[petsc-users] Error while building PETSc with MATLAB
Satish Balay
balay at mcs.anl.gov
Sun Sep 3 23:49:36 CDT 2023
You are missing one more step:
> [0] PetscInitialize(): Running on machine: MB108SMEC028
> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
No run matlab manually on "MB108SMEC028" with the command "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash"
Does this work for you? As the message indicates this command is invoked by "matlab_ls_test" - and that is failing.
Satish
On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote:
> Hi Sathish,
>
> I tried the following procedure
>
> *$make *
> CLINKER linux-opt/lib/libpetsc.so.3.13.4
> BEGINNING TO COMPILE MATLAB INTERFACE
> Building with 'gcc'.
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
> In function ‘PetscBinaryWrite’:
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
> warning: ‘err’ may be used uninitialized in this function
> [-Wmaybe-uninitialized]
> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
> | ^
>
> MEX completed successfully.
> Building with 'gcc'.
> MEX completed successfully.
> Building with 'gcc'.
> MEX completed successfully.
> Building with 'gcc'.
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
> In function ‘PetscBinaryWrite’:
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
> warning: ‘err’ may be used uninitialized in this function
> [-Wmaybe-uninitialized]
> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
> | ^
>
> MEX completed successfully.
> =========================================
> Now to check if the libraries are working do:
> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check
>
> *$make test query=requires queryval=matlab
> DATAFILESPATH=/home/vit/datafiles/*
> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab
> query=requires
> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
> not ok ksp_ksp_tutorials-ex72_12 # Error code: 139
> # [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> # [0]PETSC ERROR: Error in external library
> # [0]PETSC ERROR: Unable to start MATLAB engine on
> # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep
> 4 10:02:32 2023
> # [0]PETSC ERROR: Configure options
> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> # [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> # [0]PETSC ERROR: Petsc has generated inconsistent data
> # [0]PETSC ERROR:
> # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep
> 4 10:02:32 2023
> # [0]PETSC ERROR: Configure options
> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> # [0]PETSC ERROR:
> ------------------------------------------------------------------------
> # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> # [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> # [0]PETSC ERROR: or see
> https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
> # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS
> X to find memory corruption errors
> # [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> and run
> # [0]PETSC ERROR: to get more information on the crash.
> # [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> # [0]PETSC ERROR: Signal received
> # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Mon Sep
> 4 10:02:32 2023
> # [0]PETSC ERROR: Configure options
> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> # [0]PETSC ERROR: #3 User provided function() line 0 in unknown file
> # --------------------------------------------------------------------------
> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> # with errorcode 50162059.
> #
> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> # You may or may not see output from other processes, depending on
> # exactly when Open MPI kills them.
> # --------------------------------------------------------------------------
> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
> CC
> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
> CLINKER
> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
> TEST
> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124
> # Running problem 5
> # [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> # [0]PETSC ERROR: Error in external library
> # [0]PETSC ERROR: Unable to start MATLAB engine on
> # [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by
> vit Mon Sep 4 10:02:34 2023
> # [0]PETSC ERROR: Configure options
> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> # [0]PETSC ERROR: #2 main() line 126 in
> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
> # [0]PETSC ERROR: PETSc Option Table entries:
> # [0]PETSC ERROR: -prob_id 5
> # [0]PETSC ERROR: -tao_smonitor
> # [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
> # --------------------------------------------------------------------------
> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
> # with errorcode 126076.
> #
> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> # You may or may not see output from other processes, depending on
> # exactly when Open MPI kills them.
> # --------------------------------------------------------------------------
> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command failed
> so no diff
>
> # -------------
> # Summary
> # -------------
> # FAILED ksp_ksp_tutorials-ex72_12
> tao_leastsquares_tutorials_matlab-matlab_ls_test
> # success 0/2 tests (0.0%)
> # failed 2/2 tests (100.0%)
> # todo 0/2 tests (0.0%)
> # skip 0/2 tests (0.0%)
> #
> # Wall clock time for tests: 4 sec
> # Approximate CPU time (not incl. build time): 0.03 sec
> #
> # To rerun failed tests:
> # /usr/bin/make -f gmakefile test test-fail=1
> #
> # Timing summary (actual test time / total CPU time):
> # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec
> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec / 0.01 sec
>
> *$cd src/tao/leastsquares/tutorials/matlab/*
> *$make matlab_ls_test*
> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings
> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3
> -I/home/vit/sfw/petsc/3.13.4/include
> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include
> -I/usr/local/MATLAB/R2020b/extern/include
> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c
> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib
> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib
> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> -L/usr/local/MATLAB/R2020b/bin/glnxa64
> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib
> -L/home/vit/sfw/linux/openmpi/4.1.4/lib
> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx
> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh
> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath
> -lstdc++ -ldl -o matlab_ls_test
>
> *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test
> -tao_smonitor -prob_id 5 -info*
> [0] PetscInitialize(): PETSc successfully started: number of processors = 1
> [0] PetscGetHostName(): Rejecting domainname, likely is NIS
> MB108SMEC028.(none)
> [0] PetscInitialize(): Running on machine: MB108SMEC028
> Running problem 5
> [0] PetscCommDuplicate(): Duplicating a communicator 140155238476992
> 94202473157392 max tags = 2147483647
> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command
> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Error in external library
> [0]PETSC ERROR: Unable to start MATLAB engine on
> [0]PETSC ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named MB108SMEC028 by vit
> Mon Sep 4 10:09:56 2023
> [0]PETSC ERROR: Configure options
> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -info
> [0]PETSC ERROR: -prob_id 5
> [0]PETSC ERROR: -tao_smonitor
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
> with errorcode 126076.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
>
> Please find the attachment for configure.log and make.log files
>
> On Sun, Sep 3, 2023 at 8:00 PM Satish Balay <balay at 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.srinivas2020 at vitstudent.ac.in> wrote:
> > >
> > > > Hi Matthew,
> > > >
> > > > I am using PETSc to simulate the problems using IBAMR. I do not have
> > any
> > > > separate test files to test PETSc alone. Can you please help me how to
> > > > define this DATAFILESPATH?
> > > >
> > >
> > > That test you tried uses a certain matrix. On our machine, we point to
> > this
> > > matrix using an environment variable, DATAFILESPATH. You don't have those
> > > matrices, since they are just for testing here. That
> > > is why I suggested just using a different matrix, or running a problem
> > you
> > > care about in IBAMR.
> > >
> > > Thanks,
> > >
> > > Matt
> > >
> > >
> > > > Thanks and regards
> > > > Srinivas.
> > > >
> > > > On Sun, Sep 3, 2023 at 6:06 PM Matthew Knepley <knepley at gmail.com>
> > wrote:
> > > >
> > > >> On Sun, Sep 3, 2023 at 3:04 AM INTURU SRINIVAS 20PHD0548 via
> > petsc-users <
> > > >> petsc-users at mcs.anl.gov> wrote:
> > > >>
> > > >>> Hi Sathish,
> > > >>>
> > > >>> Thank you so much for your efforts and the support you are giving me
> > to
> > > >>> sort this out.
> > > >>>
> > > >>> I tried to follow the same procedure which you followed to build
> > Petsc
> > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04.
> > > >>>
> > > >>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
> > > >>> --with-debugging=0 --with-x=0
> > --with-matlab-dir=/usr/local/MATLAB/R2020b
> > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1*
> > > >>> Using python3 for Python
> > > >>>
> > > >>>
> > ===============================================================================
> > > >>> Configuring PETSc to compile on your system
> > > >>>
> > > >>>
> > > >>>
> > ===============================================================================
> > > >>>
> > ===============================================================================
> > > >>> It appears you do not have
> > valgrind
> > > >>> installed on your system.
> > > >>> We HIGHLY recommend you install it from www.valgrind.org
> > > >>> Or install
> > valgrind-devel or
> > > >>> equivalent using your package manager.
> > > >>> Then rerun ./configure
> > > >>>
> > > >>>
> > ===============================================================================
> > > >>> Compilers:
> > > >>>
> > > >>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
> > -fPIC
> > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > > >>> -fstack-protector -fvisibility=hidden -O3
> > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
> > > >>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
> > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC
> > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0
> > > >>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
> > > >>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3
> > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
> > > >>> Linkers:
> > > >>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
> > -shared
> > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> > -Wno-unknown-pragmas
> > > >>> -fstack-protector -fvisibility=hidden -O3
> > > >>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
> > -shared
> > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
> > -Wno-unknown-pragmas
> > > >>> -fstack-protector -fvisibility=hidden -O3
> > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl
> > > >>> make:
> > > >>> Version: 4.2
> > > >>> /usr/bin/make
> > > >>> BlasLapack:
> > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
> > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
> > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread
> > > >>> uses OpenMP; use export OMP_NUM_THREADS=<p> or -omp_num_threads
> > <p> to
> > > >>> control the number of threads
> > > >>> uses 8 byte integers
> > > >>> MPI:
> > > >>> Version: 3
> > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include
> > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec
> > --oversubscribe
> > > >>> OMPI_VERSION: 4.1.4
> > > >>> pthread:
> > > >>> cmake:
> > > >>> Version: 3.16.3
> > > >>> /usr/bin/cmake
> > > >>> regex:
> > > >>> Matlab:
> > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include
> > > >>> /usr/local/MATLAB/R2020b
> > > >>> MatlabEngine:
> > > >>> Library:
> > > >>>
> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
> > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat
> > -lut
> > > >>> -licudata -licui18n -licuuc
> > > >>> Language used to compile PETSc: C
> > > >>> PETSc:
> > > >>> PETSC_ARCH: linux-opt
> > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4
> > > >>> Scalar type: real
> > > >>> Precision: double
> > > >>> Support for __float128
> > > >>> Integer size: 4 bytes
> > > >>> shared libraries: enabled
> > > >>> Memory alignment from malloc(): 16 bytes
> > > >>>
> > > >>>
> > xxx=========================================================================xxx
> > > >>> Configure stage complete. Now build PETSc libraries with:
> > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all
> > > >>>
> > > >>>
> > xxx=========================================================================xxx
> > > >>>
> > > >>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as
> > > >>> you suggested earlier.
> > > >>>
> > > >>> *$make*
> > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o
> > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4
> > > >>> BEGINNING TO COMPILE MATLAB INTERFACE
> > > >>> Building with 'gcc'.
> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
> > > >>> In function ‘PetscBinaryWrite’:
> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
> > > >>> warning: ‘err’ may be used uninitialized in this function
> > > >>> [-Wmaybe-uninitialized]
> > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
> > > >>> | ^
> > > >>>
> > > >>> MEX completed successfully.
> > > >>> Building with 'gcc'.
> > > >>> MEX completed successfully.
> > > >>> Building with 'gcc'.
> > > >>> MEX completed successfully.
> > > >>> Building with 'gcc'.
> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
> > > >>> In function ‘PetscBinaryWrite’:
> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
> > > >>> warning: ‘err’ may be used uninitialized in this function
> > > >>> [-Wmaybe-uninitialized]
> > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
> > > >>> | ^
> > > >>>
> > > >>> MEX completed successfully.
> > > >>> =========================================
> > > >>> Now to check if the libraries are working do:
> > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check
> > > >>> ===============================================
> > > >>>
> > > >>> *$make test query=requires queryval=matlab*
> > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires
> > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
> > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
> > > >>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
> > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169
> > > >>> # [0]PETSC ERROR: --------------------- Error Message
> > > >>> --------------------------------------------------------------
> > > >>> # [0]PETSC ERROR: Unable to open file
> > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1
> > > >>>
> > > >>
> > > >> No, the problem is that you do not have DATAFILESPATH defined, so it
> > > >> cannot find the matrix to test. Try running some test of yours.
> > > >>
> > > >> Thanks,
> > > >>
> > > >> Matt
> > > >>
> > > >>
> > > >>> # [0]PETSC ERROR: See
> > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> > > >>> shooting.
> > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit
> > Sun
> > > >>> Sep 3 11:51:03 2023
> > > >>> # [0]PETSC ERROR: Configure options
> > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c
> > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c
> > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c
> > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c
> > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c
> > > >>> # [0]PETSC ERROR: #6 main() line 113 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c
> > > >>> # [0]PETSC ERROR: PETSc Option Table entries:
> > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1
> > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
> > > >>> # [0]PETSC ERROR: -pc_type lu
> > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send
> > > >>> entire error message to petsc-maint at mcs.anl.gov----------
> > > >>> #
> > > >>>
> > --------------------------------------------------------------------------
> > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
> > > >>> # with errorcode 113065.
> > > >>> #
> > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > > >>> # You may or may not see output from other processes, depending on
> > > >>> # exactly when Open MPI kills them.
> > > >>> #
> > > >>>
> > --------------------------------------------------------------------------
> > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
> > > >>> CC
> > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
> > > >>> CLINKER
> > > >>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
> > > >>> TEST
> > > >>>
> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
> > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
> > code: 124
> > > >>> # Running problem 5
> > > >>> # [0]PETSC ERROR: --------------------- Error Message
> > > >>> --------------------------------------------------------------
> > > >>> # [0]PETSC ERROR: Error in external library
> > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on
> > > >>> # [0]PETSC ERROR: See
> > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
> > > >>> shooting.
> > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named
> > MB108SMEC028 by
> > > >>> vit Sun Sep 3 11:51:05 2023
> > > >>> # [0]PETSC ERROR: Configure options
> > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
> > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> > > >>> # [0]PETSC ERROR: #2 main() line 126 in
> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
> > > >>> # [0]PETSC ERROR: PETSc Option Table entries:
> > > >>> # [0]PETSC ERROR: -prob_id 5
> > > >>> # [0]PETSC ERROR: -tao_smonitor
> > > >>> # [0]PETSC ERROR: ----------------End of Error Message -------send
> > > >>> entire error message to petsc-maint at mcs.anl.gov----------
> > > >>> #
> > > >>>
> > --------------------------------------------------------------------------
> > > >>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
> > > >>> # with errorcode 126076.
> > > >>> #
> > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > > >>> # You may or may not see output from other processes, depending on
> > > >>> # exactly when Open MPI kills them.
> > > >>> #
> > > >>>
> > --------------------------------------------------------------------------
> > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command
> > > >>> failed so no diff
> > > >>>
> > > >>> # -------------
> > > >>> # Summary
> > > >>> # -------------
> > > >>> # FAILED ksp_ksp_tutorials-ex72_12
> > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test
> > > >>> # success 0/2 tests (0.0%)
> > > >>> # failed 2/2 tests (100.0%)
> > > >>> # todo 0/2 tests (0.0%)
> > > >>> # skip 0/2 tests (0.0%)
> > > >>> #
> > > >>> # Wall clock time for tests: 3 sec
> > > >>> # Approximate CPU time (not incl. build time): 0.05 sec
> > > >>> #
> > > >>> # To rerun failed tests:
> > > >>> # /usr/bin/make -f gmakefile test test-fail=1
> > > >>> #
> > > >>> # Timing summary (actual test time / total CPU time):
> > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec
> > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec /
> > 0.02 sec
> > > >>>
> > > >>> *How to sort out this error?*
> > > >>>
> > > >>> *$cd src/tao/leastsquares/tutorials/matlab/*
> > > >>> *$make matlab_ls_test*
> > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall
> > -Wwrite-strings
> > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
> > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings
> > -Wno-strict-aliasing
> > > >>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3
> > > >>> -I/home/vit/sfw/petsc/3.13.4/include
> > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include
> > > >>> -I/usr/local/MATLAB/R2020b/extern/include
> > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c
> > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib
> > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib
> > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
> > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
> > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
> > > >>>
> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
> > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib
> > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib
> > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
> > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9
> > -Wl,-rpath,/usr/lib/x86_64-linux-gnu
> > > >>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
> > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex
> > -lmx
> > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr
> > -lmpi_mpifh
> > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread
> > -lquadmath
> > > >>> -lstdc++ -ldl -o matlab_ls_test
> > > >>>
> > > >>> I think there is a problem with the Matlab-R2020b version.
> > > >>> I am sharing the configure.log and make.log files. Please find the
> > > >>> attachment and do the needful.
> > > >>>
> > > >>>
> > > >>> Thanks and regards
> > > >>> Srinivas
> > > >>>
> > > >>>
> > > >>> On Sat, Sep 2, 2023 at 11:15 PM Satish Balay <balay at mcs.anl.gov>
> > wrote:
> > > >>>
> > > >>>> Perhaps you can try the following to get additional info - and debug
> > > >>>>
> > > >>>> Satish
> > > >>>> ----------
> > > >>>>
> > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd
> > > >>>> src/tao/leastsquares/tutorials/matlab/
> > > >>>> balay at compute-386-07
> > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
> > > >>>> make matlab_ls_test
> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC
> > -Wall
> > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > -fstack-protector
> > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings
> > -Wno-strict-aliasing
> > > >>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3
> > > >>>> -I/scratch/balay/petsc/include
> > -I/scratch/balay/petsc/linux-opt/include
> > > >>>>
> > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include
> > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include
> > > >>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib
> > > >>>> -L/scratch/balay/petsc/linux-opt/lib
> > > >>>>
> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
> > > >>>>
> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64
> > > >>>>
> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
> > > >>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib
> > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib
> > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
> > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9
> > -Wl,-rpath,/usr/lib/x86_64-linux-gnu
> > > >>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
> > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng
> > -lmex
> > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort
> > -lmpi
> > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o
> > > >>>> matlab_ls_test
> > > >>>> balay at compute-386-07
> > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
> > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test
> > > >>>> -tao_smonitor -prob_id 5 -info
> > > >>>> [0] PetscInitialize(): PETSc successfully started: number of
> > processors
> > > >>>> = 1
> > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS
> > > >>>> compute-386-07.(none)
> > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07
> > > >>>> Running problem 5
> > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689
> > > >>>> -2080374784 max tags = 268435455
> > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
> > > >>>> -glnxa64 -nodisplay -nosplash
> > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine
> > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string:
> > > >>>> TestingInitialize
> > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string:
> > > >>>> TestingInitialize
> > > >>>> 5
> > > >>>> <snip>
> > > >>>>
> > > >>>> <<<< Now verify if the above matlab command actually works for you
> > - on
> > > >>>> this machine..>>>>>
> > > >>>>
> > > >>>> balay at compute-386-07
> > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
> > > >>>> -glnxa64 -nodisplay -nosplash
> > > >>>>
> > > >>>>
> > > >>>> < M A T L A B (R) >
> > > >>>>
> > > >>>> Copyright 1984-2021 The MathWorks, Inc.
> > > >>>>
> > > >>>> R2021a (9.10.0.1602886) 64-bit (glnxa64)
> > > >>>>
> > > >>>> February 17, 2021
> > > >>>>
> > > >>>>
> > > >>>> To get started, type doc.
> > > >>>> For product information, visit www.mathworks.com.
> > > >>>>
> > > >>>> >>
> > > >>>>
> > > >>>>
> > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote:
> > > >>>>
> > > >>>> > Please don't cc: both petsc-users and petsc-maint [reverting
> > thread
> > > >>>> to petsc-users only]
> > > >>>> >
> > > >>>> > I'm not sure what is happening here. Can you send the
> > corresponding
> > > >>>> configure.log, make.log [compressed]?
> > > >>>> >
> > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04,
> > > >>>> with Matlab-R2021a - and that works:
> > > >>>> >
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch
> > > >>>> > main
> > > >>>> > release
> > > >>>> > * release-3.13
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load
> > matlab/R2021a
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab
> > > >>>> >
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure
> > > >>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/
> > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
> > > >>>> --with-debugging=0 --with-x=0
> > > >>>>
> > --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
> > > >>>>
> > --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
> > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
> > > >>>> > <snip>
> > > >>>> > Compilers:
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>> > C Compiler:
> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC
> > -Wall
> > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > -fstack-protector
> > > >>>> -fvisibility=hidden -O3
> > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
> > > >>>> > C++ Compiler:
> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall
> > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > -fstack-protector
> > > >>>> -fvisibility=hidden -O3 -fPIC
> > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
> > > >>>> > Fortran Compiler:
> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC
> > -Wall
> > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3
> > > >>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
> > > >>>> > Linkers:
> > > >>>> > Shared linker:
> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc
> > -shared -fPIC
> > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > > >>>> -fstack-protector -fvisibility=hidden -O3
> > > >>>> > Dynamic linker:
> > > >>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc
> > -shared -fPIC
> > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
> > > >>>> -fstack-protector -fvisibility=hidden -O3
> > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl
> > > >>>> > make:
> > > >>>> > Version: 4.2
> > > >>>> > /usr/bin/make
> > > >>>> > BlasLapack:
> > > >>>> > Library:
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so
> > > >>>>
> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64
> > > >>>>
> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64
> > > >>>> -liomp5 -lpthread
> > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=<p> or -omp_num_threads
> > <p>
> > > >>>> to control the number of threads
> > > >>>> > uses 8 byte integers
> > > >>>> > MPI:
> > > >>>> > Version: 4
> > > >>>> > Includes:
> > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include
> > > >>>> > Mpiexec:
> > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec
> > > >>>> > MPICH_NUMVERSION: 40002300
> > > >>>> > pthread:
> > > >>>> > Library: -lpthread
> > > >>>> > cmake:
> > > >>>> > Version: 3.16.3
> > > >>>> > /usr/bin/cmake
> > > >>>> > regex:
> > > >>>> > Matlab:
> > > >>>> > Includes:
> > > >>>>
> > -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include
> > > >>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
> > > >>>> > MatlabEngine:
> > > >>>> > Library:
> > > >>>>
> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
> > > >>>>
> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64
> > > >>>>
> > -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
> > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc
> > > >>>> > sowing:
> > > >>>> > Version: 1.1.25
> > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort
> > > >>>> > valgrind:
> > > >>>> > Language used to compile PETSc: C
> > > >>>> > PETSc:
> > > >>>> > PETSC_ARCH: linux-opt
> > > >>>> > PETSC_DIR: /scratch/balay/petsc
> > > >>>> > Scalar type: real
> > > >>>> > Precision: double
> > > >>>> > Support for __float128
> > > >>>> > Integer size: 4 bytes
> > > >>>> > shared libraries: enabled
> > > >>>> > Memory alignment from malloc(): 16 bytes
> > > >>>> >
> > > >>>>
> > xxx=========================================================================xxx
> > > >>>> > Configure stage complete. Now build PETSc libraries with:
> > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all
> > > >>>> >
> > > >>>>
> > xxx=========================================================================xxx
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make
> > > >>>>
> > > >>>>
> > > >>>>
> > > >>>> >
> > > >>>> > <snip>
> > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o
> > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6
> > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE
> > > >>>> > Building with 'gcc'.
> > > >>>> >
> > > >>>>
> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In
> > > >>>> function ‘PetscBinaryWrite’:
> > > >>>> >
> > > >>>>
> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
> > > >>>> warning: ‘err’ may be used uninitialized in this function
> > > >>>> [-Wmaybe-uninitialized]
> > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to
> > socket\n");
> > > >>>> > | ^
> > > >>>> >
> > > >>>> > MEX completed successfully.
> > > >>>> > Building with 'gcc'.
> > > >>>> > MEX completed successfully.
> > > >>>> > Building with 'gcc'.
> > > >>>> > MEX completed successfully.
> > > >>>> > Building with 'gcc'.
> > > >>>> >
> > > >>>>
> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In
> > > >>>> function ‘PetscBinaryWrite’:
> > > >>>> >
> > > >>>>
> > /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
> > > >>>> warning: ‘err’ may be used uninitialized in this function
> > > >>>> [-Wmaybe-uninitialized]
> > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to
> > socket\n");
> > > >>>> > | ^
> > > >>>> >
> > > >>>> > MEX completed successfully.
> > > >>>> > =========================================
> > > >>>> > Now to check if the libraries are working do:
> > > >>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check
> > > >>>> > =========================================
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test
> > query=requires
> > > >>>> queryval=matlab
> > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires
> > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
> > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
> > > >>>> > TEST
> > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
> > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1
> > > >>>> > # ../ex72:
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5:
> > > >>>> version `GFORTRAN_9' not found (required by
> > > >>>>
> > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12)
> > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
> > > >>>> > CC
> > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
> > > >>>> > CLINKER
> > > >>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
> > > >>>> > TEST
> > > >>>>
> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
> > > >>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
> > code:
> > > >>>> 1
> > > >>>> > # ../matlab_ls_test:
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5:
> > > >>>> version `GFORTRAN_9' not found (required by
> > > >>>>
> > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12)
> > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP
> > Command
> > > >>>> failed so no diff
> > > >>>> > <snip>
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$
> > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test
> > query=requires
> > > >>>> queryval=matlab
> > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires
> > > >>>> > TEST
> > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
> > > >>>> > ok ksp_ksp_tutorials-ex72_12
> > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12
> > > >>>> > TEST
> > > >>>>
> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
> > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test
> > > >>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test
> > > >>>> >
> > > >>>> > # -------------
> > > >>>> > # Summary
> > > >>>> > # -------------
> > > >>>> > # success 4/4 tests (100.0%)
> > > >>>> > # failed 0/4 tests (0.0%)
> > > >>>> > # todo 0/4 tests (0.0%)
> > > >>>> > # skip 0/4 tests (0.0%)
> > > >>>> > #
> > > >>>> > # Wall clock time for tests: 27 sec
> > > >>>> > # Approximate CPU time (not incl. build time): 15.190000000000001
> > sec
> > > >>>> > #
> > > >>>> > # Timing summary (actual test time / total CPU time):
> > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec /
> > 7.54
> > > >>>> sec
> > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec
> > > >>>> > balay at compute-386-07:/scratch/balay/petsc$
> > > >>>> >
> > > >>>> >
> > > >>>> >
> > > >>>> >
> > > >>>> >
> > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote:
> > > >>>> >
> > > >>>> > > Based on the suggestions given by Sathish, I have tried to
> > > >>>> configure petsc
> > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After
> > > >>>> running make
> > > >>>> > > -j 10 test command I have got the following error message.
> > > >>>> > >
> > > >>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
> > > >>>> code: 124
> > > >>>> > > # Running problem 5
> > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message
> > > >>>> > > --------------------------------------------------------------
> > > >>>> > > # [0]PETSC ERROR: Error in external library
> > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on
> > > >>>> > > # [0]PETSC ERROR: See
> > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
> > > >>>> > > for trouble shooting.
> > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
> > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named
> > > >>>> MB108SMEC028 by
> > > >>>> > > vit Sat Sep 2 12:27:22 2023
> > > >>>> > > # [0]PETSC ERROR: Configure options
> > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
> > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
> > > >>>> --with-debugging=0
> > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
> > > >>>> > > --with-matlab-engine=1
> > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>>> > > --known-64-bit-blas-indices=1
> > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
> > > >>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in
> > > >>>> > >
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
> > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries:
> > > >>>> > > # [0]PETSC ERROR: -prob_id 5
> > > >>>> > > # [0]PETSC ERROR: -tao_smonitor
> > > >>>> > > # [0]PETSC ERROR: ----------------End of Error Message
> > -------send
> > > >>>> entire
> > > >>>> > > error message to petsc-maint at mcs.anl.gov----------
> > > >>>> > > #
> > > >>>>
> > --------------------------------------------------------------------------
> > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
> > > >>>> > > # with errorcode 126076.
> > > >>>> > > #
> > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
> > > >>>> processes.
> > > >>>> > > # You may or may not see output from other processes, depending
> > on
> > > >>>> > > # exactly when Open MPI kills them.
> > > >>>> > > #
> > > >>>>
> > --------------------------------------------------------------------------
> > > >>>> > >
> > > >>>> > > I request you to help me to sort out this error.
> > > >>>> > >
> > > >>>> > > Thanks
> > > >>>> > > Srinivas
> > > >>>> > >
> > > >>>> > >
> > > >>>> > > On Fri, Sep 1, 2023 at 11:42 PM Amneet Bhalla <
> > > >>>> mail2amneet at gmail.com> wrote:
> > > >>>> > >
> > > >>>> > > > I think there should be two hyphens in
> > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>>> > > >
> > > >>>> > > > i.e.:
> > > >>>> > > >
> > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>>> > > >
> > > >>>> > > > On Fri, Sep 1, 2023 at 10:25 AM INTURU SRINIVAS 20PHD0548 via
> > > >>>> petsc-users <
> > > >>>> > > > petsc-users at mcs.anl.gov> wrote:
> > > >>>> > > >
> > > >>>> > > >> Thank you Sathish.I will try this
> > > >>>> > > >>
> > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay <balay at mcs.anl.gov>
> > > >>>> wrote:
> > > >>>> > > >>
> > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work
> > > >>>> here].
> > > >>>> > > >>>
> > > >>>> > > >>> i.e:
> > > >>>> > > >>>
> > > >>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
> > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> > PETSC_ARCH=linux-opt
> > > >>>> > > >>> --with-debugging=0 --with-x=0 \
> > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b
> > > >>>> --with-matlab-engine=1
> > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b
> > > >>>> --known-64-bit-blas-indices=1
> > > >>>> > > >>>
> > > >>>> > > >>> Satish
> > > >>>> > > >>>
> > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via
> > petsc-users
> > > >>>> wrote:
> > > >>>> > > >>>
> > > >>>> > > >>> > Hi Satish,
> > > >>>> > > >>> >
> > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir
> > > >>>> > > >>> > --known-64-bit-blas-indices=1
> > > >>>> > > >>> >
> > > >>>> > > >>> > Is this what you are suggesting?
> > > >>>> > > >>> >
> > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay <
> > balay at mcs.anl.gov>
> > > >>>> wrote:
> > > >>>> > > >>> >
> > > >>>> > > >>> > > Also:
> > > >>>> > > >>> > >
> > > >>>> > > >>> > > '-known-64-bit-blas-indices=1',
> > > >>>> > > >>> > >
> > > >>>> > > >>> > > Note: most externalpackages might not work in this mode.
> > > >>>> > > >>> > >
> > > >>>> > > >>> > > [we can't really over come such dependency/conflicts
> > across
> > > >>>> packages]
> > > >>>> > > >>> > >
> > > >>>> > > >>> > > Satish
> > > >>>> > > >>> > >
> > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote:
> > > >>>> > > >>> > >
> > > >>>> > > >>> > > > Here is the matlab test that runs in CI
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict
> > with
> > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring
> > > >>>> -known-64-bit-blas-indices=1
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with
> > > >>>> matlab - to
> > > >>>> > > >>> have a
> > > >>>> > > >>> > > compatible build
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir,
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > Satish
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via
> > > >>>> petsc-users
> > > >>>> > > >>> wrote:
> > > >>>> > > >>> > > >
> > > >>>> > > >>> > > > > Hi Amneet,
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not
> > > >>>> working. It is
> > > >>>> > > >>> > > showing
> > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions.
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with
> > > >>>> libmesh and
> > > >>>> > > >>> this is
> > > >>>> > > >>> > > for
> > > >>>> > > >>> > > > > general usage not only for WEC. This I tried without
> > > >>>> linking
> > > >>>> > > >>> Matlab
> > > >>>> > > >>> > > with
> > > >>>> > > >>> > > > > PETSc. Here also I got the error while configuring
> > > >>>> libmesh 1.6.2
> > > >>>> > > >>> that
> > > >>>> > > >>> > > PETSc
> > > >>>> > > >>> > > > > was not found but --enable-petsc-required is
> > specified.
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > The reason for specifically asking for libmesh with
> > > >>>> PETSc and
> > > >>>> > > >>> Matlab
> > > >>>> > > >>> > > is in
> > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated
> > geometries
> > > >>>> it is
> > > >>>> > > >>> > > mentioned to
> > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct.
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > For the past 10 days I am trying these various
> > things
> > > >>>> and ended
> > > >>>> > > >>> up with
> > > >>>> > > >>> > > > > errors.
> > > >>>> > > >>> > > > > I want to solve this and proceed further to do my
> > > >>>> research work.
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > Please help me to solve this as soon as possible.
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > Thanks and Regards
> > > >>>> > > >>> > > > > Srinivas
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla <
> > > >>>> mail2amneet at gmail.com>
> > > >>>> > > >>> > > wrote:
> > > >>>> > > >>> > > > >
> > > >>>> > > >>> > > > > > Hi Srinivas,
> > > >>>> > > >>> > > > > >
> > > >>>> > > >>> > > > > > As discussed earlier you don’t need libMesh for
> > the
> > > >>>> WEC
> > > >>>> > > >>> application.
> > > >>>> > > >>> > > You
> > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with
> > > >>>> Matlab.
> > > >>>> > > >>> > > > > >
> > > >>>> > > >>> > > > > > Do you have a specific reason for wanting to build
> > > >>>> libMesh?
> > > >>>> > > >>> > > > > >
> > > >>>> > > >>> > > > > > Thanks,
> > > >>>> > > >>> > > > > > —Amneet
> > > >>>> > > >>> > > > > >
> > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS
> > > >>>> 20PHD0548 via
> > > >>>> > > >>> > > petsc-users
> > > >>>> > > >>> > > > > > <petsc-users at mcs.anl.gov> wrote:
> > > >>>> > > >>> > > > > >
> > > >>>> > > >>> > > > > >> Hi,
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all
> > > >>>> occurrences
> > > >>>> > > >>> of
> > > >>>> > > >>> > > "-lut
> > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make
> > test"
> > > >>>> got the
> > > >>>> > > >>> > > following
> > > >>>> > > >>> > > > > >> errors
> > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug:
> > > >>>> > > >>> > > > > >> TEST
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
> > > >>>> > > >>> > > > > >> not ok
> > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
> > > >>>> > > >>> Error
> > > >>>> > > >>> > > code: 124
> > > >>>> > > >>> > > > > >> # Running problem 5
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error
> > Message
> > > >>>> > > >>> > > > > >>
> > > >>>> --------------------------------------------------------------
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine
> > on
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See
> > > >>>> > > >>> > > > > >>
> > https://www.mcs.anl.gov/petsc/documentation/faq.html
> > > >>>> for
> > > >>>> > > >>> trouble
> > > >>>> > > >>> > > > > >> shooting.
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4,
> > Aug
> > > >>>> 01, 2020
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a
> > linux-debug
> > > >>>> named
> > > >>>> > > >>> > > MB108SMEC028
> > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
> > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
> > > >>>> > > >>> > > > > >>
> > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
> > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
> > > >>>> > > >>> --with-debugging=1
> > > >>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1
> > > >>>> --with-x=0
> > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/
> > > >>>> > > >>> --with-matlab-engine=1
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>>
> > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate()
> > line
> > > >>>> 67 in
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries:
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error
> > > >>>> Message
> > > >>>> > > >>> -------send
> > > >>>> > > >>> > > entire
> > > >>>> > > >>> > > > > >> error message to
> > petsc-maint at mcs.anl.gov----------
> > > >>>> > > >>> > > > > >> #
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > --------------------------------------------------------------------------
> > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator
> > > >>>> > > >>> MPI_COMM_SELF
> > > >>>> > > >>> > > > > >> # with errorcode 126076.
> > > >>>> > > >>> > > > > >> #
> > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to
> > kill
> > > >>>> all MPI
> > > >>>> > > >>> > > processes.
> > > >>>> > > >>> > > > > >> # You may or may not see output from other
> > processes,
> > > >>>> > > >>> depending on
> > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them.
> > > >>>> > > >>> > > > > >> #
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > --------------------------------------------------------------------------
> > > >>>> > > >>> > > > > >> ok
> > tao_leastsquares_tutorials_matlab-matlab_ls_test
> > > >>>> # SKIP
> > > >>>> > > >>> Command
> > > >>>> > > >>> > > > > >> failed so no diff
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt
> > > >>>> > > >>> > > > > >> TEST
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
> > > >>>> > > >>> > > > > >> not ok
> > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
> > > >>>> > > >>> Error
> > > >>>> > > >>> > > code: 124
> > > >>>> > > >>> > > > > >> # Running problem 5
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error
> > Message
> > > >>>> > > >>> > > > > >>
> > > >>>> --------------------------------------------------------------
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine
> > on
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See
> > > >>>> > > >>> > > > > >>
> > https://www.mcs.anl.gov/petsc/documentation/faq.html
> > > >>>> for
> > > >>>> > > >>> trouble
> > > >>>> > > >>> > > > > >> shooting.
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4,
> > Aug
> > > >>>> 01, 2020
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a
> > linux-opt
> > > >>>> named
> > > >>>> > > >>> > > MB108SMEC028 by
> > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
> > > >>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
> > > >>>> > > >>> > > > > >>
> > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
> > > >>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
> > > >>>> > > >>> --COPTFLAGS=-O3
> > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3
> > > >>>> --PETSC_ARCH=linux-opt
> > > >>>> > > >>> > > --with-debugging=0
> > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0
> > > >>>> --download-fblaslapack=1
> > > >>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/
> > > >>>> > > >>> --with-matlab-engine=1
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>>
> > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate()
> > line
> > > >>>> 67 in
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>>
> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries:
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
> > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error
> > > >>>> Message
> > > >>>> > > >>> -------send
> > > >>>> > > >>> > > entire
> > > >>>> > > >>> > > > > >> error message to
> > petsc-maint at mcs.anl.gov----------
> > > >>>> > > >>> > > > > >> #
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > --------------------------------------------------------------------------
> > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator
> > > >>>> > > >>> MPI_COMM_SELF
> > > >>>> > > >>> > > > > >> # with errorcode 126076.
> > > >>>> > > >>> > > > > >> #
> > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to
> > kill
> > > >>>> all MPI
> > > >>>> > > >>> > > processes.
> > > >>>> > > >>> > > > > >> # You may or may not see output from other
> > processes,
> > > >>>> > > >>> depending on
> > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them.
> > > >>>> > > >>> > > > > >> #
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > --------------------------------------------------------------------------
> > > >>>> > > >>> > > > > >> ok
> > tao_leastsquares_tutorials_matlab-matlab_ls_test
> > > >>>> # SKIP
> > > >>>> > > >>> Command
> > > >>>> > > >>> > > > > >> failed so no diff.
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5
> > version. I
> > > >>>> am
> > > >>>> > > >>> sharing the
> > > >>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and
> > > >>>> petsc
> > > >>>> > > >>> 3.17.5.
> > > >>>> > > >>> > > Please find
> > > >>>> > > >>> > > > > >> the attachment and do the needful.
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >> Thanks and regards
> > > >>>> > > >>> > > > > >> Srinivas
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56 PM Satish Balay <
> > > >>>> > > >>> balay at mcs.anl.gov>
> > > >>>> > > >>> > > wrote:
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's
> > > >>>> > > >>> configure.log/make.log
> > > >>>> > > >>> > > for
> > > >>>> > > >>> > > > > >>> petsc-3.17
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> >>>>
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> Matlab:
> > > >>>> > > >>> > > > > >>> Includes:
> > > >>>> -I/usr/local/MATLAB/R2020b/extern/include
> > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b
> > > >>>> > > >>> > > > > >>> MatlabEngine:
> > > >>>> > > >>> > > > > >>> Library:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
> > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
> > -leng
> > > >>>> -lmex
> > > >>>> > > >>> -lmx
> > > >>>> > > >>> > > -lmat -lut
> > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc
> > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C
> > > >>>> > > >>> > > > > >>> <<<<<
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are
> > seeing:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>>
> > https://gitlab.com/petsc/petsc/-/jobs/4904566768
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> >>>
> > > >>>> > > >>> > > > > >>> Matlab:
> > > >>>> > > >>> > > > > >>> Includes:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include
> > > >>>> > > >>> > > > > >>> Libraries:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
> > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat
> > > >>>> > > >>> > > > > >>> Executable:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>>
> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a
> > > >>>> > > >>> > > > > >>> mex:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex
> > > >>>> > > >>> > > > > >>> matlab:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab
> > > >>>> > > >>> > > > > >>> -glnxa64
> > > >>>> > > >>> > > > > >>> <<<
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not
> > > >>>> preset here.
> > > >>>> > > >>> This
> > > >>>> > > >>> > > might
> > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions.
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> You can:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> - edit
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>>
> > > >>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables
> > > >>>> > > >>> > > and
> > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata
> > -licui18n
> > > >>>> -licuuc"
> > > >>>> > > >>> > > > > >>> - now run 'make all' in
> > '/home/vit/sfw/petsc/3.13.4'
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> And see if the build works now.
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> Satish
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548
> > via
> > > >>>> > > >>> petsc-users
> > > >>>> > > >>> > > wrote:
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>> > I am sharing the log files while building
> > > >>>> petsc3.13.4 with
> > > >>>> > > >>> > > matlab and
> > > >>>> > > >>> > > > > >>> also
> > > >>>> > > >>> > > > > >>> > the log file while building libmesh with
> > > >>>> petsc3.17.5 and
> > > >>>> > > >>> matlab.
> > > >>>> > > >>> > > > > >>> Building
> > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done
> > successfully.
> > > >>>> But
> > > >>>> > > >>> libmesh is
> > > >>>> > > >>> > > not
> > > >>>> > > >>> > > > > >>> able to
> > > >>>> > > >>> > > > > >>> > find the petsc
> > > >>>> > > >>> > > > > >>> > Please find the attachments.
> > > >>>> > > >>> > > > > >>> >
> > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31 PM Satish Balay <
> > > >>>> > > >>> balay at mcs.anl.gov>
> > > >>>> > > >>> > > > > >>> wrote:
> > > >>>> > > >>> > > > > >>> >
> > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from both
> > > >>>> petsc-3.13 and
> > > >>>> > > >>> 3.17 [or
> > > >>>> > > >>> > > 3.19].
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs
> > friendly to
> > > >>>> mailing
> > > >>>> > > >>> list -
> > > >>>> > > >>> > > or
> > > >>>> > > >>> > > > > >>> send
> > > >>>> > > >>> > > > > >>> > > them to petsc-maint]
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or
> > 3.19?]
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>> > > Satish
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS
> > 20PHD0548
> > > >>>> via
> > > >>>> > > >>> petsc-users
> > > >>>> > > >>> > > wrote:
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file while
> > building
> > > >>>> > > >>> petsc-3.13.4
> > > >>>> > > >>> > > with
> > > >>>> > > >>> > > > > >>> Matlab.
> > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do the
> > needful.
> > > >>>> > > >>> > > > > >>> > > >
> > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19 AM INTURU
> > > >>>> SRINIVAS
> > > >>>> > > >>> 20PHD0548 <
> > > >>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in>
> > wrote:
> > > >>>> > > >>> > > > > >>> > > >
> > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During
> > building
> > > >>>> of
> > > >>>> > > >>> libmesh, the
> > > >>>> > > >>> > > error
> > > >>>> > > >>> > > > > >>> shows
> > > >>>> > > >>> > > > > >>> > > > > petsc was not found
> > > >>>> > > >>> > > > > >>> > > > >
> > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43 PM Satish
> > > >>>> Balay <
> > > >>>> > > >>> > > balay at mcs.anl.gov>
> > > >>>> > > >>> > > > > >>> > > wrote:
> > > >>>> > > >>> > > > > >>> > > > >
> > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says
> > > >>>> petsc-3.17
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5?
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > > >> Satish
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS
> > > >>>> 20PHD0548 via
> > > >>>> > > >>> > > petsc-users
> > > >>>> > > >>> > > > > >>> wrote:
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > > >> > Hello,
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for
> > > >>>> working on
> > > >>>> > > >>> the
> > > >>>> > > >>> > > > > >>> simulation
> > > >>>> > > >>> > > > > >>> > > using
> > > >>>> > > >>> > > > > >>> > > > >> IBAMR
> > > >>>> > > >>> > > > > >>> > > > >> > open software. While building the
> > PETSc,
> > > >>>> using the
> > > >>>> > > >>> > > following
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD
> > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug
> > > >>>> > > >>> > > > > >>> > > > >> > ./configure \
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \
> > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \
> > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \
> > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \
> > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
> > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>>
> > > >>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > make -j4
> > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > I got the following error
> > > >>>> > > >>> > > > > >>> > > > >> > CLINKER
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>>
> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
> > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual':
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEnginePut'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineEvaluate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGet'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
> > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian':
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEnginePut'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineEvaluate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGet'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
> > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders':
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGet'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
> > > >>>> > > >>> > > > > >>> > > > >> > function `main':
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineCreate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineEvaluate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineEvaluate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGetArray'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGetArray'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGetArray'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGetArray'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineGetArray'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineEvaluate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineEvaluate'
> > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > >
> > > >>>> > > >>>
> > > >>>>
> > /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158:
> > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
> > > >>>> `PetscMatlabEngineDestroy'
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit
> > > >>>> status
> > > >>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185:
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>>
> > > >>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test]
> > > >>>> > > >>> > > > > >>> > > > >> Error 1
> > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished
> > jobs....
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> > Thank you
> > > >>>> > > >>> > > > > >>> > > > >> > Srinivas
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >> >
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > > >>
> > > >>>> > > >>> > > > > >>> > > >
> > > >>>> > > >>> > > > > >>> > > >
> > > >>>> > > >>> > > > > >>> > >
> > > >>>> > > >>> > > > > >>> >
> > > >>>> > > >>> > > > > >>> >
> > > >>>> > > >>> > > > > >>>
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >>
> > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore
> > > >>>> Institute of
> > > >>>> > > >>> > > Technology.
> > > >>>> > > >>> > > > > >> The contents of this email may contain legally
> > > >>>> protected
> > > >>>> > > >>> > > confidential or
> > > >>>> > > >>> > > > > >> privileged information of “Vellore Institute of
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> > > >>>> > > >>> If
> > > >>>> > > >>> > > you are
> > > >>>> > > >>> > > > > >> not the intended recipient, you should not
> > > >>>> disseminate,
> > > >>>> > > >>> distribute
> > > >>>> > > >>> > > or copy
> > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately
> > > >>>> and destroy
> > > >>>> > > >>> all
> > > >>>> > > >>> > > copies of
> > > >>>> > > >>> > > > > >> this message and any attachments. If you have
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> > > >>>> > > >>> > > > > >> 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.*
> > > >
> > >
> > >
> > >
> >
>
>
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