[petsc-users] Error while building PETSc with MATLAB
Satish Balay
balay at mcs.anl.gov
Sun Sep 3 09:30:51 CDT 2023
To use datafiles in the test suite:
cd $HOME
git clone https://gitlab.com/petsc/datafiles
<configure should now pick up this location and set DATAFILESPATH - or set manually with make>
make test query=requires queryval=matlab DATAFILESPATH=$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=<p> or -omp_num_threads <p> 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
> >>>> <snip>
> >>>>
> >>>> <<<< 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
> >>>> > <snip>
> >>>> > 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=<p> or -omp_num_threads <p>
> >>>> 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
> >>>>
> >>>>
> >>>>
> >>>> >
> >>>> > <snip>
> >>>> > 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
> >>>> > <snip>
> >>>> > 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
> >>>> > > >>> > > > > > <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 <
> >>>> > > >>> 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/
> >> <http://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.*
> >
>
>
>
More information about the petsc-users
mailing list