<div dir="ltr"><div>Hi,</div><div><br></div><div>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</div><div>in petsc/3.13.4/linux-debug:<br></div><div>TEST linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts<br>not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124<br># Running problem 5<br># [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br># [0]PETSC ERROR: Error in external library<br># [0]PETSC ERROR: Unable to start MATLAB engine on <br># [0]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.<br># [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 <br># [0]PETSC ERROR: ../matlab_ls_test on a linux-debug named MB108SMEC028 by vit Fri Sep 1 10:01:11 2023<br># [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/<br># [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c<br># [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c<br># [0]PETSC ERROR: PETSc Option Table entries:<br># [0]PETSC ERROR: -prob_id 5<br># [0]PETSC ERROR: -tao_smonitor<br># [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint@mcs.anl.gov----------<br># --------------------------------------------------------------------------<br># MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF<br># with errorcode 126076.<br># <br># NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br># You may or may not see output from other processes, depending on<br># exactly when Open MPI kills them.<br># --------------------------------------------------------------------------<br> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff</div><div><br></div><div>in petsc/3.13.4/linux-opt</div><div> TEST linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts<br>not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124<br># Running problem 5<br># [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------<br># [0]PETSC ERROR: Error in external library<br># [0]PETSC ERROR: Unable to start MATLAB engine on <br># [0]PETSC ERROR: See <a href="https://www.mcs.anl.gov/petsc/documentation/faq.html">https://www.mcs.anl.gov/petsc/documentation/faq.html</a> for trouble shooting.<br># [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 <br># [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by vit Fri Sep 1 10:34:12 2023<br># [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/<br># [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c<br># [0]PETSC ERROR: #2 main() line 126 in /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c<br># [0]PETSC ERROR: PETSc Option Table entries:<br># [0]PETSC ERROR: -prob_id 5<br># [0]PETSC ERROR: -tao_smonitor<br># [0]PETSC ERROR: ----------------End of Error Message -------send entire error message to petsc-maint@mcs.anl.gov----------<br># --------------------------------------------------------------------------<br># MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF<br># with errorcode 126076.<br># <br># NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br># You may or may not see output from other processes, depending on<br># exactly when Open MPI kills them.<br># --------------------------------------------------------------------------<br> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed so no diff.</div><div><br></div><div>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.</div><div><br></div><div>Thanks and regards</div><div>Srinivas<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Aug 29, 2023 at 10:56 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov">balay@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Well - you sent in libmesh log not petsc's configure.log/make.log for petsc-3.17<br>
<br>
Anyway - with petsc-3.13 - you have:<br>
<br>
>>>><br>
<br>
Matlab:<br>
Includes: -I/usr/local/MATLAB/R2020b/extern/include<br>
/usr/local/MATLAB/R2020b<br>
MatlabEngine:<br>
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<br>
Language used to compile PETSc: C<br>
<<<<<<br>
<br>
With petsc-3.19 (and matlab-R2022a) - we are seeing:<br>
<br>
<a href="https://gitlab.com/petsc/petsc/-/jobs/4904566768" rel="noreferrer" target="_blank">https://gitlab.com/petsc/petsc/-/jobs/4904566768</a><br>
<br>
>>><br>
Matlab:<br>
Includes: -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include<br>
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<br>
Executable: /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a<br>
mex: /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex<br>
matlab: /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab -glnxa64<br>
<<<<br>
<br>
I.e "-lut -licudata -licui18n -licuuc" are not preset here. This might be a change wrt newer matlab versions.<br>
<br>
You can:<br>
<br>
- edit /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables and remove all occurrences of "-lut -licudata -licui18n -licuuc"<br>
- now run 'make all' in '/home/vit/sfw/petsc/3.13.4'<br>
<br>
And see if the build works now.<br>
<br>
Satish<br>
<br>
On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote:<br>
<br>
> I am sharing the log files while building petsc3.13.4 with matlab and also<br>
> the log file while building libmesh with petsc3.17.5 and matlab. Building<br>
> petsc 3.17.5 with matlab was done successfully. But libmesh is not able to<br>
> find the petsc<br>
> Please find the attachments.<br>
> <br>
> On Tue, Aug 29, 2023 at 7:31 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>> wrote:<br>
> <br>
> > Send configure.log, make.log from both petsc-3.13 and 3.17 [or 3.19].<br>
> ><br>
> > [you can gzip them to make the logs friendly to mailing list - or send<br>
> > them to petsc-maint]<br>
> ><br>
> > And does test suite work with 3.17? [or 3.19?]<br>
> ><br>
> > Satish<br>
> ><br>
> > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote:<br>
> ><br>
> > > I am sharing the make.log file while building petsc-3.13.4 with Matlab.<br>
> > > Please find the attachment and do the needful.<br>
> > ><br>
> > > On Tue, Aug 29, 2023 at 10:19 AM INTURU SRINIVAS 20PHD0548 <<br>
> > > <a href="mailto:inturu.srinivas2020@vitstudent.ac.in" target="_blank">inturu.srinivas2020@vitstudent.ac.in</a>> wrote:<br>
> > ><br>
> > > > I tried with petsc-3.17.5. During building of libmesh, the error shows<br>
> > > > petsc was not found<br>
> > > ><br>
> > > > On Mon, Aug 28, 2023 at 9:43 PM Satish Balay <<a href="mailto:balay@mcs.anl.gov" target="_blank">balay@mcs.anl.gov</a>><br>
> > wrote:<br>
> > > ><br>
> > > >> <a href="https://ibamr.github.io/linux" rel="noreferrer" target="_blank">https://ibamr.github.io/linux</a> says petsc-3.17<br>
> > > >><br>
> > > >> Here you are using 3.13<br>
> > > >><br>
> > > >> Can you retry with petsc-3.17.5?<br>
> > > >><br>
> > > >> Satish<br>
> > > >><br>
> > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote:<br>
> > > >><br>
> > > >> > Hello,<br>
> > > >> ><br>
> > > >> > I want to build PETSc with MATLAB for working on the simulation<br>
> > using<br>
> > > >> IBAMR<br>
> > > >> > open software. While building the PETSc, using the following<br>
> > > >> ><br>
> > > >> > export PETSC_DIR=$PWD<br>
> > > >> > export PETSC_ARCH=linux-debug<br>
> > > >> > ./configure \<br>
> > > >> > --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \<br>
> > > >> > --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \<br>
> > > >> > --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \<br>
> > > >> > --with-debugging=1 \<br>
> > > >> > --download-hypre=1 \<br>
> > > >> > --download-fblaslapack=1 \<br>
> > > >> > --with-x=0 \<br>
> > > >> > --with-matlab-dir=/usr/local/MATLAB/R2020b/<br>
> > > >> > --with-matlab-engine=1<br>
> > > >> > --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/<br>
> > > >> ><br>
> > > >> > make -j4<br>
> > > >> > make -j4 test<br>
> > > >> ><br>
> > > >> > I got the following error<br>
> > > >> > CLINKER<br>
> > > >> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in<br>
> > > >> > function `EvaluateResidual':<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32:<br>
> > > >> > undefined reference to `PetscMatlabEnginePut'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33:<br>
> > > >> > undefined reference to `PetscMatlabEngineEvaluate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35:<br>
> > > >> > undefined reference to `PetscMatlabEngineGet'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in<br>
> > > >> > function `EvaluateJacobian':<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46:<br>
> > > >> > undefined reference to `PetscMatlabEnginePut'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47:<br>
> > > >> > undefined reference to `PetscMatlabEngineEvaluate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49:<br>
> > > >> > undefined reference to `PetscMatlabEngineGet'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in<br>
> > > >> > function `TaoPounders':<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75:<br>
> > > >> > undefined reference to `PetscMatlabEngineGet'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in<br>
> > > >> > function `main':<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126:<br>
> > > >> > undefined reference to `PetscMatlabEngineCreate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127:<br>
> > > >> > undefined reference to `PetscMatlabEngineEvaluate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139:<br>
> > > >> > undefined reference to `PetscMatlabEngineEvaluate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140:<br>
> > > >> > undefined reference to `PetscMatlabEngineGetArray'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142:<br>
> > > >> > undefined reference to `PetscMatlabEngineGetArray'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144:<br>
> > > >> > undefined reference to `PetscMatlabEngineGetArray'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146:<br>
> > > >> > undefined reference to `PetscMatlabEngineGetArray'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148:<br>
> > > >> > undefined reference to `PetscMatlabEngineGetArray'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154:<br>
> > > >> > undefined reference to `PetscMatlabEngineEvaluate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157:<br>
> > > >> > undefined reference to `PetscMatlabEngineEvaluate'<br>
> > > >> > /usr/bin/ld:<br>
> > > >> ><br>
> > > >><br>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158:<br>
> > > >> > undefined reference to `PetscMatlabEngineDestroy'<br>
> > > >> ><br>
> > > >> > collect2: error: ld returned 1 exit status<br>
> > > >> > make: *** [gmakefile.test:185:<br>
> > > >> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test]<br>
> > > >> Error 1<br>
> > > >> > make: *** Waiting for unfinished jobs....<br>
> > > >> ><br>
> > > >> > Please help me to solve this issue<br>
> > > >> ><br>
> > > >> > Thank you<br>
> > > >> > Srinivas<br>
> > > >> ><br>
> > > >> ><br>
> > > >><br>
> > > >><br>
> > ><br>
> > ><br>
> ><br>
> <br>
> <br>
</blockquote></div>
<br>
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