have to changed to be compiled in the latest version On Tue, Sep 26, 2023 at 8:44 AM Satish Balay wrote: > We generally recommend getting a basic build going for such use case - > and then migrate it to latest version as old versions have more issues > [as you might be encountering now] > > Also - you haven't responded to my follow-up regarding the issue you > are encountering. > > If you are having build issues - you might want to recheck the > installation instructions (for petsc-3.4) - and send us relevant logs. > > Satish > > On Tue, 26 Sep 2023, Ivan Luthfi wrote: > > > the reason I install the old version is because i try to run an old code > > file that was compiled with the same version > > > > On Tue, Sep 26, 2023 at 4:20 AM Satish Balay wrote: > > > > > > > > What are you looking at? Send 'ls' from PETSC_DIR/PETSC_ARCH/lib > > > > > > Perhaps its a shared library build - and you have libpetsc.so? > > > > > > BTW: the current release is 3.19 - and you are attempting to build a > super > > > old version 3.4. > > > > > > We recommend using the latest version to avoid build and other > > > compatibility issues. > > > > > > Satish > > > > > > On Tue, 26 Sep 2023, Ivan Luthfi wrote: > > > > > > > Dear developers, > > > > I cannot find libpetsc.a in my library. > > > > Do you have any suggestion how can I figure this out. > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Mon Sep 25 19:58:05 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Mon, 25 Sep 2023 19:58:05 -0500 (CDT) Subject: [petsc-users] I cannot find my libpetsc.a in my installation pets-3.4.5 In-Reply-To: References: <6eb555a7-73b9-9637-d833-4dcb1a7702fa@mcs.anl.gov> Message-ID: On Tue, 26 Sep 2023, Ivan Luthfi wrote: > Sorry, In the petsc_lib i only found out the libpetsc.so, but not > libpetsc.a, > > are they functionality the same ? yes. You would run 'make check' after the build - to verify if PETSc examples are able to compile, link correctly [to this libpetsc.so] - and run And then - you should be able to use it similarly with your application code. If there are issues with building your application code - compare the compile command used for the petsc examples with the compile command used for your application code Note: configure option --with-shared-libraries=1 [default] builds petsc shared library - i.e libpetsc.so. And if you use --with-shared-libraries=0 - it will build petsc as static library - i.e libpetsc.a A compiler (linker) will look for shared library and use it if found. If not found - it will look for a static version of the library - and use it if found. Satish > > thank you for your recommendation, i will try as your recommendation step > by step, because the code uses some deprecated function that I have to > changed to be compiled in the latest version > > On Tue, Sep 26, 2023 at 8:44 AM Satish Balay wrote: > > > We generally recommend getting a basic build going for such use case - > > and then migrate it to latest version as old versions have more issues > > [as you might be encountering now] > > > > Also - you haven't responded to my follow-up regarding the issue you > > are encountering. > > > > If you are having build issues - you might want to recheck the > > installation instructions (for petsc-3.4) - and send us relevant logs. > > > > Satish > > > > On Tue, 26 Sep 2023, Ivan Luthfi wrote: > > > > > the reason I install the old version is because i try to run an old code > > > file that was compiled with the same version > > > > > > On Tue, Sep 26, 2023 at 4:20 AM Satish Balay wrote: > > > > > > > > > > > What are you looking at? Send 'ls' from PETSC_DIR/PETSC_ARCH/lib > > > > > > > > Perhaps its a shared library build - and you have libpetsc.so? > > > > > > > > BTW: the current release is 3.19 - and you are attempting to build a > > super > > > > old version 3.4. > > > > > > > > We recommend using the latest version to avoid build and other > > > > compatibility issues. > > > > > > > > Satish > > > > > > > > On Tue, 26 Sep 2023, Ivan Luthfi wrote: > > > > > > > > > Dear developers, > > > > > I cannot find libpetsc.a in my library. > > > > > Do you have any suggestion how can I figure this out. > > > > > > > > > > > > > > > > > > > > > From inturu.srinivas2020 at vitstudent.ac.in Tue Sep 26 11:04:49 2023 From: inturu.srinivas2020 at vitstudent.ac.in (INTURU SRINIVAS 20PHD0548) Date: Tue, 26 Sep 2023 21:34:49 +0530 Subject: [petsc-users] Error while building PETSc with MATLAB In-Reply-To: <3AF4D6DD-D536-4A17-8C07-2F7FBB34078A@petsc.dev> References: <07d75222-fe7f-3025-2f1e-1b8059f7bb7d@mcs.anl.gov> <361a87cb-a5c7-3145-06d4-e6dd81c10277@mcs.anl.gov> <02d23617-cdfd-9b93-084f-8ff851d71522@mcs.anl.gov> <79d53f28-1f4a-b494-7e41-02ba75db97aa@mcs.anl.gov> <2168f3b5-4913-e7aa-bb8e-abc98b8bdd31@mcs.anl.gov> <752d85e2-4641-0082-f0a3-54bd8ed6dcb8@mcs.anl.gov> <5FE30E52-A88C-47D3-A81D-EE9028FA7735@petsc.dev> <67B7E3F1-F2B2-491D-964F-F0835BCD6A18@petsc.dev> <35978ADC-57E1-4422-A14D-49E43ED91FA3@petsc.dev> <58283126-56CF-4741-B264-3C7E68AA3655@petsc.dev> <3AF4D6DD-D536-4A17-8C07-2F7FBB34078A@petsc.dev> Message-ID: Hi everyone, With the help of the Matlab technical support team the issue is resolved. The error is associated with setting the PATH for MATLAB. This is resolved using the following commands before configuring PETSc with Matlab. *LD_LIBRARY_PATH=matlabroot/bin/glnxa64:matlabroot/sys/os/glnxa64:LD_LIBRARY_PATH * *export LD_LIBRARY_PATH* Now, PETSc with Matlab is successfully built. Thank you to everyone for all of your support. With regards Srinivas On Sat, Sep 9, 2023 at 11:52?PM Barry Smith wrote: > > I don't understand. The directory only has two files in it? They begin > with libMatlab? My directory has over 100 files. > > Barry > > > On Sep 9, 2023, at 1:24 AM, INTURU SRINIVAS 20PHD0548 < > inturu.srinivas2020 at vitstudent.ac.in> wrote: > > I am sending the outputs available in the directory > /usr/local/MATLAB/R2020b/extern/bin/glnxa64. > Please find the attached files. > > > Thanks and regards > Srinivas > > On Fri, Sep 8, 2023 at 11:58?PM Barry Smith wrote: > >> >> I expect a libmx.so in the >> directory /usr/local/MATLAB/R2020b/extern/bin/glnxa64. Do an ls on that >> directory and send all the output >> >> >> >> On Sep 8, 2023, at 10:33 AM, INTURU SRINIVAS 20PHD0548 < >> inturu.srinivas2020 at vitstudent.ac.in> wrote: >> >> Hi Barry, >> >> I tried to run Matlab Engine C example provided in the link " >> https://in.mathworks.com/help/matlab/matlab_external/build-unix-engine-example.html >> " >> >> *in Matlab:* copyfile(fullfile(matlabroot,'extern','examples','eng_mat','engdemo.c'),'.','f') >> mex -v -client engine engdemo.c >> >> *in linux terminal :* LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64 >> >> export LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH >> >> *./engdemo* >> ./engdemo: error while loading shared libraries: libmx.so: cannot open shared object file: No such file or directory >> >> how to sort out this error? Is this the right way to check MatlabEngine with C? >> >> Thanks and regards >> >> Srinivas >> >> >> >> On Wed, Sep 6, 2023 at 11:47?PM Barry Smith wrote: >> >>> >>> Ok, so the C++ binding for Matlab engine is working on your machine. >>> PETSc uses the C binding which links against different libraries but, one >>> would think the C binding would work for sure if the C++ binding works. Can >>> you try a Matlab Engine C example provided by Matlab? >>> >>> >>> >>> >>> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 < >>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> >>> Hi Amneet, >>> >>> I repeated the same procedure again and this time it is working. >>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp >>> -lMatlabDataArray -lMatlabEngine* >>> >>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >>> *$export LD_LIBRARY_PATH* >>> *$./a.out* >>> Square root of -2 is 0 + 1.41421i >>> Square root of 2 is 1.41421 + 0i >>> Square root of 6 is 2.44949 + 0i >>> Square root of 8 is 2.82843 + 0i >>> I don't know how it is working this time? >>> >>> Thanks and regards >>> Srinivas >>> >>> >>> On Wed, Sep 6, 2023 at 12:17?PM INTURU SRINIVAS 20PHD0548 < >>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>> >>>> Hi Amneet, >>>> I tried the following example to run a matlab engine. >>>> >>>> #include "MatlabDataArray.hpp" >>>> #include "MatlabEngine.hpp" >>>> #include >>>> void callSQRT() { >>>> >>>> using namespace matlab::engine; >>>> >>>> // Start MATLAB engine synchronously >>>> std::unique_ptr matlabPtr = startMATLAB(); >>>> >>>> //Create MATLAB data array factory >>>> matlab::data::ArrayFactory factory; >>>> >>>> // Define a four-element typed array >>>> matlab::data::TypedArray const argArray = >>>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 }); >>>> >>>> // Call MATLAB sqrt function on the data array >>>> matlab::data::Array const results = matlabPtr->feval(u"sqrt", >>>> argArray); >>>> >>>> // Display results >>>> for (int i = 0; i < results.getNumberOfElements(); i++) { >>>> double a = argArray[i]; >>>> std::complex v = results[i]; >>>> double realPart = v.real(); >>>> double imgPart = v.imag(); >>>> std::cout << "Square root of " << a << " is " << >>>> realPart << " + " << imgPart << "i" << std::endl; >>>> } >>>> } >>>> >>>> int main() { >>>> callSQRT(); >>>> return 0; >>>> } >>>> >>>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L >>>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp >>>> -lMatlabDataArray -lMatlabEngine* >>>> >>>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64* >>>> *$export LD_LIBRARY_PATH* >>>> *$./a.out* >>>> Starting >>>> Error: The import statement 'import matlab.internal.engine.input' >>>> cannot be found or cannot be imported. Imported names must end with '.*' or >>>> be fully qualified. >>>> >>>> terminate called after throwing an instance of >>>> 'matlab::engine::EngineException' >>>> what(): MATLAB process cannot be created. >>>> Aborted (core dumped) >>>> >>>> I got the above error for Matlab R2020b. Please help me to sort out >>>> this. >>>> >>>> Thanks and regards >>>> Srinivas >>>> >>>> On Tue, Sep 5, 2023 at 11:39?PM Amneet Bhalla >>>> wrote: >>>> >>>>> BTW, what Barry is suggesting is the following: >>>>> >>>>> Compile a sample code with a command line this: >>>>> >>>>> >>>>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/ >>>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine >>>>> >>>>> >>>>> This command is provided here: >>>>> >>>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html >>>>> >>>>> >>>>> A sample MATLAB code is here: >>>>> >>>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html >>>>> >>>>> >>>>> (You can just pick a few lines of code from here to create a barebone example) >>>>> >>>>> >>>>> On Tue, Sep 5, 2023 at 11:02?AM Amneet Bhalla >>>>> wrote: >>>>> >>>>>> Srinivas --- Do you have a different version of MATLAB that you can >>>>>> install? If your organization has a MATLAB license, you can install recent >>>>>> versions of MATLAB from mathworks.com >>>>>> >>>>>> On Tue, Sep 5, 2023 at 10:37?AM Barry Smith wrote: >>>>>> >>>>>>> >>>>>>> Ok, I have no suggestions. It seems to be more an issue with the >>>>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine >>>>>>> (in the Matlab documentation) and try it to see if it works. >>>>>>> >>>>>>> Barry >>>>>>> >>>>>>> >>>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 < >>>>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>> >>>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen(""); >>>>>>> I got the same errors for petsc 3.17.5 >>>>>>> >>>>>>> >>>>>>> *make all* >>>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o >>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> MEX completed successfully. >>>>>>> Building with 'gcc'. >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>> In function ?PetscBinaryWrite?: >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>> [-Wmaybe-uninitialized] >>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>> | ^ >>>>>>> >>>>>>> MEX completed successfully. >>>>>>> ========================================= >>>>>>> ========================================= >>>>>>> Now to check if the libraries are working do: >>>>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check >>>>>>> >>>>>>> *make test query=requires queryval=matlab >>>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>> queryval=matlab query=requires >>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>> -------------------------------------------------------------- >>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>>> shooting. >>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>> Tue Sep 5 21:39:22 2023 >>>>>>> # [0]PETSC ERROR: Configure options >>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 >>>>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>> --known-64-bit-blas-indices=1 >>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83 >>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332 >>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245 >>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>> # [0]PETSC ERROR: #9 main() at >>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>> # with errorcode 85. >>>>>>> # >>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>>>>> # You may or may not see output from other processes, depending on >>>>>>> # exactly when Open MPI kills them. >>>>>>> # >>>>>>> -------------------------------------------------------------------------- >>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>> >>>>>>> >>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>> # >>>>>>> # To rerun failed tests: >>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>> >>>>>>> Thanks and regards >>>>>>> Srinivas >>>>>>> >>>>>>> On Tue, Sep 5, 2023 at 9:05?PM Barry Smith wrote: >>>>>>> >>>>>>>> >>>>>>>> The error is occuring during >>>>>>>> >>>>>>>> e->ep = engOpen(buffer); >>>>>>>> >>>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab >>>>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to >>>>>>>> assume the problem is occuring when engOpen() is attempting to connect the >>>>>>>> stdout and stdin from the Matlab session that is launched to the >>>>>>>> executable. >>>>>>>> >>>>>>>> You can try the following. In 3.17.5 edit the >>>>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line >>>>>>>> >>>>>>>> e->ep = engOpen(buffer); >>>>>>>> >>>>>>>> replace it with >>>>>>>> >>>>>>>> e->ep = engOpen(""); >>>>>>>> >>>>>>>> Now in the PETSc directory do make all (it should recompile one >>>>>>>> file) and then run the >>>>>>>> >>>>>>>> make test query=requires queryval=matlab >>>>>>>> DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> >>>>>>>> again >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via >>>>>>>> petsc-users wrote: >>>>>>>> >>>>>>>> Hi Amneeth, >>>>>>>> >>>>>>>> I think the errors are different with petsc 3.17.5 >>>>>>>> >>>>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx >>>>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>> >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> The version of PETSc you are using is out-of-date, we recommend >>>>>>>> updating to the new release >>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5 >>>>>>>> https://petsc.org/release/download/ >>>>>>>> >>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>>>>>> >>>>>>>> ============================================================================================= >>>>>>>> Configuring PETSc to compile on your >>>>>>>> system >>>>>>>> >>>>>>>> ============================================================================================= >>>>>>>> Compilers: >>>>>>>> >>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings >>>>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector >>>>>>>> -fvisibility=hidden -O3 >>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings >>>>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC >>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall >>>>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3 >>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>> Linkers: >>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall >>>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch >>>>>>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>> BlasLapack: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread >>>>>>>> uses OpenMP; use export OMP_NUM_THREADS=

or -omp_num_threads >>>>>>>>

to control the number of threads >>>>>>>> uses 8 byte integers >>>>>>>> MPI: >>>>>>>> Version: 3 >>>>>>>> mpiexec: /usr/bin/mpiexec >>>>>>>> Implementation: openmpi >>>>>>>> OMPI_VERSION: 4.0.3 >>>>>>>> pthread: >>>>>>>> cmake: >>>>>>>> Version: 3.16.3 >>>>>>>> /usr/bin/cmake >>>>>>>> regex: >>>>>>>> Matlab: >>>>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>> /usr/local/MATLAB/R2020b >>>>>>>> MatlabEngine: >>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat >>>>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher >>>>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c >>>>>>>> Language used to compile PETSc: C >>>>>>>> PETSc: >>>>>>>> PETSC_ARCH: linux-opt >>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>> Prefix: >>>>>>>> Scalar type: real >>>>>>>> Precision: double >>>>>>>> Support for __float128 >>>>>>>> Integer size: 4 bytes >>>>>>>> Single library: yes >>>>>>>> Shared libraries: yes >>>>>>>> Memory alignment from malloc(): 16 bytes >>>>>>>> Using GNU make: /usr/bin/make >>>>>>>> >>>>>>>> xxx=========================================================================xxx >>>>>>>> Configure stage complete. Now build PETSc libraries with: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 >>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>> >>>>>>>> xxx=========================================================================xxx >>>>>>>> >>>>>>>> *$make* >>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5 >>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>>> [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> MEX completed successfully. >>>>>>>> Building with 'gcc'. >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>> In function ?PetscBinaryWrite?: >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6: >>>>>>>> warning: ?err? may be used uninitialized in this function >>>>>>>> [-Wmaybe-uninitialized] >>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); >>>>>>>> | ^ >>>>>>>> >>>>>>>> MEX completed successfully. >>>>>>>> ========================================= >>>>>>>> ========================================= >>>>>>>> Now to check if the libraries are working do: >>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt >>>>>>>> check >>>>>>>> >>>>>>>> *$make test query=requires queryval=matlab >>>>>>>> DATAFILESPATH=/home/vit/datafiles/* >>>>>>>> /usr/bin/python3 >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py >>>>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt >>>>>>>> --testdir=./linux-opt/tests >>>>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>> queryval=matlab query=requires >>>>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85 >>>>>>>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>> -------------------------------------------------------------- >>>>>>>> # [0]PETSC ERROR: Error in external library >>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with >>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble >>>>>>>> shooting. >>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022 >>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit >>>>>>>> Tue Sep 5 10:15:57 2023 >>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc >>>>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 >>>>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0 >>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82 >>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331 >>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244 >>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144 >>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020 >>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131 >>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990 >>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407 >>>>>>>> # [0]PETSC ERROR: #9 main() at >>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305 >>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0 >>>>>>>> # [0]PETSC ERROR: -error_output_stdout >>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1 >>>>>>>> # [0]PETSC ERROR: -malloc_dump >>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>> # [0]PETSC ERROR: -pc_type lu >>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0 >>>>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send >>>>>>>> entire error message to petsc-maint at mcs.anl.gov---------- >>>>>>>> # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>>>>>> # with errorcode 85. >>>>>>>> # >>>>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>> processes. >>>>>>>> # You may or may not see output from other processes, depending on >>>>>>>> # exactly when Open MPI kills them. >>>>>>>> # >>>>>>>> -------------------------------------------------------------------------- >>>>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>> >>>>>>>> >>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>> # >>>>>>>> # To rerun failed tests: >>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>> >>>>>>>> To get the info of the error there is no specific probe id reported. >>>>>>>> >>>>>>>> How to check error info and proceed further? >>>>>>>> >>>>>>>> Thanks and regards >>>>>>>> Srinivas >>>>>>>> >>>>>>>> On Tue, Sep 5, 2023 at 1:08?AM Amneet Bhalla >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new >>>>>>>>> configure options that Satish mentioned? >>>>>>>>> >>>>>>>>> On Sun, Sep 3, 2023 at 10:19?PM INTURU SRINIVAS 20PHD0548 via >>>>>>>>> petsc-users wrote: >>>>>>>>> >>>>>>>>>> Sorry for missing that. >>>>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>>> -nosplash* >>>>>>>>>> >>>>>>>>>> < M A T L A B (R) > >>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc. >>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64) >>>>>>>>>> November 23, 2020 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> To get started, type doc. >>>>>>>>>> For product information, visit www.mathworks.com. >>>>>>>>>> >>>>>>>>>> Thanks and regards >>>>>>>>>> Srinivas >>>>>>>>>> >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19?AM Satish Balay >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> You are missing one more step: >>>>>>>>>>> >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash >>>>>>>>>>> >>>>>>>>>>> No run matlab manually on "MB108SMEC028" with the command >>>>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" >>>>>>>>>>> >>>>>>>>>>> Does this work for you? As the message indicates this command is >>>>>>>>>>> invoked by "matlab_ls_test" - and that is failing. >>>>>>>>>>> >>>>>>>>>>> Satish >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>> > Hi Sathish, >>>>>>>>>>> > >>>>>>>>>>> > I tried the following procedure >>>>>>>>>>> > >>>>>>>>>>> > *$make * >>>>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > Building with 'gcc'. >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > In function ?PetscBinaryWrite?: >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > warning: ?err? may be used uninitialized in this function >>>>>>>>>>> > [-Wmaybe-uninitialized] >>>>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to >>>>>>>>>>> socket\n"); >>>>>>>>>>> > | ^ >>>>>>>>>>> > >>>>>>>>>>> > MEX completed successfully. >>>>>>>>>>> > ========================================= >>>>>>>>>>> > Now to check if the libraries are working do: >>>>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt >>>>>>>>>>> check >>>>>>>>>>> > >>>>>>>>>>> > *$make test query=requires queryval=matlab >>>>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/* >>>>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ >>>>>>>>>>> queryval=matlab >>>>>>>>>>> > query=requires >>>>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > TEST >>>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>>> vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>>> vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: >>>>>>>>>>> > >>>>>>>>>>> ------------------------------------------------------------------------ >>>>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation >>>>>>>>>>> Violation, >>>>>>>>>>> > probably memory access out of range >>>>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or >>>>>>>>>>> -on_error_attach_debugger >>>>>>>>>>> > # [0]PETSC ERROR: or see >>>>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind >>>>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and >>>>>>>>>>> Apple Mac OS >>>>>>>>>>> > X to find memory corruption errors >>>>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes, >>>>>>>>>>> recompile, link, >>>>>>>>>>> > and run >>>>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash. >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Signal received >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by >>>>>>>>>>> vit Mon Sep >>>>>>>>>>> > 4 10:02:32 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in >>>>>>>>>>> unknown file >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_WORLD >>>>>>>>>>> > # with errorcode 50162059. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> processes. >>>>>>>>>>> > # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff >>>>>>>>>>> > CC >>>>>>>>>>> > >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > CLINKER >>>>>>>>>>> > >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > TEST >>>>>>>>>>> > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> Error code: 124 >>>>>>>>>>> > # Running problem 5 >>>>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > # [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named >>>>>>>>>>> MB108SMEC028 by >>>>>>>>>>> > vit Mon Sep 4 10:02:34 2023 >>>>>>>>>>> > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > # with errorcode 126076. >>>>>>>>>>> > # >>>>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> processes. >>>>>>>>>>> > # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > # exactly when Open MPI kills them. >>>>>>>>>>> > # >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>> Command failed >>>>>>>>>>> > so no diff >>>>>>>>>>> > >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # Summary >>>>>>>>>>> > # ------------- >>>>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > # success 0/2 tests (0.0%) >>>>>>>>>>> > # failed 2/2 tests (100.0%) >>>>>>>>>>> > # todo 0/2 tests (0.0%) >>>>>>>>>>> > # skip 0/2 tests (0.0%) >>>>>>>>>>> > # >>>>>>>>>>> > # Wall clock time for tests: 4 sec >>>>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec >>>>>>>>>>> > # >>>>>>>>>>> > # To rerun failed tests: >>>>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > # >>>>>>>>>>> > # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec >>>>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec >>>>>>>>>>> / 0.01 sec >>>>>>>>>>> > >>>>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > *$make matlab_ls_test* >>>>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>> -Wwrite-strings >>>>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> -Wno-strict-aliasing >>>>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> matlab_ls_test.c >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng >>>>>>>>>>> -lmex -lmx >>>>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr >>>>>>>>>>> -lmpi_mpifh >>>>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>>> -lpthread -lquadmath >>>>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > >>>>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>>> ./matlab_ls_test >>>>>>>>>>> > -tao_smonitor -prob_id 5 -info* >>>>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of >>>>>>>>>>> processors = 1 >>>>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS >>>>>>>>>>> > MB108SMEC028.(none) >>>>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028 >>>>>>>>>>> > Running problem 5 >>>>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>>> 140155238476992 >>>>>>>>>>> > 94202473157392 max tags = 2147483647 >>>>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with >>>>>>>>>>> command >>>>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay >>>>>>>>>>> -nosplash >>>>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > -------------------------------------------------------------- >>>>>>>>>>> > [0]PETSC ERROR: Error in external library >>>>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > [0]PETSC ERROR: See >>>>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > for trouble shooting. >>>>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 >>>>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named >>>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>>> > Mon Sep 4 10:09:56 2023 >>>>>>>>>>> > [0]PETSC ERROR: Configure options >>>>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 >>>>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in >>>>>>>>>>> > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c >>>>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > [0]PETSC ERROR: -info >>>>>>>>>>> > [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send entire >>>>>>>>>>> > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF >>>>>>>>>>> > with errorcode 126076. >>>>>>>>>>> > >>>>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI >>>>>>>>>>> processes. >>>>>>>>>>> > You may or may not see output from other processes, depending >>>>>>>>>>> on >>>>>>>>>>> > exactly when Open MPI kills them. >>>>>>>>>>> > >>>>>>>>>>> > Please find the attachment for configure.log and make.log files >>>>>>>>>>> > >>>>>>>>>>> > On Sun, Sep 3, 2023 at 8:00?PM Satish Balay >>>>>>>>>>> wrote: >>>>>>>>>>> > >>>>>>>>>>> > > To use datafiles in the test suite: >>>>>>>>>>> > > >>>>>>>>>>> > > cd $HOME >>>>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles >>>>>>>>>>> > > >>>>>>>>>> DATAFILESPATH - or set >>>>>>>>>>> > > manually with make> >>>>>>>>>>> > > >>>>>>>>>>> > > make test query=requires queryval=matlab >>>>>>>>>>> DATAFILESPATH=$HOME/datafiles >>>>>>>>>>> > > >>>>>>>>>>> > > Satish >>>>>>>>>>> > > >>>>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote: >>>>>>>>>>> > > >>>>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47?AM INTURU SRINIVAS 20PHD0548 < >>>>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote: >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Hi Matthew, >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I >>>>>>>>>>> do not have >>>>>>>>>>> > > any >>>>>>>>>>> > > > > separate test files to test PETSc alone. Can you please >>>>>>>>>>> help me how to >>>>>>>>>>> > > > > define this DATAFILESPATH? >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, >>>>>>>>>>> we point to >>>>>>>>>>> > > this >>>>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You >>>>>>>>>>> don't have those >>>>>>>>>>> > > > matrices, since they are just for testing here. That >>>>>>>>>>> > > > is why I suggested just using a different matrix, or >>>>>>>>>>> running a problem >>>>>>>>>>> > > you >>>>>>>>>>> > > > care about in IBAMR. >>>>>>>>>>> > > > >>>>>>>>>>> > > > Thanks, >>>>>>>>>>> > > > >>>>>>>>>>> > > > Matt >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > > Thanks and regards >>>>>>>>>>> > > > > Srinivas. >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06?PM Matthew Knepley < >>>>>>>>>>> knepley at gmail.com> >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04?AM INTURU SRINIVAS >>>>>>>>>>> 20PHD0548 via >>>>>>>>>>> > > petsc-users < >>>>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote: >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> Hi Sathish, >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thank you so much for your efforts and the support you >>>>>>>>>>> are giving me >>>>>>>>>>> > > to >>>>>>>>>>> > > > >>> sort this out. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I tried to follow the same procedure which you >>>>>>>>>>> followed to build >>>>>>>>>>> > > Petsc >>>>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$./configure >>>>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1* >>>>>>>>>>> > > > >>> Using python3 for Python >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> Configuring PETSc to compile on your >>>>>>>>>>> system >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> It appears you >>>>>>>>>>> do not have >>>>>>>>>>> > > valgrind >>>>>>>>>>> > > > >>> installed on your system. >>>>>>>>>>> > > > >>> We HIGHLY recommend you install it from >>>>>>>>>>> www.valgrind.org >>>>>>>>>>> > > > >>> Or install >>>>>>>>>>> > > valgrind-devel or >>>>>>>>>>> > > > >>> equivalent using your package manager. >>>>>>>>>>> > > > >>> Then rerun ./configure >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> =============================================================================== >>>>>>>>>>> > > > >>> Compilers: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> C Compiler: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -fPIC >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> C++ Compiler: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0 >>>>>>>>>>> > > > >>> Fortran Compiler: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0 >>>>>>>>>>> -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu >>>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>> Linkers: >>>>>>>>>>> > > > >>> Shared linker: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Dynamic linker: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > -shared >>>>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> > > -Wno-unknown-pragmas >>>>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl >>>>>>>>>>> > > > >>> make: >>>>>>>>>>> > > > >>> Version: 4.2 >>>>>>>>>>> > > > >>> /usr/bin/make >>>>>>>>>>> > > > >>> BlasLapack: >>>>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 >>>>>>>>>>> -lpthread >>>>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>>> -omp_num_threads >>>>>>>>>>> > >

to >>>>>>>>>>> > > > >>> control the number of threads >>>>>>>>>>> > > > >>> uses 8 byte integers >>>>>>>>>>> > > > >>> MPI: >>>>>>>>>>> > > > >>> Version: 3 >>>>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> > > > >>> Mpiexec: >>>>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec >>>>>>>>>>> > > --oversubscribe >>>>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4 >>>>>>>>>>> > > > >>> pthread: >>>>>>>>>>> > > > >>> cmake: >>>>>>>>>>> > > > >>> Version: 3.16.3 >>>>>>>>>>> > > > >>> /usr/bin/cmake >>>>>>>>>>> > > > >>> regex: >>>>>>>>>>> > > > >>> Matlab: >>>>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>> Library: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng >>>>>>>>>>> -lmex -lmx -lmat >>>>>>>>>>> > > -lut >>>>>>>>>>> > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>> Language used to compile PETSc: C >>>>>>>>>>> > > > >>> PETSc: >>>>>>>>>>> > > > >>> PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> > > > >>> Scalar type: real >>>>>>>>>>> > > > >>> Precision: double >>>>>>>>>>> > > > >>> Support for __float128 >>>>>>>>>>> > > > >>> Integer size: 4 bytes >>>>>>>>>>> > > > >>> shared libraries: enabled >>>>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries >>>>>>>>>>> with: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata >>>>>>>>>>> -licui18n -licuuc as >>>>>>>>>>> > > > >>> you suggested earlier. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make* >>>>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4 >>>>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>>> to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> Building with 'gcc'. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: >>>>>>>>>>> > > > >>> In function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing >>>>>>>>>>> to socket\n"); >>>>>>>>>>> > > > >>> | ^ >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> MEX completed successfully. >>>>>>>>>>> > > > >>> ========================================= >>>>>>>>>>> > > > >>> Now to check if the libraries are working do: >>>>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 >>>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>> =============================================== >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$make test query=requires queryval=matlab* >>>>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>> TEST >>>>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH >>>>>>>>>>> defined, so it >>>>>>>>>>> > > > >> cannot find the matrix to test. Try running some test >>>>>>>>>>> of yours. >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Thanks, >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> Matt >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>>>>> 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named >>>>>>>>>>> MB108SMEC028 by vit >>>>>>>>>>> > > Sun >>>>>>>>>>> > > > >>> Sep 3 11:51:03 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 >>>>>>>>>>> PetscViewerFileSetUp_BinarySTDIO() line 1444 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line >>>>>>>>>>> 1511 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in >>>>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send >>>>>>>>>>> > > > >>> entire error message to >>>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 113065. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>>> MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so >>>>>>>>>>> no diff >>>>>>>>>>> > > > >>> CC >>>>>>>>>>> > > > >>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>> CLINKER >>>>>>>>>>> > > > >>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>> TEST >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>> not ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: 124 >>>>>>>>>>> > > > >>> # Running problem 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message >>>>>>>>>>> > > > >>> >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> for trouble >>>>>>>>>>> > > > >>> shooting. >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug >>>>>>>>>>> 01, 2020 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt >>>>>>>>>>> named >>>>>>>>>>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> --with-debugging=0 >>>>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 >>>>>>>>>>> in >>>>>>>>>>> > > > >>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message >>>>>>>>>>> -------send >>>>>>>>>>> > > > >>> entire error message to >>>>>>>>>>> petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_SELF >>>>>>>>>>> > > > >>> # with errorcode 126076. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all >>>>>>>>>>> MPI processes. >>>>>>>>>>> > > > >>> # You may or may not see output from other processes, >>>>>>>>>>> depending on >>>>>>>>>>> > > > >>> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> SKIP Command >>>>>>>>>>> > > > >>> failed so no diff >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # Summary >>>>>>>>>>> > > > >>> # ------------- >>>>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>> # success 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # failed 2/2 tests (100.0%) >>>>>>>>>>> > > > >>> # todo 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # skip 0/2 tests (0.0%) >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec >>>>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # To rerun failed tests: >>>>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1 >>>>>>>>>>> > > > >>> # >>>>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time): >>>>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec >>>>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: >>>>>>>>>>> 0.02 sec / >>>>>>>>>>> > > 0.02 sec >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *How to sort out this error?* >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/* >>>>>>>>>>> > > > >>> *$make matlab_ls_test* >>>>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall >>>>>>>>>>> > > -Wwrite-strings >>>>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas >>>>>>>>>>> -fstack-protector >>>>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include >>>>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include >>>>>>>>>>> matlab_ls_test.c >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib >>>>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib >>>>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm >>>>>>>>>>> -leng -lmex >>>>>>>>>>> > > -lmx >>>>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 >>>>>>>>>>> -lmpi_usempi_ignore_tkr >>>>>>>>>>> > > -lmpi_mpifh >>>>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>>> -lpthread >>>>>>>>>>> > > -lquadmath >>>>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b >>>>>>>>>>> version. >>>>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. >>>>>>>>>>> Please find the >>>>>>>>>>> > > > >>> attachment and do the needful. >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> Thanks and regards >>>>>>>>>>> > > > >>> Srinivas >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15?PM Satish Balay < >>>>>>>>>>> balay at mcs.anl.gov> >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>>> Perhaps you can try the following to get additional >>>>>>>>>>> info - and debug >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Satish >>>>>>>>>>> > > > >>>> ---------- >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd >>>>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/ >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> make matlab_ls_test >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings >>>>>>>>>>> > > -Wno-strict-aliasing >>>>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector >>>>>>>>>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include >>>>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> >>>>>>>>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> matlab_ls_test.c >>>>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib >>>>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 >>>>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu >>>>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu >>>>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas >>>>>>>>>>> -lpthread -lm -leng >>>>>>>>>>> > > -lmex >>>>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ >>>>>>>>>>> -ldl -lmpifort >>>>>>>>>>> > > -lmpi >>>>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath >>>>>>>>>>> -lstdc++ -ldl -o >>>>>>>>>>> > > > >>>> matlab_ls_test >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>>> ./matlab_ls_test >>>>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started: >>>>>>>>>>> number of >>>>>>>>>>> > > processors >>>>>>>>>>> > > > >>>> = 1 >>>>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely >>>>>>>>>>> is NIS >>>>>>>>>>> > > > >>>> compute-386-07.(none) >>>>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: >>>>>>>>>>> compute-386-07 >>>>>>>>>>> > > > >>>> Running problem 5 >>>>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator >>>>>>>>>>> 1140850689 >>>>>>>>>>> > > > >>>> -2080374784 max tags = 268435455 >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine >>>>>>>>>>> with command >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB >>>>>>>>>>> string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating >>>>>>>>>>> Matlab string: >>>>>>>>>>> > > > >>>> TestingInitialize >>>>>>>>>>> > > > >>>> 5 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually >>>>>>>>>>> works for you >>>>>>>>>>> > > - on >>>>>>>>>>> > > > >>>> this machine..>>>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> balay at compute-386-07 >>>>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$ >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> < M A T L A B (R) > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> Copyright 1984-2021 The >>>>>>>>>>> MathWorks, Inc. >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) >>>>>>>>>>> 64-bit (glnxa64) >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> February 17, 2021 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> To get started, type doc. >>>>>>>>>>> > > > >>>> For product information, visit www.mathworks.com. >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users >>>>>>>>>>> wrote: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint >>>>>>>>>>> [reverting >>>>>>>>>>> > > thread >>>>>>>>>>> > > > >>>> to petsc-users only] >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send >>>>>>>>>>> the >>>>>>>>>>> > > corresponding >>>>>>>>>>> > > > >>>> configure.log, make.log [compressed]? >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) >>>>>>>>>>> on Ubuntu-20.04, >>>>>>>>>>> > > > >>>> with Matlab-R2021a - and that works: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git >>>>>>>>>>> branch >>>>>>>>>>> > > > >>>> > main >>>>>>>>>>> > > > >>>> > release >>>>>>>>>>> > > > >>>> > * release-3.13 >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module >>>>>>>>>>> load >>>>>>>>>>> > > matlab/R2021a >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which >>>>>>>>>>> matlab >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> ./configure >>>>>>>>>>> > > > >>>> >>>>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/ >>>>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > Compilers: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > C Compiler: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>>> 9.4.0 >>>>>>>>>>> > > > >>>> > C++ Compiler: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall >>>>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > -fstack-protector >>>>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC >>>>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) >>>>>>>>>>> 9.4.0 >>>>>>>>>>> > > > >>>> > Fortran Compiler: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC >>>>>>>>>>> > > -Wall >>>>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3 >>>>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu >>>>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0 >>>>>>>>>>> > > > >>>> > Linkers: >>>>>>>>>>> > > > >>>> > Shared linker: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Dynamic linker: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc >>>>>>>>>>> > > -shared -fPIC >>>>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing >>>>>>>>>>> -Wno-unknown-pragmas >>>>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3 >>>>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ >>>>>>>>>>> -ldl >>>>>>>>>>> > > > >>>> > make: >>>>>>>>>>> > > > >>>> > Version: 4.2 >>>>>>>>>>> > > > >>>> > /usr/bin/make >>>>>>>>>>> > > > >>>> > BlasLapack: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64 >>>>>>>>>>> > > > >>>> -liomp5 -lpthread >>>>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=

or >>>>>>>>>>> -omp_num_threads >>>>>>>>>>> > >

>>>>>>>>>>> > > > >>>> to control the number of threads >>>>>>>>>>> > > > >>>> > uses 8 byte integers >>>>>>>>>>> > > > >>>> > MPI: >>>>>>>>>>> > > > >>>> > Version: 4 >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include >>>>>>>>>>> > > > >>>> > Mpiexec: >>>>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec >>>>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300 >>>>>>>>>>> > > > >>>> > pthread: >>>>>>>>>>> > > > >>>> > Library: -lpthread >>>>>>>>>>> > > > >>>> > cmake: >>>>>>>>>>> > > > >>>> > Version: 3.16.3 >>>>>>>>>>> > > > >>>> > /usr/bin/cmake >>>>>>>>>>> > > > >>>> > regex: >>>>>>>>>>> > > > >>>> > Matlab: >>>>>>>>>>> > > > >>>> > Includes: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a >>>>>>>>>>> > > > >>>> > MatlabEngine: >>>>>>>>>>> > > > >>>> > Library: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64 >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n >>>>>>>>>>> -licuuc >>>>>>>>>>> > > > >>>> > sowing: >>>>>>>>>>> > > > >>>> > Version: 1.1.25 >>>>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort >>>>>>>>>>> > > > >>>> > valgrind: >>>>>>>>>>> > > > >>>> > Language used to compile PETSc: C >>>>>>>>>>> > > > >>>> > PETSc: >>>>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt >>>>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc >>>>>>>>>>> > > > >>>> > Scalar type: real >>>>>>>>>>> > > > >>>> > Precision: double >>>>>>>>>>> > > > >>>> > Support for __float128 >>>>>>>>>>> > > > >>>> > Integer size: 4 bytes >>>>>>>>>>> > > > >>>> > shared libraries: enabled >>>>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc >>>>>>>>>>> libraries with: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>>> PETSC_ARCH=linux-opt all >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> xxx=========================================================================xxx >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6 >>>>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>>> writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > Building with 'gcc'. >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In >>>>>>>>>>> > > > >>>> function ?PetscBinaryWrite?: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: >>>>>>>>>>> > > > >>>> warning: ?err? may be used uninitialized in this >>>>>>>>>>> function >>>>>>>>>>> > > > >>>> [-Wmaybe-uninitialized] >>>>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error >>>>>>>>>>> writing to >>>>>>>>>>> > > socket\n"); >>>>>>>>>>> > > > >>>> > | ^ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > MEX completed successfully. >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > Now to check if the libraries are working do: >>>>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc >>>>>>>>>>> PETSC_ARCH=linux-opt check >>>>>>>>>>> > > > >>>> > ========================================= >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make >>>>>>>>>>> test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>> linux-opt/tests/ksp/ksp/tutorials/ex72.o >>>>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1 >>>>>>>>>>> > > > >>>> > # ../ex72: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed >>>>>>>>>>> so no diff >>>>>>>>>>> > > > >>>> > CC >>>>>>>>>>> > > > >>>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o >>>>>>>>>>> > > > >>>> > CLINKER >>>>>>>>>>> > > > >>>> >>>>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > not ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > code: >>>>>>>>>>> > > > >>>> 1 >>>>>>>>>>> > > > >>>> > # ../matlab_ls_test: >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5: >>>>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12) >>>>>>>>>>> > > > >>>> > ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP >>>>>>>>>>> > > Command >>>>>>>>>>> > > > >>>> failed so no diff >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 >>>>>>>>>>> make test >>>>>>>>>>> > > query=requires >>>>>>>>>>> > > > >>>> queryval=matlab >>>>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts >>>>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12 >>>>>>>>>>> > > > >>>> > TEST >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > ok >>>>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # Summary >>>>>>>>>>> > > > >>>> > # ------------- >>>>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%) >>>>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%) >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec >>>>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time): >>>>>>>>>>> 15.190000000000001 >>>>>>>>>>> > > sec >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU >>>>>>>>>>> time): >>>>>>>>>>> > > > >>>> > # >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / >>>>>>>>>>> > > 7.54 >>>>>>>>>>> > > > >>>> sec >>>>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec >>>>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote: >>>>>>>>>>> > > > >>>> > >>>>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have >>>>>>>>>>> tried to >>>>>>>>>>> > > > >>>> configure petsc >>>>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not >>>>>>>>>>> successful. After >>>>>>>>>>> > > > >>>> running make >>>>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error >>>>>>>>>>> message. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > not ok >>>>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error >>>>>>>>>>> > > > >>>> code: 124 >>>>>>>>>>> > > > >>>> > > # Running problem 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error >>>>>>>>>>> Message >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> > > for trouble shooting. >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, >>>>>>>>>>> Aug 01, 2020 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a >>>>>>>>>>> linux-opt named >>>>>>>>>>> > > > >>>> MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> --with-debugging=0 >>>>>>>>>>> > > > >>>> > > --with-x=0 >>>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() >>>>>>>>>>> line 67 in >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries: >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error >>>>>>>>>>> Message >>>>>>>>>>> > > -------send >>>>>>>>>>> > > > >>>> entire >>>>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator >>>>>>>>>>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to >>>>>>>>>>> kill all MPI >>>>>>>>>>> > > > >>>> processes. >>>>>>>>>>> > > > >>>> > > # You may or may not see output from other >>>>>>>>>>> processes, depending >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > # >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > I request you to help me to sort out this error. >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > Thanks >>>>>>>>>>> > > > >>>> > > Srinivas >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42?PM Amneet Bhalla < >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com> wrote: >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > > I think there should be two hyphens in >>>>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > i.e.: >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25?AM INTURU SRINIVAS >>>>>>>>>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> petsc-users < >>>>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote: >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay < >>>>>>>>>>> balay at mcs.anl.gov> >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if >>>>>>>>>>> hypre will work >>>>>>>>>>> > > > >>>> here]. >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> i.e: >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> ./configure >>>>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 >>>>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 >>>>>>>>>>> > > PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> Satish >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 >>>>>>>>>>> via >>>>>>>>>>> > > petsc-users >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >>> > Hi Satish, >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir >>>>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting? >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay < >>>>>>>>>>> > > balay at mcs.anl.gov> >>>>>>>>>>> > > > >>>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > Also: >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1', >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not >>>>>>>>>>> work in this mode. >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such >>>>>>>>>>> dependency/conflicts >>>>>>>>>>> > > across >>>>>>>>>>> > > > >>>> packages] >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via >>>>>>>>>>> petsc-users wrote: >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> config/examples/arch-ci-linux-matlab-ilp64.py >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit >>>>>>>>>>> integers] conflict >>>>>>>>>>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring >>>>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1 >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64 >>>>>>>>>>> blas/lapack with >>>>>>>>>>> > > > >>>> matlab - to >>>>>>>>>>> > > > >>>> > > >>> have a >>>>>>>>>>> > > > >>>> > > >>> > > compatible build >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir, >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS >>>>>>>>>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet, >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with >>>>>>>>>>> MATLAB is not >>>>>>>>>>> > > > >>>> working. It is >>>>>>>>>>> > > > >>>> > > >>> > > showing >>>>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 >>>>>>>>>>> versions. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC >>>>>>>>>>> cluster with >>>>>>>>>>> > > > >>>> libmesh and >>>>>>>>>>> > > > >>>> > > >>> this is >>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This >>>>>>>>>>> I tried without >>>>>>>>>>> > > > >>>> linking >>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error >>>>>>>>>>> while configuring >>>>>>>>>>> > > > >>>> libmesh 1.6.2 >>>>>>>>>>> > > > >>>> > > >>> that >>>>>>>>>>> > > > >>>> > > >>> > > PETSc >>>>>>>>>>> > > > >>>> > > >>> > > > > was not found but >>>>>>>>>>> --enable-petsc-required is >>>>>>>>>>> > > specified. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking >>>>>>>>>>> for libmesh with >>>>>>>>>>> > > > >>>> PETSc and >>>>>>>>>>> > > > >>>> > > >>> Matlab >>>>>>>>>>> > > > >>>> > > >>> > > is in >>>>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for >>>>>>>>>>> complicated >>>>>>>>>>> > > geometries >>>>>>>>>>> > > > >>>> it is >>>>>>>>>>> > > > >>>> > > >>> > > mentioned to >>>>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh >>>>>>>>>>> construct. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying >>>>>>>>>>> these various >>>>>>>>>>> > > things >>>>>>>>>>> > > > >>>> and ended >>>>>>>>>>> > > > >>>> > > >>> up with >>>>>>>>>>> > > > >>>> > > >>> > > > > errors. >>>>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed >>>>>>>>>>> further to do my >>>>>>>>>>> > > > >>>> research work. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon >>>>>>>>>>> as possible. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards >>>>>>>>>>> > > > >>>> > > >>> > > > > Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet >>>>>>>>>>> Bhalla < >>>>>>>>>>> > > > >>>> mail2amneet at gmail.com> >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas, >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don?t need >>>>>>>>>>> libMesh for >>>>>>>>>>> > > the >>>>>>>>>>> > > > >>>> WEC >>>>>>>>>>> > > > >>>> > > >>> application. >>>>>>>>>>> > > > >>>> > > >>> > > You >>>>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 >>>>>>>>>>> that builds with >>>>>>>>>>> > > > >>>> Matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for >>>>>>>>>>> wanting to build >>>>>>>>>>> > > > >>>> libMesh? >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > Thanks, >>>>>>>>>>> > > > >>>> > > >>> > > > > > ?Amneet >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM >>>>>>>>>>> INTURU SRINIVAS >>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > > > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Hi, >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 >>>>>>>>>>> by removing all >>>>>>>>>>> > > > >>>> occurrences >>>>>>>>>>> > > > >>>> > > >>> of >>>>>>>>>>> > > > >>>> > > >>> > > "-lut >>>>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When >>>>>>>>>>> I ran "make >>>>>>>>>>> > > test" >>>>>>>>>>> > > > >>>> got the >>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>> > > > >>>> > > >>> > > > > >> errors >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>>> --------------------- Error >>>>>>>>>>> > > Message >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in >>>>>>>>>>> external library >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>>>>> MATLAB engine >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> for >>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>>>>> Version 3.13.4, >>>>>>>>>>> > > Aug >>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>>> ../matlab_ls_test on a >>>>>>>>>>> > > linux-debug >>>>>>>>>>> > > > >>>> named >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>>> > > >>> --with-debugging=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 >>>>>>>>>>> --download-fblaslapack=1 >>>>>>>>>>> > > > >>>> --with-x=0 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>>>>> PetscMatlabEngineCreate() >>>>>>>>>>> > > line >>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line >>>>>>>>>>> 126 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option >>>>>>>>>>> Table entries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>>> ----------------End of Error >>>>>>>>>>> > > > >>>> Message >>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 >>>>>>>>>>> in communicator >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>>>>> Open MPI to >>>>>>>>>>> > > kill >>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output >>>>>>>>>>> from other >>>>>>>>>>> > > processes, >>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt >>>>>>>>>>> > > > >>>> > > >>> > > > > >> TEST >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not ok >>>>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # >>>>>>>>>>> > > > >>>> > > >>> Error >>>>>>>>>>> > > > >>>> > > >>> > > code: 124 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>>> --------------------- Error >>>>>>>>>>> > > Message >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> -------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in >>>>>>>>>>> external library >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start >>>>>>>>>>> MATLAB engine >>>>>>>>>>> > > on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html >>>>>>>>>>> > > > >>>> for >>>>>>>>>>> > > > >>>> > > >>> trouble >>>>>>>>>>> > > > >>>> > > >>> > > > > >> shooting. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release >>>>>>>>>>> Version 3.13.4, >>>>>>>>>>> > > Aug >>>>>>>>>>> > > > >>>> 01, 2020 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>>> ../matlab_ls_test on a >>>>>>>>>>> > > linux-opt >>>>>>>>>>> > > > >>>> named >>>>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by >>>>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90 >>>>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3 >>>>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt >>>>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0 >>>>>>>>>>> > > > >>>> --download-fblaslapack=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 >>>>>>>>>>> PetscMatlabEngineCreate() >>>>>>>>>>> > > line >>>>>>>>>>> > > > >>>> 67 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line >>>>>>>>>>> 126 in >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option >>>>>>>>>>> Table entries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5 >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: >>>>>>>>>>> ----------------End of Error >>>>>>>>>>> > > > >>>> Message >>>>>>>>>>> > > > >>>> > > >>> -------send >>>>>>>>>>> > > > >>>> > > >>> > > entire >>>>>>>>>>> > > > >>>> > > >>> > > > > >> error message to >>>>>>>>>>> > > petsc-maint at mcs.anl.gov---------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 >>>>>>>>>>> in communicator >>>>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes >>>>>>>>>>> Open MPI to >>>>>>>>>>> > > kill >>>>>>>>>>> > > > >>>> all MPI >>>>>>>>>>> > > > >>>> > > >>> > > processes. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output >>>>>>>>>>> from other >>>>>>>>>>> > > processes, >>>>>>>>>>> > > > >>>> > > >>> depending on >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> # >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -------------------------------------------------------------------------- >>>>>>>>>>> > > > >>>> > > >>> > > > > >> ok >>>>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test >>>>>>>>>>> > > > >>>> # SKIP >>>>>>>>>>> > > > >>>> > > >>> Command >>>>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc >>>>>>>>>>> 3.17.5 >>>>>>>>>>> > > version. I >>>>>>>>>>> > > > >>>> am >>>>>>>>>>> > > > >>>> > > >>> sharing the >>>>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both >>>>>>>>>>> petsc 3.13.4 and >>>>>>>>>>> > > > >>>> petsc >>>>>>>>>>> > > > >>>> > > >>> 3.17.5. >>>>>>>>>>> > > > >>>> > > >>> > > Please find >>>>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards >>>>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56?PM >>>>>>>>>>> Satish Balay < >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log >>>>>>>>>>> not petsc's >>>>>>>>>>> > > > >>>> > > >>> configure.log/make.log >>>>>>>>>>> > > > >>>> > > >>> > > for >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you >>>>>>>>>>> have: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Library: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 >>>>>>>>>>> > > -leng >>>>>>>>>>> > > > >>>> -lmex >>>>>>>>>>> > > > >>>> > > >>> -lmx >>>>>>>>>>> > > > >>>> > > >>> > > -lmat -lut >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: >>>>>>>>>>> C >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<< >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and >>>>>>>>>>> matlab-R2022a) - we are >>>>>>>>>>> > > seeing: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> mex: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> <<< >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n >>>>>>>>>>> -licuuc" are not >>>>>>>>>>> > > > >>>> preset here. >>>>>>>>>>> > > > >>>> > > >>> This >>>>>>>>>>> > > > >>>> > > >>> > > might >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab >>>>>>>>>>> versions. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> You can: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables >>>>>>>>>>> > > > >>>> > > >>> > > and >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut >>>>>>>>>>> -licudata >>>>>>>>>>> > > -licui18n >>>>>>>>>>> > > > >>>> -licuuc" >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in >>>>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU >>>>>>>>>>> SRINIVAS 20PHD0548 >>>>>>>>>>> > > via >>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files >>>>>>>>>>> while building >>>>>>>>>>> > > > >>>> petsc3.13.4 with >>>>>>>>>>> > > > >>>> > > >>> > > matlab and >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> also >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building >>>>>>>>>>> libmesh with >>>>>>>>>>> > > > >>>> petsc3.17.5 and >>>>>>>>>>> > > > >>>> > > >>> matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Building >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was >>>>>>>>>>> done >>>>>>>>>>> > > successfully. >>>>>>>>>>> > > > >>>> But >>>>>>>>>>> > > > >>>> > > >>> libmesh is >>>>>>>>>>> > > > >>>> > > >>> > > not >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> able to >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31?PM >>>>>>>>>>> Satish Balay < >>>>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log >>>>>>>>>>> from both >>>>>>>>>>> > > > >>>> petsc-3.13 and >>>>>>>>>>> > > > >>>> > > >>> 3.17 [or >>>>>>>>>>> > > > >>>> > > >>> > > 3.19]. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make >>>>>>>>>>> the logs >>>>>>>>>>> > > friendly to >>>>>>>>>>> > > > >>>> mailing >>>>>>>>>>> > > > >>>> > > >>> list - >>>>>>>>>>> > > > >>>> > > >>> > > or >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> send >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with >>>>>>>>>>> 3.17? [or >>>>>>>>>>> > > 3.19?] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU >>>>>>>>>>> SRINIVAS >>>>>>>>>>> > > 20PHD0548 >>>>>>>>>>> > > > >>>> via >>>>>>>>>>> > > > >>>> > > >>> petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log >>>>>>>>>>> file while >>>>>>>>>>> > > building >>>>>>>>>>> > > > >>>> > > >>> petsc-3.13.4 >>>>>>>>>>> > > > >>>> > > >>> > > with >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment >>>>>>>>>>> and do the >>>>>>>>>>> > > needful. >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at >>>>>>>>>>> 10:19?AM INTURU >>>>>>>>>>> > > > >>>> SRINIVAS >>>>>>>>>>> > > > >>>> > > >>> 20PHD0548 < >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> inturu.srinivas2020 at vitstudent.ac.in> >>>>>>>>>>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with >>>>>>>>>>> petsc-3.17.5. During >>>>>>>>>>> > > building >>>>>>>>>>> > > > >>>> of >>>>>>>>>>> > > > >>>> > > >>> libmesh, the >>>>>>>>>>> > > > >>>> > > >>> > > error >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> shows >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at >>>>>>>>>>> 9:43?PM Satish >>>>>>>>>>> > > > >>>> Balay < >>>>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> https://ibamr.github.io/linux says >>>>>>>>>>> > > > >>>> petsc-3.17 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with >>>>>>>>>>> petsc-3.17.5? >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, >>>>>>>>>>> INTURU SRINIVAS >>>>>>>>>>> > > > >>>> 20PHD0548 via >>>>>>>>>>> > > > >>>> > > >>> > > petsc-users >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello, >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc >>>>>>>>>>> with MATLAB for >>>>>>>>>>> > > > >>>> working on >>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While >>>>>>>>>>> building the >>>>>>>>>>> > > PETSc, >>>>>>>>>>> > > > >>>> using the >>>>>>>>>>> > > > >>>> > > >>> > > following >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export >>>>>>>>>>> PETSC_ARCH=linux-debug >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> --download-fblaslapack=1 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> --with-matlab-engine=1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/ >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following >>>>>>>>>>> error >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>>>>> `EvaluateResidual': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function >>>>>>>>>>> `EvaluateJacobian': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEnginePut' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGet' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main': >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineCreate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > >>>>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to >>>>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy' >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld >>>>>>>>>>> returned 1 exit >>>>>>>>>>> > > > >>>> status >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** >>>>>>>>>>> [gmakefile.test:185: >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> >>>>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test] >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1 >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for >>>>>>>>>>> unfinished >>>>>>>>>>> > > jobs.... >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to >>>>>>>>>>> solve this issue >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent >>>>>>>>>>> from Vellore >>>>>>>>>>> > > > >>>> Institute of >>>>>>>>>>> > > > >>>> > > >>> > > Technology. >>>>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may >>>>>>>>>>> contain legally >>>>>>>>>>> > > > >>>> protected >>>>>>>>>>> > > > >>>> > > >>> > > confidential or >>>>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of ?Vellore >>>>>>>>>>> Institute of >>>>>>>>>>> > > > >>>> Technology?. >>>>>>>>>>> > > > >>>> > > >>> If >>>>>>>>>>> > > > >>>> > > >>> > > you are >>>>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you >>>>>>>>>>> should not >>>>>>>>>>> > > > >>>> disseminate, >>>>>>>>>>> > > > >>>> > > >>> distribute >>>>>>>>>>> > > > >>>> > > >>> > > or copy >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the >>>>>>>>>>> sender immediately >>>>>>>>>>> > > > >>>> and destroy >>>>>>>>>>> > > > >>>> > > >>> all >>>>>>>>>>> > > > >>>> > > >>> > > copies of >>>>>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. >>>>>>>>>>> If you have >>>>>>>>>>> > > > >>>> received this >>>>>>>>>>> > > > >>>> > > >>> email >>>>>>>>>>> > > > >>>> > > >>> > > in error, >>>>>>>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender >>>>>>>>>>> by reply email >>>>>>>>>>> > > and >>>>>>>>>>> > > > >>>> delete >>>>>>>>>>> > > > >>>> > > >>> the >>>>>>>>>>> > > > >>>> > > >>> > > original >>>>>>>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies >>>>>>>>>>> without reading >>>>>>>>>>> > > them.* >>>>>>>>>>> > > > >>>> > > >>> > > > > >> >>>>>>>>>>> > > > >>>> > > >>> > > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > > >>>>>>>>>>> > > > >>>> > > >>> > > > >>>>>>>>>>> > > > >>>> > > >>> > > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> > >>>>>>>>>>> > > > >>>> > > >>> >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore >>>>>>>>>>> Institute of >>>>>>>>>>> > > > >>>> Technology. >>>>>>>>>>> > > > >>>> > > >> The contents of this email may contain legally >>>>>>>>>>> protected >>>>>>>>>>> > > > >>>> confidential or >>>>>>>>>>> > > > >>>> > > >> privileged information of ?Vellore Institute of >>>>>>>>>>> > > Technology?. If >>>>>>>>>>> > > > >>>> you are >>>>>>>>>>> > > > >>>> > > >> not the intended recipient, you should not >>>>>>>>>>> disseminate, >>>>>>>>>>> > > > >>>> distribute or copy >>>>>>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender >>>>>>>>>>> immediately and destroy >>>>>>>>>>> > > > >>>> all copies of >>>>>>>>>>> > > > >>>> > > >> this message and any attachments. If you have >>>>>>>>>>> received this >>>>>>>>>>> > > > >>>> email in error, >>>>>>>>>>> > > > >>>> > > >> please promptly notify the sender by reply >>>>>>>>>>> email and delete >>>>>>>>>>> > > the >>>>>>>>>>> > > > >>>> original >>>>>>>>>>> > > > >>>> > > >> email and any backup copies without reading >>>>>>>>>>> them.* >>>>>>>>>>> > > > >>>> > > >> >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > -- >>>>>>>>>>> > > > >>>> > > > --Amneet >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> > > >>>>>>>>>>> > > > >>>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore >>>>>>>>>>> Institute of >>>>>>>>>>> > > Technology. >>>>>>>>>>> > > > >>> The contents of this email may contain legally >>>>>>>>>>> protected >>>>>>>>>>> > > confidential or >>>>>>>>>>> > > > >>> privileged information of ?Vellore Institute of >>>>>>>>>>> Technology?. If you >>>>>>>>>>> > > are >>>>>>>>>>> > > > >>> not the intended recipient, you should not >>>>>>>>>>> disseminate, distribute >>>>>>>>>>> > > or copy >>>>>>>>>>> > > > >>> this e-mail. Please notify the sender immediately and >>>>>>>>>>> destroy all >>>>>>>>>>> > > copies of >>>>>>>>>>> > > > >>> this message and any attachments. If you have received >>>>>>>>>>> this email in >>>>>>>>>>> > > error, >>>>>>>>>>> > > > >>> please promptly notify the sender by reply email and >>>>>>>>>>> delete the >>>>>>>>>>> > > original >>>>>>>>>>> > > > >>> email and any backup copies without reading them.* >>>>>>>>>>> > > > >>> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> -- >>>>>>>>>>> > > > >> What most experimenters take for granted before they >>>>>>>>>>> begin their >>>>>>>>>>> > > > >> experiments is infinitely more interesting than any >>>>>>>>>>> results to which >>>>>>>>>>> > > their >>>>>>>>>>> > > > >> experiments lead. >>>>>>>>>>> > > > >> -- Norbert Wiener >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> https://www.cse.buffalo.edu/~knepley/ >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > >> >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > >>>>>>>>>>> > > > > *Disclaimer:This message was sent from Vellore Institute >>>>>>>>>>> of Technology. >>>>>>>>>>> > > > > The contents of this email may contain legally protected >>>>>>>>>>> confidential >>>>>>>>>>> > > or >>>>>>>>>>> > > > > privileged information of ?Vellore Institute of >>>>>>>>>>> Technology?. If you >>>>>>>>>>> > > are >>>>>>>>>>> > > > > not the intended recipient, you should not disseminate, >>>>>>>>>>> distribute or >>>>>>>>>>> > > copy >>>>>>>>>>> > > > > this e-mail. Please notify the sender immediately and >>>>>>>>>>> destroy all >>>>>>>>>>> > > copies of >>>>>>>>>>> > > > > this message and any attachments. If you have received >>>>>>>>>>> this email in >>>>>>>>>>> > > error, >>>>>>>>>>> > > > > please promptly notify the sender by reply email and >>>>>>>>>>> delete the >>>>>>>>>>> > > original >>>>>>>>>>> > > > > email and any backup copies without reading them.* >>>>>>>>>>> > > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > > >>>>>>>>>>> > > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>>>> Technology. The contents of this email may contain legally protected >>>>>>>>>> confidential or privileged information of ?Vellore Institute of >>>>>>>>>> Technology?. If you are not the intended recipient, you should not >>>>>>>>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>>>>>>>> immediately and destroy all copies of this message and any attachments. If >>>>>>>>>> you have received this email in error, please promptly notify the sender by >>>>>>>>>> reply email and delete the original email and any backup copies without >>>>>>>>>> reading them.* >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> --Amneet >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>>> Technology. The contents of this email may contain legally protected >>>>>>>> confidential or privileged information of ?Vellore Institute of >>>>>>>> Technology?. If you are not the intended recipient, you should not >>>>>>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>>>>>> immediately and destroy all copies of this message and any attachments. If >>>>>>>> you have received this email in error, please promptly notify the sender by >>>>>>>> reply email and delete the original email and any backup copies without >>>>>>>> reading them.* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> *Disclaimer:This message was sent from Vellore Institute of >>>>>>> Technology. The contents of this email may contain legally protected >>>>>>> confidential or privileged information of ?Vellore Institute of >>>>>>> Technology?. If you are not the intended recipient, you should not >>>>>>> disseminate, distribute or copy this e-mail. Please notify the sender >>>>>>> immediately and destroy all copies of this message and any attachments. If >>>>>>> you have received this email in error, please promptly notify the sender by >>>>>>> reply email and delete the original email and any backup copies without >>>>>>> reading them.* >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> --Amneet >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> -- >>>>> --Amneet >>>>> >>>>> >>>>> >>>>> >>> >>> *Disclaimer:This message was sent from Vellore Institute of Technology. >>> The contents of this email may contain legally protected confidential or >>> privileged information of ?Vellore Institute of Technology?. If you are >>> not the intended recipient, you should not disseminate, distribute or copy >>> this e-mail. Please notify the sender immediately and destroy all copies of >>> this message and any attachments. If you have received this email in error, >>> please promptly notify the sender by reply email and delete the original >>> email and any backup copies without reading them.* >>> >>> >>> >> >> *Disclaimer:This message was sent from Vellore Institute of Technology. >> The contents of this email may contain legally protected confidential or >> privileged information of ?Vellore Institute of Technology?. If you are >> not the intended recipient, you should not disseminate, distribute or copy >> this e-mail. Please notify the sender immediately and destroy all copies of >> this message and any attachments. If you have received this email in error, >> please promptly notify the sender by reply email and delete the original >> email and any backup copies without reading them.* >> >> >> > > *Disclaimer:This message was sent from Vellore Institute of Technology. > The contents of this email may contain legally protected confidential or > privileged information of ?Vellore Institute of Technology?. If you are > not the intended recipient, you should not disseminate, distribute or copy > this e-mail. Please notify the sender immediately and destroy all copies of > this message and any attachments. If you have received this email in error, > please promptly notify the sender by reply email and delete the original > email and any backup copies without reading them.* > > > > -- **Disclaimer:* This message was sent from Vellore Institute of Technology. ? The contents of this email may contain legally protected confidential or privileged information of ?Vellore Institute of Technology?.? If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments. If you have received this email in error, please promptly notify the sender by reply email and delete the original email and any backup copies without reading them.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From ptackley at gmail.com Thu Sep 28 05:29:28 2023 From: ptackley at gmail.com (Paul Tackley) Date: Thu, 28 Sep 2023 12:29:28 +0200 Subject: [petsc-users] Xcode 15.0 breaks PETSc configure? Message-ID: Hello, PETSc was working fine on my M1 Mac until I upgraded to Xcode 15.0 - now I can?t even configure it. There seems to be a problem related to C and C++ in Xcode 15.0. ?Cxx libraries cannot directly be used with C as linker?. Stdout message pasted below and configure.log file attached. Thanks for any advice. Paul % gcc --version Apple clang version 15.0.0 (clang-1500.0.40.1) Target: arm64-apple-darwin22.6.0 % g++ --version Apple clang version 15.0.0 (clang-1500.0.40.1) Target: arm64-apple-darwin22.6.0 ********************************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------------- Cxx libraries cannot directly be used with C as linker. If you don't need the C++ compiler to build external packages or for you application you can run ./configure with --with-cxx=0. Otherwise you need a different combination of C and C++ compilers ********************************************************************************************* File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/configure.py", line 462, in petsc_configure framework.configure(out = sys.stdout) File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1438, in configure self.processChildren() File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1426, in processChildren self.serialEvaluation(self.childGraph) File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1401, in serialEvaluation child.configure() File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/compilers.py", line 1463, in configure self.executeTest(self.checkCxxLibraries) File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/base.py", line 138, in executeTest ret = test(*args,**kargs) ^^^^^^^^^^^^^^^^^^^ File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/compilers.py", line 695, in checkCxxLibraries raise RuntimeError("Cxx libraries cannot directly be used with C as linker.\n\ ? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 1431946 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Thu Sep 28 08:56:31 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Thu, 28 Sep 2023 08:56:31 -0500 (CDT) Subject: [petsc-users] Xcode 15.0 breaks PETSc configure? In-Reply-To: References: Message-ID: <9fa15540-0c89-c7e5-b892-40b25ad81613@mcs.anl.gov> petsc git repo main branch has fixes for xcode-15. Can you give it a try? Satish On Thu, 28 Sep 2023, Paul Tackley wrote: > Hello, > > PETSc was working fine on my M1 Mac until I upgraded to Xcode 15.0 - now I can?t even configure it. There seems to be a problem related to C and C++ in Xcode 15.0. ?Cxx libraries cannot directly be used with C as linker?. Stdout message pasted below and configure.log file attached. > > Thanks for any advice. > Paul > > > % gcc --version > > Apple clang version 15.0.0 (clang-1500.0.40.1) > > Target: arm64-apple-darwin22.6.0 > > > % g++ --version > > Apple clang version 15.0.0 (clang-1500.0.40.1) > > Target: arm64-apple-darwin22.6.0 > > > > ********************************************************************************************* > > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > > --------------------------------------------------------------------------------------------- > > Cxx libraries cannot directly be used with C as linker. > > If you don't need the C++ compiler to build external packages or for you application you > > can run > > ./configure with --with-cxx=0. Otherwise you need a different combination of C and C++ > > compilers > > ********************************************************************************************* > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/configure.py", line 462, in petsc_configure > > framework.configure(out = sys.stdout) > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1438, in configure > > self.processChildren() > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1426, in processChildren > > self.serialEvaluation(self.childGraph) > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1401, in serialEvaluation > > child.configure() > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/compilers.py", line 1463, in configure > > self.executeTest(self.checkCxxLibraries) > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/base.py", line 138, in executeTest > > ret = test(*args,**kargs) > > ^^^^^^^^^^^^^^^^^^^ > > File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/compilers.py", line 695, in checkCxxLibraries > > raise RuntimeError("Cxx libraries cannot directly be used with C as linker.\n\ > > From erdemguer at proton.me Thu Sep 28 14:37:58 2023 From: erdemguer at proton.me (erdemguer) Date: Thu, 28 Sep 2023 19:37:58 +0000 Subject: [petsc-users] Parallel DMPlex Message-ID: Hi, I am currently using DMPlex in my code. It runs serially at the moment, but I'm interested in adding parallel options. Here is my workflow: Create a DMPlex mesh from GMSH. Reorder it with DMPlexPermute. Create necessary pre-processing arrays related to the mesh/problem. Create field(s) with multi-dofs. Create residual vectors. Define a function to calculate the residual for each cell and, use SNES. As you can see, I'm not using FV or FE structures (most examples do). Now, I'm trying to implement this in parallel using a similar approach. However, I'm struggling to understand how to create corresponding vectors and how to obtain index sets for each processor. Is there a tutorial or paper that covers this topic? Thank you. Guer. Sent with [Proton Mail](https://proton.me/) secure email. -------------- next part -------------- An HTML attachment was scrubbed... URL: From knepley at gmail.com Thu Sep 28 14:42:53 2023 From: knepley at gmail.com (Matthew Knepley) Date: Thu, 28 Sep 2023 15:42:53 -0400 Subject: [petsc-users] Parallel DMPlex In-Reply-To: References: Message-ID: On Thu, Sep 28, 2023 at 3:38?PM erdemguer via petsc-users < petsc-users at mcs.anl.gov> wrote: > Hi, > > I am currently using DMPlex in my code. It runs serially at the moment, > but I'm interested in adding parallel options. Here is my workflow: > > Create a DMPlex mesh from GMSH. > Reorder it with DMPlexPermute. > Create necessary pre-processing arrays related to the mesh/problem. > Create field(s) with multi-dofs. > Create residual vectors. > Define a function to calculate the residual for each cell and, use SNES. > As you can see, I'm not using FV or FE structures (most examples do). Now, > I'm trying to implement this in parallel using a similar approach. However, > I'm struggling to understand how to create corresponding vectors and how to > obtain index sets for each processor. Is there a tutorial or paper that > covers this topic? > The intention was that there is enough information in the manual to do this. Using PetscFE/PetscFV is not required. However, I strongly encourage you to use PetscSection. Without this, it would be incredibly hard to do what you want. Once the DM has a Section, it can do things like automatically create vectors and matrices for you. It can redistribute them, subset them, etc. The Section describes how dofs are assigned to pieces of the mesh (mesh points). This is in the manual, and there are a few examples that do it by hand. So I suggest changing your code to use PetscSection, and then letting us know if things still do not work. Thanks, Matt > Thank you. > Guer. > > Sent with Proton Mail secure email. > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ptackley at gmail.com Fri Sep 29 06:44:15 2023 From: ptackley at gmail.com (Paul Tackley) Date: Fri, 29 Sep 2023 13:44:15 +0200 Subject: [petsc-users] Xcode 15.0 breaks PETSc configure? In-Reply-To: <9fa15540-0c89-c7e5-b892-40b25ad81613@mcs.anl.gov> References: <9fa15540-0c89-c7e5-b892-40b25ad81613@mcs.anl.gov> Message-ID: <78B20F28-F6B0-4E48-928F-C69773D891B1@gmail.com> It works. The current git main branch configures and compiles with Xcode-15 on my M1 Mac. Thank you, Paul > On 28 Sep 2023, at 15:56, Satish Balay wrote: > > petsc git repo main branch has fixes for xcode-15. Can you give it a try? > > Satish > > On Thu, 28 Sep 2023, Paul Tackley wrote: > >> Hello, >> >> PETSc was working fine on my M1 Mac until I upgraded to Xcode 15.0 - now I can?t even configure it. There seems to be a problem related to C and C++ in Xcode 15.0. ?Cxx libraries cannot directly be used with C as linker?. Stdout message pasted below and configure.log file attached. >> >> Thanks for any advice. >> Paul >> >> >> % gcc --version >> >> Apple clang version 15.0.0 (clang-1500.0.40.1) >> >> Target: arm64-apple-darwin22.6.0 >> >> >> % g++ --version >> >> Apple clang version 15.0.0 (clang-1500.0.40.1) >> >> Target: arm64-apple-darwin22.6.0 >> >> >> >> ********************************************************************************************* >> >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >> >> --------------------------------------------------------------------------------------------- >> >> Cxx libraries cannot directly be used with C as linker. >> >> If you don't need the C++ compiler to build external packages or for you application you >> >> can run >> >> ./configure with --with-cxx=0. Otherwise you need a different combination of C and C++ >> >> compilers >> >> ********************************************************************************************* >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/configure.py", line 462, in petsc_configure >> >> framework.configure(out = sys.stdout) >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1438, in configure >> >> self.processChildren() >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1426, in processChildren >> >> self.serialEvaluation(self.childGraph) >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/framework.py", line 1401, in serialEvaluation >> >> child.configure() >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/compilers.py", line 1463, in configure >> >> self.executeTest(self.checkCxxLibraries) >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/base.py", line 138, in executeTest >> >> ret = test(*args,**kargs) >> >> ^^^^^^^^^^^^^^^^^^^ >> >> File "/Users/pjt/Software/PETSc/petsc-3.19.5/config/BuildSystem/config/compilers.py", line 695, in checkCxxLibraries >> >> raise RuntimeError("Cxx libraries cannot directly be used with C as linker.\n\ >> >> From ivanluthfi5 at gmail.com Fri Sep 29 11:59:01 2023 From: ivanluthfi5 at gmail.com (Ivan Luthfi) Date: Sat, 30 Sep 2023 00:59:01 +0800 Subject: [petsc-users] Issue when configuring my petsc-3.20.0 Message-ID: Hi team, I have an issue when I configure my petsc with the following script: ./configure --with-fc=0 --download-f2cblaslapack=1 --with-blaslapack-lib=libsunperf.a --with-blas-lib=libblas.a --with-lapack-lib=liblapack.a --download-make --with-cc=gcc --with-cxx=/home/ivanluthfi1/openmpi/opt-4.1.1/bin/mpicxx --download-cmake --download-superlu_dist --with-superlud-lib=libsuperlu_dist_3.3.a --download-parmetis --with-parmetis-lib=libparmetis.a --with-cc=/home/ivanluthfi1/openmpi/opt-4.1.1/bin/mpicc --download-metis --with-metis-lib=libmetis.a Here is the configure.log message: PETSc Error: No output file produced Rejecting compiler flag -std=c++11 due to nonzero status from link ********************************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): --------------------------------------------------------------------------------------------- Using C++ dialect C++11 as lower bound due to package(s): - SuperLU_DIST But C++ compiler (/home/ivanluthfi1/openmpi/opt-4.1.1/bin/mpicxx) appears non-compliant with C++11 or didn't accept: - -std=gnu++20 - -std=c++20 - -std=gnu++17 - -std=c++17 - -std=gnu++14 - -std=c++14 - -std=gnu++11 - -std=c++11 ********************************************************************************************* File "/home/ivanluthfi1/petsc/config/configure.py", line 462, in petsc_configure framework.configure(out = sys.stdout) File "/home/ivanluthfi1/petsc/config/BuildSystem/config/framework.py", line 1447, in configure self.processChildren() File "/home/ivanluthfi1/petsc/config/BuildSystem/config/framework.py", line 1435, in processChildren self.serialEvaluation(self.childGraph) File "/home/ivanluthfi1/petsc/config/BuildSystem/config/framework.py", line 1410, in serialEvaluation child.configure() File "/home/ivanluthfi1/petsc/config/BuildSystem/config/setCompilers.py", line 2786, in configure self.executeTest(self.checkCxxDialect,args=[LANG],kargs={'isGNUish':isGNUish}) File "/home/ivanluthfi1/petsc/config/BuildSystem/config/base.py", line 138, in executeTest ret = test(*args,**kargs) File "/home/ivanluthfi1/petsc/config/BuildSystem/config/setCompilers.py", line 1225, in checkCxxDialect raise ConfigureSetupError(mess) ================================================================================ Finishing configure run at Sat, 30 Sep 2023 00:52:35 +0800 Please help me, I need to configure it with metis, parmetis, superlud, blas, and lapack. -------------- next part -------------- An HTML attachment was scrubbed... URL: From balay at mcs.anl.gov Fri Sep 29 12:04:39 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Fri, 29 Sep 2023 12:04:39 -0500 (CDT) Subject: [petsc-users] Issue when configuring my petsc-3.20.0 In-Reply-To: References: Message-ID: Can you send us the complete configure.log file [as attachment] - perhaps to petsc-maint at mcs.anl.gov Satish On Sat, 30 Sep 2023, Ivan Luthfi wrote: > Hi team, > I have an issue when I configure my petsc with the following script: > > ./configure --with-fc=0 --download-f2cblaslapack=1 --with-blaslapack-lib=libsunperf.a --with-blas-lib=libblas.a --with-lapack-lib=liblapack.a --download-make --with-cc=gcc --with-cxx=/home/ivanluthfi1/openmpi/opt-4.1.1/bin/mpicxx --download-cmake --download-superlu_dist --with-superlud-lib=libsuperlu_dist_3.3.a --download-parmetis --with-parmetis-lib=libparmetis.a --with-cc=/home/ivanluthfi1/openmpi/opt-4.1.1/bin/mpicc --download-metis --with-metis-lib=libmetis.a > > Here is the configure.log message: > > PETSc Error: No output file produced > Rejecting compiler flag -std=c++11 due to nonzero status from link > ********************************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > --------------------------------------------------------------------------------------------- > Using C++ dialect C++11 as lower bound due to package(s): > - SuperLU_DIST > But C++ compiler (/home/ivanluthfi1/openmpi/opt-4.1.1/bin/mpicxx) appears non-compliant > with C++11 or didn't accept: > - -std=gnu++20 > - -std=c++20 > - -std=gnu++17 > - -std=c++17 > - -std=gnu++14 > - -std=c++14 > - -std=gnu++11 > - -std=c++11 > ********************************************************************************************* > File "/home/ivanluthfi1/petsc/config/configure.py", line 462, in petsc_configure > framework.configure(out = sys.stdout) > File "/home/ivanluthfi1/petsc/config/BuildSystem/config/framework.py", line 1447, in configure > self.processChildren() > File "/home/ivanluthfi1/petsc/config/BuildSystem/config/framework.py", line 1435, in processChildren > self.serialEvaluation(self.childGraph) > File "/home/ivanluthfi1/petsc/config/BuildSystem/config/framework.py", line 1410, in serialEvaluation > child.configure() > File "/home/ivanluthfi1/petsc/config/BuildSystem/config/setCompilers.py", line 2786, in configure > self.executeTest(self.checkCxxDialect,args=[LANG],kargs={'isGNUish':isGNUish}) > File "/home/ivanluthfi1/petsc/config/BuildSystem/config/base.py", line 138, in executeTest > ret = test(*args,**kargs) > File "/home/ivanluthfi1/petsc/config/BuildSystem/config/setCompilers.py", line 1225, in checkCxxDialect > raise ConfigureSetupError(mess) > ================================================================================ > Finishing configure run at Sat, 30 Sep 2023 00:52:35 +0800 > > Please help me, I need to configure it with metis, parmetis, superlud, blas, and lapack. > > From bsmith at petsc.dev Fri Sep 29 13:23:44 2023 From: bsmith at petsc.dev (Barry Smith) Date: Fri, 29 Sep 2023 14:23:44 -0400 Subject: [petsc-users] Spring 2024 PETSc meeting and release announcement 3.20 References: Message-ID: <2FBFCF80-8A3E-4A00-B0D1-9C067130AD77@petsc.dev> The May 23-24, 2024 PETSc annual meeting in Cologne Germany website is now available: https://cds.uni-koeln.de/en/workshops/petsc-2024/home Please register and start making your travel plans. We are pleased to announce the release of PETSc version 3.20.0 at https://petsc.org/release/download/ A list of the major changes and updates can be found at https://petsc.org/release/changes/320/ The release tarball location is changed from https://ftp.mcs.anl.gov/pub/petsc to https://web.cels.anl.gov/projects/petsc/download The final update to petsc-3.19 i.e petsc-3.19.6 is also available We recommend upgrading to PETSc 3.20.0 soon. As always, please report problems to petsc-maint at mcs.anl.gov and ask questions at petsc-users at mcs.anl.gov This release includes contributions from David Ham Iglesia Dolci Jack Betteridge Koki Sagiyama Marcin Rogowski Nathan Collier Aidan Hamilton Albert Cowie Barry Smith Blaise Bourdin Connor Ward David Andrs David Wells Duncan Campbell Hansol Suh Hong Zhang Jacob Faibussowitsch James Wright Jed Brown jeremy theler Joseph Pusztay Jose Roman Junchao Zhang Lisandro Dalcin Mark Adams Matthew Knepley Mr. Hong Zhang Pablo Brubeck Pierre Jolivet Pieter Ghysels Richard Tran Mills Satish Balay Sebastian Grimberg Stefano Zampini Suyash Tandon Toby Isaac YANG Zongze Zach Atkins and bug reports/proposed improvements received from Carl-Johan Thore Chris Douglas Daniel at OLCF Duan Junming Edoardo alinovi Philip Fackler Frederic Vi Getnet Betrie Aron Graham Hongrui Yu James Wright Jin Chen Jonas Lundgren Karsten Lettmann Boris Kaus LEONARDO MUTTI Maciej Lewkowicz maitri ksh Milan Pelletier Mr. Hong Zhang Ngoc Mai Monica Huynh Peng Wang S?bastien Gilles Daniel Taller Vibhas Mishra Wei Liu Li Xiaoye As always, thanks for your support, Barry -------------- next part -------------- An HTML attachment was scrubbed... URL: From ivanluthfi5 at gmail.com Sat Sep 30 00:00:46 2023 From: ivanluthfi5 at gmail.com (Ivan Luthfi) Date: Sat, 30 Sep 2023 13:00:46 +0800 Subject: [petsc-users] Error when configure cmake Message-ID: <7EE795B2-7B7D-4238-8476-00396A54DD08@gmail.com> I am trying to configure my pets-3.13.6, but I have an error when running configure on cmake. Please help me on this. Here is the following configure.log. -------------- next part -------------- A non-text attachment was scrubbed... Name: configure.log Type: application/octet-stream Size: 551406 bytes Desc: not available URL: From pierre.jolivet at lip6.fr Sat Sep 30 00:07:32 2023 From: pierre.jolivet at lip6.fr (Pierre Jolivet) Date: Sat, 30 Sep 2023 07:07:32 +0200 Subject: [petsc-users] Error when configure cmake In-Reply-To: <7EE795B2-7B7D-4238-8476-00396A54DD08@gmail.com> References: <7EE795B2-7B7D-4238-8476-00396A54DD08@gmail.com> Message-ID: You are using g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23). You need to use a less ancient C++ compiler. Please send logs to petsc-maint, not petsc-users. Thanks, Pierre > On 30 Sep 2023, at 7:00?AM, Ivan Luthfi wrote: > > I am trying to configure my pets-3.13.6, but I have an error when running configure on cmake. Please help me on this. Here is the following configure.log. > > From balay at mcs.anl.gov Sat Sep 30 00:16:24 2023 From: balay at mcs.anl.gov (Satish Balay) Date: Sat, 30 Sep 2023 00:16:24 -0500 (CDT) Subject: [petsc-users] Error when configure cmake In-Reply-To: References: <7EE795B2-7B7D-4238-8476-00396A54DD08@gmail.com> Message-ID: <862738b7-b2e7-a8df-b7d8-b94c27be1933@mcs.anl.gov> Here --download-cmake is failing [due to the old version of c++ compiler]. You can try installing an older version manually instead of --download-cmake Or you might be able to install a newer gcc/g++ easily [if its not already installed on your machine]. For ex: git clone https://github.com/spack/spack/ cd spack ./bin/spack install gcc at 7.5.0 Satish On Sat, 30 Sep 2023, Pierre Jolivet wrote: > You are using g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-23). > You need to use a less ancient C++ compiler. > Please send logs to petsc-maint, not petsc-users. > > Thanks, > Pierre > > > On 30 Sep 2023, at 7:00?AM, Ivan Luthfi wrote: > > > > I am trying to configure my pets-3.13.6, but I have an error when running configure on cmake. Please help me on this. Here is the following configure.log. > > > > >