You are missing one more step: > [0] PetscInitialize(): Running on machine: MB108SMEC028 > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash" Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing. Satish On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote: > Hi Sathish, > > I tried the following procedure > > *$make * > CLINKER linux-opt/lib/libpetsc.so.3.13.4 > BEGINNING TO COMPILE MATLAB INTERFACE > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ‘PetscBinaryWrite’: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ‘err’ may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > MEX completed successfully. > Building with 'gcc'. > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c: > In function ‘PetscBinaryWrite’: > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6: > warning: ‘err’ may be used uninitialized in this function > [-Wmaybe-uninitialized] > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n"); > | ^ > > MEX completed successfully. > ========================================= > Now to check if the libraries are working do: > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check > > *$make test query=requires queryval=matlab > DATAFILESPATH=/home/vit/datafiles/* > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab > query=requires > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72 > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > 4 10:02:32 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Petsc has generated inconsistent data > # [0]PETSC ERROR: > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > 4 10:02:32 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: > ------------------------------------------------------------------------ > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > # [0]PETSC ERROR: or see > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS > X to find memory corruption errors > # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > and run > # [0]PETSC ERROR: to get more information on the crash. > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Signal received > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep > 4 10:02:32 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file > # -------------------------------------------------------------------------- > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD > # with errorcode 50162059. > # > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > # You may or may not see output from other processes, depending on > # exactly when Open MPI kills them. > # -------------------------------------------------------------------------- > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff > CC > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o > CLINKER > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test > TEST > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124 > # Running problem 5 > # [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > # [0]PETSC ERROR: Error in external library > # [0]PETSC ERROR: Unable to start MATLAB engine on > # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by > vit Mon Sep 4 10:02:34 2023 > # [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > # [0]PETSC ERROR: #2 main() line 126 in > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c > # [0]PETSC ERROR: PETSc Option Table entries: > # [0]PETSC ERROR: -prob_id 5 > # [0]PETSC ERROR: -tao_smonitor > # [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-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: 4 sec > # Approximate CPU time (not incl. build time): 0.03 sec > # > # To rerun failed tests: > # /usr/bin/make -f gmakefile test test-fail=1 > # > # Timing summary (actual test time / total CPU time): > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec > > *$cd src/tao/leastsquares/tutorials/matlab/* > *$make matlab_ls_test* > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3 > -I/home/vit/sfw/petsc/3.13.4/include > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include > -I/usr/local/MATLAB/R2020b/extern/include > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -L/usr/local/MATLAB/R2020b/bin/glnxa64 > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib > -L/home/vit/sfw/linux/openmpi/4.1.4/lib > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9 > -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath > -lstdc++ -ldl -o matlab_ls_test > > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test > -tao_smonitor -prob_id 5 -info* > [0] PetscInitialize(): PETSc successfully started: number of processors = 1 > [0] PetscGetHostName(): Rejecting domainname, likely is NIS > MB108SMEC028.(none) > [0] PetscInitialize(): Running on machine: MB108SMEC028 > Running problem 5 > [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992 > 94202473157392 max tags = 2147483647 > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Error in external library > [0]PETSC ERROR: Unable to start MATLAB engine on > [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html > for trouble shooting. > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020 > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit > Mon Sep 4 10:09:56 2023 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3 > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b > --with-blaslapack-dir=/usr/local/MATLAB/R2020b > --known-64-bit-blas-indices=1 --with-matlab-engine=1 > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -info > [0]PETSC ERROR: -prob_id 5 > [0]PETSC ERROR: -tao_smonitor > [0]PETSC ERROR: ----------------End of Error Message -------send entire > error message to petsc-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. > > Please find the attachment for configure.log and make.log files > > On Sun, Sep 3, 2023 at 8:00 PM Satish Balay <ba...@mcs.anl.gov> wrote: > > > 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.* > > > > > > > > > > > > > > > > >