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.srinivas2...@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 <knep...@gmail.com> wrote: > > > >> On Sun, Sep 3, 2023 at 3:04 AM INTURU SRINIVAS 20PHD0548 via petsc-users < > >> petsc-users@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-ma...@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-ma...@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 <ba...@mcs.anl.gov> wrote: > >>> > >>>> Perhaps you can try the following to get additional info - and debug > >>>> > >>>> Satish > >>>> ---------- > >>>> > >>>> balay@compute-386-07:/scratch/balay/petsc$ cd > >>>> src/tao/leastsquares/tutorials/matlab/ > >>>> balay@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@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@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@compute-386-07:/scratch/balay/petsc$ git branch > >>>> > main > >>>> > release > >>>> > * release-3.13 > >>>> > balay@compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a > >>>> > balay@compute-386-07:/scratch/balay/petsc$ which matlab > >>>> > > >>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab > >>>> > balay@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@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@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@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@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-ma...@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 < > >>>> mail2amn...@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@mcs.anl.gov> wrote: > >>>> > > > > >>>> > > >> Thank you Sathish.I will try this > >>>> > > >> > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay <ba...@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 <ba...@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 < > >>>> mail2amn...@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@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-ma...@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-ma...@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 < > >>>> > > >>> ba...@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 < > >>>> > > >>> ba...@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.srinivas2...@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 < > >>>> > > >>> > > ba...@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.* > > > > >