[petsc-users] Error while building PETSc with MATLAB
Matthew Knepley
knepley at gmail.com
Sun Sep 3 07:55:22 CDT 2023
On Sun, Sep 3, 2023 at 8:47 AM INTURU SRINIVAS 20PHD0548 <
inturu.srinivas2020 at vitstudent.ac.in> wrote:
> Hi Matthew,
>
> I am using PETSc to simulate the problems using IBAMR. I do not have any
> separate test files to test PETSc alone. Can you please help me how to
> define this DATAFILESPATH?
>
That test you tried uses a certain matrix. On our machine, we point to this
matrix using an environment variable, DATAFILESPATH. You don't have those
matrices, since they are just for testing here. That
is why I suggested just using a different matrix, or running a problem you
care about in IBAMR.
Thanks,
Matt
> Thanks and regards
> Srinivas.
>
> On Sun, Sep 3, 2023 at 6:06 PM Matthew Knepley <knepley at gmail.com> wrote:
>
>> On Sun, Sep 3, 2023 at 3:04 AM INTURU SRINIVAS 20PHD0548 via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>> Hi Sathish,
>>>
>>> Thank you so much for your efforts and the support you are giving me to
>>> sort this out.
>>>
>>> I tried to follow the same procedure which you followed to build Petsc
>>> 3.13.4 with Matlab-R2020b on Ubuntu20.04.
>>>
>>> *$./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>> --with-debugging=0 --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1*
>>> Using python3 for Python
>>>
>>> ===============================================================================
>>> Configuring PETSc to compile on your system
>>>
>>>
>>> ===============================================================================
>>> ===============================================================================
>>> It appears you do not have valgrind
>>> installed on your system.
>>> We HIGHLY recommend you install it from www.valgrind.org
>>> Or install valgrind-devel or
>>> equivalent using your package manager.
>>> Then rerun ./configure
>>>
>>> ===============================================================================
>>> Compilers:
>>>
>>> C Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC
>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>> -fstack-protector -fvisibility=hidden -O3
>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>> C++ Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>> -fstack-protector -fvisibility=hidden -O3 -fPIC
>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0
>>> Fortran Compiler: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>> -fPIC -Wall -ffree-line-length-0 -Wno-unused-dummy-argument -O3
>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>> Linkers:
>>> Shared linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared
>>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>> -fstack-protector -fvisibility=hidden -O3
>>> Dynamic linker: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -shared
>>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>> -fstack-protector -fvisibility=hidden -O3
>>> Libraries linked against: -lquadmath -lstdc++ -ldl
>>> make:
>>> Version: 4.2
>>> /usr/bin/make
>>> BlasLapack:
>>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5 -lpthread
>>> uses OpenMP; use export OMP_NUM_THREADS=<p> or -omp_num_threads <p> to
>>> control the number of threads
>>> uses 8 byte integers
>>> MPI:
>>> Version: 3
>>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include
>>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec --oversubscribe
>>> OMPI_VERSION: 4.1.4
>>> pthread:
>>> cmake:
>>> Version: 3.16.3
>>> /usr/bin/cmake
>>> regex:
>>> Matlab:
>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include
>>> /usr/local/MATLAB/R2020b
>>> MatlabEngine:
>>> Library:
>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat -lut
>>> -licudata -licui18n -licuuc
>>> Language used to compile PETSc: C
>>> PETSc:
>>> PETSC_ARCH: linux-opt
>>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4
>>> Scalar type: real
>>> Precision: double
>>> Support for __float128
>>> Integer size: 4 bytes
>>> shared libraries: enabled
>>> Memory alignment from malloc(): 16 bytes
>>>
>>> xxx=========================================================================xxx
>>> Configure stage complete. Now build PETSc libraries with:
>>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt all
>>>
>>> xxx=========================================================================xxx
>>>
>>> Then I removed all occurrences of -lut -licudata -licui18n -licuuc as
>>> you suggested earlier.
>>>
>>> *$make*
>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o
>>> CLINKER linux-opt/lib/libpetsc.so.3.13.4
>>> BEGINNING TO COMPILE MATLAB INTERFACE
>>> Building with 'gcc'.
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>> In function ‘PetscBinaryWrite’:
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>> warning: ‘err’ may be used uninitialized in this function
>>> [-Wmaybe-uninitialized]
>>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>> | ^
>>>
>>> MEX completed successfully.
>>> Building with 'gcc'.
>>> MEX completed successfully.
>>> Building with 'gcc'.
>>> MEX completed successfully.
>>> Building with 'gcc'.
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>> In function ‘PetscBinaryWrite’:
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>> warning: ‘err’ may be used uninitialized in this function
>>> [-Wmaybe-uninitialized]
>>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>> | ^
>>>
>>> MEX completed successfully.
>>> =========================================
>>> Now to check if the libraries are working do:
>>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt check
>>> ===============================================
>>>
>>> *$make test query=requires queryval=matlab*
>>> Using MAKEFLAGS: -- queryval=matlab query=requires
>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169
>>> # [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [0]PETSC ERROR: Unable to open file
>>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1
>>>
>>
>> No, the problem is that you do not have DATAFILESPATH defined, so it
>> cannot find the matrix to test. Try running some test of yours.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> # [0]PETSC ERROR: See
>>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>> shooting.
>>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Sun
>>> Sep 3 11:51:03 2023
>>> # [0]PETSC ERROR: Configure options
>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO() line 1444 in
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c
>>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511 in
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c
>>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c
>>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in
>>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c
>>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in
>>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c
>>> # [0]PETSC ERROR: #6 main() line 113 in
>>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c
>>> # [0]PETSC ERROR: PETSc Option Table entries:
>>> # [0]PETSC ERROR: -f0 /matrices/arco1
>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
>>> # [0]PETSC ERROR: -pc_type lu
>>> # [0]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> #
>>> --------------------------------------------------------------------------
>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
>>> # with errorcode 113065.
>>> #
>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> # You may or may not see output from other processes, depending on
>>> # exactly when Open MPI kills them.
>>> #
>>> --------------------------------------------------------------------------
>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
>>> CC
>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
>>> CLINKER
>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>> TEST
>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code: 124
>>> # Running problem 5
>>> # [0]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [0]PETSC ERROR: Error in external library
>>> # [0]PETSC ERROR: Unable to start MATLAB engine on
>>> # [0]PETSC ERROR: See
>>> https://www.mcs.anl.gov/petsc/documentation/faq.html for trouble
>>> shooting.
>>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named MB108SMEC028 by
>>> vit Sun Sep 3 11:51:05 2023
>>> # [0]PETSC ERROR: Configure options
>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>> # [0]PETSC ERROR: #2 main() line 126 in
>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>> # [0]PETSC ERROR: PETSc Option Table entries:
>>> # [0]PETSC ERROR: -prob_id 5
>>> # [0]PETSC ERROR: -tao_smonitor
>>> # [0]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> #
>>> --------------------------------------------------------------------------
>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
>>> # with errorcode 126076.
>>> #
>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> # You may or may not see output from other processes, depending on
>>> # exactly when Open MPI kills them.
>>> #
>>> --------------------------------------------------------------------------
>>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command
>>> failed so no diff
>>>
>>> # -------------
>>> # Summary
>>> # -------------
>>> # FAILED ksp_ksp_tutorials-ex72_12
>>> tao_leastsquares_tutorials_matlab-matlab_ls_test
>>> # success 0/2 tests (0.0%)
>>> # failed 2/2 tests (100.0%)
>>> # todo 0/2 tests (0.0%)
>>> # skip 0/2 tests (0.0%)
>>> #
>>> # Wall clock time for tests: 3 sec
>>> # Approximate CPU time (not incl. build time): 0.05 sec
>>> #
>>> # To rerun failed tests:
>>> # /usr/bin/make -f gmakefile test test-fail=1
>>> #
>>> # Timing summary (actual test time / total CPU time):
>>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec
>>> # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.02 sec / 0.02 sec
>>>
>>> *How to sort out this error?*
>>>
>>> *$cd src/tao/leastsquares/tutorials/matlab/*
>>> *$make matlab_ls_test*
>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall -Wwrite-strings
>>> -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3
>>> -I/home/vit/sfw/petsc/3.13.4/include
>>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include
>>> -I/usr/local/MATLAB/R2020b/extern/include
>>> -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c
>>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib
>>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib
>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib
>>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib
>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
>>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex -lmx
>>> -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh
>>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lquadmath
>>> -lstdc++ -ldl -o matlab_ls_test
>>>
>>> I think there is a problem with the Matlab-R2020b version.
>>> I am sharing the configure.log and make.log files. Please find the
>>> attachment and do the needful.
>>>
>>>
>>> Thanks and regards
>>> Srinivas
>>>
>>>
>>> On Sat, Sep 2, 2023 at 11:15 PM Satish Balay <balay at mcs.anl.gov> wrote:
>>>
>>>> Perhaps you can try the following to get additional info - and debug
>>>>
>>>> Satish
>>>> ----------
>>>>
>>>> balay at compute-386-07:/scratch/balay/petsc$ cd
>>>> src/tao/leastsquares/tutorials/matlab/
>>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
>>>> make matlab_ls_test
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall
>>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
>>>> -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3
>>>> -I/scratch/balay/petsc/include -I/scratch/balay/petsc/linux-opt/include
>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include
>>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include
>>>> matlab_ls_test.c -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib
>>>> -L/scratch/balay/petsc/linux-opt/lib
>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64
>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib
>>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib
>>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
>>>> -L/usr/lib/gcc/x86_64-linux-gnu/9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>>>> -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
>>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas -lpthread -lm -leng -lmex
>>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++ -ldl -lmpifort -lmpi
>>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lstdc++ -ldl -o
>>>> matlab_ls_test
>>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
>>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 ./matlab_ls_test
>>>> -tao_smonitor -prob_id 5 -info
>>>> [0] PetscInitialize(): PETSc successfully started: number of processors
>>>> = 1
>>>> [0] PetscGetHostName(): Rejecting domainname, likely is NIS
>>>> compute-386-07.(none)
>>>> [0] PetscInitialize(): Running on machine: compute-386-07
>>>> Running problem 5
>>>> [0] PetscCommDuplicate(): Duplicating a communicator 1140850689
>>>> -2080374784 max tags = 268435455
>>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command
>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
>>>> -glnxa64 -nodisplay -nosplash
>>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine
>>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB string:
>>>> TestingInitialize
>>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab string:
>>>> TestingInitialize
>>>> 5
>>>> <snip>
>>>>
>>>> <<<< Now verify if the above matlab command actually works for you - on
>>>> this machine..>>>>>
>>>>
>>>> balay at compute-386-07:/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
>>>> -glnxa64 -nodisplay -nosplash
>>>>
>>>>
>>>> < M A T L A B (R) >
>>>>
>>>> Copyright 1984-2021 The MathWorks, Inc.
>>>>
>>>> R2021a (9.10.0.1602886) 64-bit (glnxa64)
>>>>
>>>> February 17, 2021
>>>>
>>>>
>>>> To get started, type doc.
>>>> For product information, visit www.mathworks.com.
>>>>
>>>> >>
>>>>
>>>>
>>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote:
>>>>
>>>> > Please don't cc: both petsc-users and petsc-maint [reverting thread
>>>> to petsc-users only]
>>>> >
>>>> > I'm not sure what is happening here. Can you send the corresponding
>>>> configure.log, make.log [compressed]?
>>>> >
>>>> > Here is my attempt to reproduce (with petsc-3.13) on Ubuntu-20.04,
>>>> with Matlab-R2021a - and that works:
>>>> >
>>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch
>>>> > main
>>>> > release
>>>> > * release-3.13
>>>> > balay at compute-386-07:/scratch/balay/petsc$ module load matlab/R2021a
>>>> > balay at compute-386-07:/scratch/balay/petsc$ which matlab
>>>> >
>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
>>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure
>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/
>>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>> --with-debugging=0 --with-x=0
>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>> > <snip>
>>>> > Compilers:
>>>>
>>>>
>>>>
>>>> > C Compiler:
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC -Wall
>>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>>>> -fvisibility=hidden -O3
>>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>> > C++ Compiler:
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall
>>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>>>> -fvisibility=hidden -O3 -fPIC
>>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>> > Fortran Compiler:
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC -Wall
>>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3
>>>> > Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>> > Linkers:
>>>> > Shared linker:
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC
>>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>>> -fstack-protector -fvisibility=hidden -O3
>>>> > Dynamic linker:
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -shared -fPIC
>>>> -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>>> -fstack-protector -fvisibility=hidden -O3
>>>> > Libraries linked against: -lquadmath -lstdc++ -ldl
>>>> > make:
>>>> > Version: 4.2
>>>> > /usr/bin/make
>>>> > BlasLapack:
>>>> > Library:
>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so
>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64
>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64
>>>> -liomp5 -lpthread
>>>> > uses OpenMP; use export OMP_NUM_THREADS=<p> or -omp_num_threads <p>
>>>> to control the number of threads
>>>> > uses 8 byte integers
>>>> > MPI:
>>>> > Version: 4
>>>> > Includes: -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include
>>>> > Mpiexec: /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec
>>>> > MPICH_NUMVERSION: 40002300
>>>> > pthread:
>>>> > Library: -lpthread
>>>> > cmake:
>>>> > Version: 3.16.3
>>>> > /usr/bin/cmake
>>>> > regex:
>>>> > Matlab:
>>>> > Includes:
>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include
>>>> > /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
>>>> > MatlabEngine:
>>>> > Library:
>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64
>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc
>>>> > sowing:
>>>> > Version: 1.1.25
>>>> > /scratch/balay/petsc/linux-opt/bin/bfort
>>>> > valgrind:
>>>> > Language used to compile PETSc: C
>>>> > PETSc:
>>>> > PETSC_ARCH: linux-opt
>>>> > PETSC_DIR: /scratch/balay/petsc
>>>> > Scalar type: real
>>>> > Precision: double
>>>> > Support for __float128
>>>> > Integer size: 4 bytes
>>>> > shared libraries: enabled
>>>> > Memory alignment from malloc(): 16 bytes
>>>> >
>>>> xxx=========================================================================xxx
>>>> > Configure stage complete. Now build PETSc libraries with:
>>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt all
>>>> >
>>>> xxx=========================================================================xxx
>>>> > balay at compute-386-07:/scratch/balay/petsc$ make
>>>>
>>>>
>>>>
>>>> >
>>>> > <snip>
>>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o
>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6
>>>> > BEGINNING TO COMPILE MATLAB INTERFACE
>>>> > Building with 'gcc'.
>>>> >
>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In
>>>> function ‘PetscBinaryWrite’:
>>>> >
>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>> warning: ‘err’ may be used uninitialized in this function
>>>> [-Wmaybe-uninitialized]
>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>> > | ^
>>>> >
>>>> > MEX completed successfully.
>>>> > Building with 'gcc'.
>>>> > MEX completed successfully.
>>>> > Building with 'gcc'.
>>>> > MEX completed successfully.
>>>> > Building with 'gcc'.
>>>> >
>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In
>>>> function ‘PetscBinaryWrite’:
>>>> >
>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>> warning: ‘err’ may be used uninitialized in this function
>>>> [-Wmaybe-uninitialized]
>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>> > | ^
>>>> >
>>>> > MEX completed successfully.
>>>> > =========================================
>>>> > Now to check if the libraries are working do:
>>>> > make PETSC_DIR=/scratch/balay/petsc PETSC_ARCH=linux-opt check
>>>> > =========================================
>>>> > balay at compute-386-07:/scratch/balay/petsc$ make test query=requires
>>>> queryval=matlab
>>>> > Using MAKEFLAGS: -- queryval=matlab query=requires
>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1
>>>> > # ../ex72:
>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5:
>>>> version `GFORTRAN_9' not found (required by
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12)
>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
>>>> > CC
>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
>>>> > CLINKER
>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>> > TEST
>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error code:
>>>> 1
>>>> > # ../matlab_ls_test:
>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5:
>>>> version `GFORTRAN_9' not found (required by
>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12)
>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP Command
>>>> failed so no diff
>>>> > <snip>
>>>> > balay at compute-386-07:/scratch/balay/petsc$
>>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make test query=requires
>>>> queryval=matlab
>>>> > Using MAKEFLAGS: -- queryval=matlab query=requires
>>>> > TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>> > ok ksp_ksp_tutorials-ex72_12
>>>> > ok diff-ksp_ksp_tutorials-ex72_12
>>>> > TEST
>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>> > ok diff-tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>> >
>>>> > # -------------
>>>> > # Summary
>>>> > # -------------
>>>> > # success 4/4 tests (100.0%)
>>>> > # failed 0/4 tests (0.0%)
>>>> > # todo 0/4 tests (0.0%)
>>>> > # skip 0/4 tests (0.0%)
>>>> > #
>>>> > # Wall clock time for tests: 27 sec
>>>> > # Approximate CPU time (not incl. build time): 15.190000000000001 sec
>>>> > #
>>>> > # Timing summary (actual test time / total CPU time):
>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 6.47 sec / 7.54
>>>> sec
>>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec
>>>> > balay at compute-386-07:/scratch/balay/petsc$
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote:
>>>> >
>>>> > > Based on the suggestions given by Sathish, I have tried to
>>>> configure petsc
>>>> > > 3.13.4 with Matlab-R2020b. But, it was not successful. After
>>>> running make
>>>> > > -j 10 test command I have got the following error message.
>>>> > >
>>>> > > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
>>>> code: 124
>>>> > > # Running problem 5
>>>> > > # [0]PETSC ERROR: --------------------- Error Message
>>>> > > --------------------------------------------------------------
>>>> > > # [0]PETSC ERROR: Error in external library
>>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>> > > # [0]PETSC ERROR: See
>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>> > > for trouble shooting.
>>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named
>>>> MB108SMEC028 by
>>>> > > vit Sat Sep 2 12:27:22 2023
>>>> > > # [0]PETSC ERROR: Configure options
>>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>> --with-debugging=0
>>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>> > > --with-matlab-engine=1
>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>> > > --known-64-bit-blas-indices=1
>>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>> > > # [0]PETSC ERROR: #2 main() line 126 in
>>>> > >
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>> > > # [0]PETSC ERROR: PETSc Option Table entries:
>>>> > > # [0]PETSC ERROR: -prob_id 5
>>>> > > # [0]PETSC ERROR: -tao_smonitor
>>>> > > # [0]PETSC ERROR: ----------------End of Error Message -------send
>>>> entire
>>>> > > error message to petsc-maint at mcs.anl.gov----------
>>>> > > #
>>>> --------------------------------------------------------------------------
>>>> > > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
>>>> > > # with errorcode 126076.
>>>> > > #
>>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
>>>> processes.
>>>> > > # You may or may not see output from other processes, depending on
>>>> > > # exactly when Open MPI kills them.
>>>> > > #
>>>> --------------------------------------------------------------------------
>>>> > >
>>>> > > I request you to help me to sort out this error.
>>>> > >
>>>> > > Thanks
>>>> > > Srinivas
>>>> > >
>>>> > >
>>>> > > On Fri, Sep 1, 2023 at 11:42 PM Amneet Bhalla <
>>>> mail2amneet at gmail.com> wrote:
>>>> > >
>>>> > > > I think there should be two hyphens in
>>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>> > > >
>>>> > > > i.e.:
>>>> > > >
>>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>> > > >
>>>> > > > On Fri, Sep 1, 2023 at 10:25 AM INTURU SRINIVAS 20PHD0548 via
>>>> petsc-users <
>>>> > > > petsc-users at mcs.anl.gov> wrote:
>>>> > > >
>>>> > > >> Thank you Sathish.I will try this
>>>> > > >>
>>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay <balay at mcs.anl.gov>
>>>> wrote:
>>>> > > >>
>>>> > > >>> yes [and remove fblaslapack. don't know if hypre will work
>>>> here].
>>>> > > >>>
>>>> > > >>> i.e:
>>>> > > >>>
>>>> > > >>> ./configure --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>> > > >>> --with-debugging=0 --with-x=0 \
>>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>> --with-matlab-engine=1
>>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>> --known-64-bit-blas-indices=1
>>>> > > >>>
>>>> > > >>> Satish
>>>> > > >>>
>>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users
>>>> wrote:
>>>> > > >>>
>>>> > > >>> > Hi Satish,
>>>> > > >>> >
>>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir
>>>> > > >>> > --known-64-bit-blas-indices=1
>>>> > > >>> >
>>>> > > >>> > Is this what you are suggesting?
>>>> > > >>> >
>>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay <balay at mcs.anl.gov>
>>>> wrote:
>>>> > > >>> >
>>>> > > >>> > > Also:
>>>> > > >>> > >
>>>> > > >>> > > '-known-64-bit-blas-indices=1',
>>>> > > >>> > >
>>>> > > >>> > > Note: most externalpackages might not work in this mode.
>>>> > > >>> > >
>>>> > > >>> > > [we can't really over come such dependency/conflicts across
>>>> packages]
>>>> > > >>> > >
>>>> > > >>> > > Satish
>>>> > > >>> > >
>>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via petsc-users wrote:
>>>> > > >>> > >
>>>> > > >>> > > > Here is the matlab test that runs in CI
>>>> > > >>> > > >
>>>> > > >>> > > > https://gitlab.com/petsc/petsc/-/jobs/4904566768
>>>> > > >>> > > >
>>>> > > >>> > > > config/examples/arch-ci-linux-matlab-ilp64.py
>>>> > > >>> > > >
>>>> > > >>> > > > # Note: regular BLAS [with 32-bit integers] conflict with
>>>> > > >>> > > > # MATLAB BLAS - hence requiring
>>>> -known-64-bit-blas-indices=1
>>>> > > >>> > > >
>>>> > > >>> > > > Ah - so you need to use the ilp64 blas/lapack with
>>>> matlab - to
>>>> > > >>> have a
>>>> > > >>> > > compatible build
>>>> > > >>> > > >
>>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir,
>>>> > > >>> > > >
>>>> > > >>> > > > Satish
>>>> > > >>> > > >
>>>> > > >>> > > >
>>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via
>>>> petsc-users
>>>> > > >>> wrote:
>>>> > > >>> > > >
>>>> > > >>> > > > > Hi Amneet,
>>>> > > >>> > > > >
>>>> > > >>> > > > > Without libmesh, even for PETSc with MATLAB is not
>>>> working. It is
>>>> > > >>> > > showing
>>>> > > >>> > > > > error for both 3.13.4 and 3.17.5 versions.
>>>> > > >>> > > > >
>>>> > > >>> > > > > I am trying to install IBAMR in HPC cluster with
>>>> libmesh and
>>>> > > >>> this is
>>>> > > >>> > > for
>>>> > > >>> > > > > general usage not only for WEC. This I tried without
>>>> linking
>>>> > > >>> Matlab
>>>> > > >>> > > with
>>>> > > >>> > > > > PETSc. Here also I got the error while configuring
>>>> libmesh 1.6.2
>>>> > > >>> that
>>>> > > >>> > > PETSc
>>>> > > >>> > > > > was not found but --enable-petsc-required is specified.
>>>> > > >>> > > > >
>>>> > > >>> > > > > The reason for specifically asking for libmesh with
>>>> PETSc and
>>>> > > >>> Matlab
>>>> > > >>> > > is in
>>>> > > >>> > > > > the cfd-mpc-wecs application for complicated geometries
>>>> it is
>>>> > > >>> > > mentioned to
>>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct.
>>>> > > >>> > > > >
>>>> > > >>> > > > > For the past 10 days I am trying these various things
>>>> and ended
>>>> > > >>> up with
>>>> > > >>> > > > > errors.
>>>> > > >>> > > > > I want to solve this and proceed further to do my
>>>> research work.
>>>> > > >>> > > > >
>>>> > > >>> > > > > Please help me to solve this as soon as possible.
>>>> > > >>> > > > >
>>>> > > >>> > > > >
>>>> > > >>> > > > > Thanks and Regards
>>>> > > >>> > > > > Srinivas
>>>> > > >>> > > > >
>>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla <
>>>> mail2amneet at gmail.com>
>>>> > > >>> > > wrote:
>>>> > > >>> > > > >
>>>> > > >>> > > > > > Hi Srinivas,
>>>> > > >>> > > > > >
>>>> > > >>> > > > > > As discussed earlier you don’t need libMesh for the
>>>> WEC
>>>> > > >>> application.
>>>> > > >>> > > You
>>>> > > >>> > > > > > can just work with PETSc 3.17.5 that builds with
>>>> Matlab.
>>>> > > >>> > > > > >
>>>> > > >>> > > > > > Do you have a specific reason for wanting to build
>>>> libMesh?
>>>> > > >>> > > > > >
>>>> > > >>> > > > > > Thanks,
>>>> > > >>> > > > > > —Amneet
>>>> > > >>> > > > > >
>>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU SRINIVAS
>>>> 20PHD0548 via
>>>> > > >>> > > petsc-users
>>>> > > >>> > > > > > <petsc-users at mcs.anl.gov> wrote:
>>>> > > >>> > > > > >
>>>> > > >>> > > > > >> Hi,
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by removing all
>>>> occurrences
>>>> > > >>> of
>>>> > > >>> > > "-lut
>>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran "make test"
>>>> got the
>>>> > > >>> > > following
>>>> > > >>> > > > > >> errors
>>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug:
>>>> > > >>> > > > > >> TEST
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>> > > >>> > > > > >> not ok
>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>> > > >>> Error
>>>> > > >>> > > code: 124
>>>> > > >>> > > > > >> # Running problem 5
>>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message
>>>> > > >>> > > > > >>
>>>> --------------------------------------------------------------
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>> > > >>> > > > > >> # [0]PETSC ERROR: See
>>>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>> for
>>>> > > >>> trouble
>>>> > > >>> > > > > >> shooting.
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug
>>>> 01, 2020
>>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-debug
>>>> named
>>>> > > >>> > > MB108SMEC028
>>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
>>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>> > > >>> --with-debugging=1
>>>> > > >>> > > > > >> --download-hypre=1 --download-fblaslapack=1
>>>> --with-x=0
>>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>> > > >>> --with-matlab-engine=1
>>>> > > >>> > > > > >>
>>>> > > >>>
>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line
>>>> 67 in
>>>> > > >>> > > > > >>
>>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries:
>>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
>>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
>>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error
>>>> Message
>>>> > > >>> -------send
>>>> > > >>> > > entire
>>>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov----------
>>>> > > >>> > > > > >> #
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> --------------------------------------------------------------------------
>>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator
>>>> > > >>> MPI_COMM_SELF
>>>> > > >>> > > > > >> # with errorcode 126076.
>>>> > > >>> > > > > >> #
>>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill
>>>> all MPI
>>>> > > >>> > > processes.
>>>> > > >>> > > > > >> # You may or may not see output from other processes,
>>>> > > >>> depending on
>>>> > > >>> > > > > >> # exactly when Open MPI kills them.
>>>> > > >>> > > > > >> #
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> --------------------------------------------------------------------------
>>>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>> # SKIP
>>>> > > >>> Command
>>>> > > >>> > > > > >> failed so no diff
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt
>>>> > > >>> > > > > >> TEST
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>> > > >>> > > > > >> not ok
>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>> > > >>> Error
>>>> > > >>> > > code: 124
>>>> > > >>> > > > > >> # Running problem 5
>>>> > > >>> > > > > >> # [0]PETSC ERROR: --------------------- Error Message
>>>> > > >>> > > > > >>
>>>> --------------------------------------------------------------
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external library
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>> > > >>> > > > > >> # [0]PETSC ERROR: See
>>>> > > >>> > > > > >> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>> for
>>>> > > >>> trouble
>>>> > > >>> > > > > >> shooting.
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug
>>>> 01, 2020
>>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt
>>>> named
>>>> > > >>> > > MB108SMEC028 by
>>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023
>>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
>>>> > > >>> > > > > >> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>> > > >>> > > > > >> --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>> > > >>> > > > > >> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>> > > >>> --COPTFLAGS=-O3
>>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3
>>>> --PETSC_ARCH=linux-opt
>>>> > > >>> > > --with-debugging=0
>>>> > > >>> > > > > >> --download-hypre=1 --with-x=0
>>>> --download-fblaslapack=1
>>>> > > >>> > > > > >> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>> > > >>> --with-matlab-engine=1
>>>> > > >>> > > > > >>
>>>> > > >>>
>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>> > > >>> > > > > >> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line
>>>> 67 in
>>>> > > >>> > > > > >>
>>>> > > >>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table entries:
>>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
>>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
>>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of Error
>>>> Message
>>>> > > >>> -------send
>>>> > > >>> > > entire
>>>> > > >>> > > > > >> error message to petsc-maint at mcs.anl.gov----------
>>>> > > >>> > > > > >> #
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> --------------------------------------------------------------------------
>>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in communicator
>>>> > > >>> MPI_COMM_SELF
>>>> > > >>> > > > > >> # with errorcode 126076.
>>>> > > >>> > > > > >> #
>>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open MPI to kill
>>>> all MPI
>>>> > > >>> > > processes.
>>>> > > >>> > > > > >> # You may or may not see output from other processes,
>>>> > > >>> depending on
>>>> > > >>> > > > > >> # exactly when Open MPI kills them.
>>>> > > >>> > > > > >> #
>>>> > > >>> > > > > >>
>>>> > > >>> > >
>>>> > > >>>
>>>> --------------------------------------------------------------------------
>>>> > > >>> > > > > >> ok tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>> # SKIP
>>>> > > >>> Command
>>>> > > >>> > > > > >> failed so no diff.
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5 version. I
>>>> am
>>>> > > >>> sharing the
>>>> > > >>> > > > > >> config.log and make.log for both petsc 3.13.4 and
>>>> petsc
>>>> > > >>> 3.17.5.
>>>> > > >>> > > Please find
>>>> > > >>> > > > > >> the attachment and do the needful.
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >> Thanks and regards
>>>> > > >>> > > > > >> Srinivas
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56 PM Satish Balay <
>>>> > > >>> balay at mcs.anl.gov>
>>>> > > >>> > > wrote:
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >>> Well - you sent in libmesh log not petsc's
>>>> > > >>> configure.log/make.log
>>>> > > >>> > > for
>>>> > > >>> > > > > >>> petsc-3.17
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have:
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> >>>>
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> Matlab:
>>>> > > >>> > > > > >>> Includes:
>>>> -I/usr/local/MATLAB/R2020b/extern/include
>>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b
>>>> > > >>> > > > > >>> MatlabEngine:
>>>> > > >>> > > > > >>> Library:
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng
>>>> -lmex
>>>> > > >>> -lmx
>>>> > > >>> > > -lmat -lut
>>>> > > >>> > > > > >>> -licudata -licui18n -licuuc
>>>> > > >>> > > > > >>> Language used to compile PETSc: C
>>>> > > >>> > > > > >>> <<<<<
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) - we are seeing:
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> https://gitlab.com/petsc/petsc/-/jobs/4904566768
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> >>>
>>>> > > >>> > > > > >>> Matlab:
>>>> > > >>> > > > > >>> Includes:
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include
>>>> > > >>> > > > > >>> Libraries:
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
>>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat
>>>> > > >>> > > > > >>> Executable:
>>>> > > >>> > > > > >>>
>>>> > > >>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a
>>>> > > >>> > > > > >>> mex:
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex
>>>> > > >>> > > > > >>> matlab:
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab
>>>> > > >>> > > > > >>> -glnxa64
>>>> > > >>> > > > > >>> <<<
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc" are not
>>>> preset here.
>>>> > > >>> This
>>>> > > >>> > > might
>>>> > > >>> > > > > >>> be a change wrt newer matlab versions.
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> You can:
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> - edit
>>>> > > >>> > > > > >>>
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables
>>>> > > >>> > > and
>>>> > > >>> > > > > >>> remove all occurrences of "-lut -licudata -licui18n
>>>> -licuuc"
>>>> > > >>> > > > > >>> - now run 'make all' in '/home/vit/sfw/petsc/3.13.4'
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> And see if the build works now.
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> Satish
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548 via
>>>> > > >>> petsc-users
>>>> > > >>> > > wrote:
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>> > I am sharing the log files while building
>>>> petsc3.13.4 with
>>>> > > >>> > > matlab and
>>>> > > >>> > > > > >>> also
>>>> > > >>> > > > > >>> > the log file while building libmesh with
>>>> petsc3.17.5 and
>>>> > > >>> matlab.
>>>> > > >>> > > > > >>> Building
>>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done successfully.
>>>> But
>>>> > > >>> libmesh is
>>>> > > >>> > > not
>>>> > > >>> > > > > >>> able to
>>>> > > >>> > > > > >>> > find the petsc
>>>> > > >>> > > > > >>> > Please find the attachments.
>>>> > > >>> > > > > >>> >
>>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31 PM Satish Balay <
>>>> > > >>> balay at mcs.anl.gov>
>>>> > > >>> > > > > >>> wrote:
>>>> > > >>> > > > > >>> >
>>>> > > >>> > > > > >>> > > Send configure.log, make.log from both
>>>> petsc-3.13 and
>>>> > > >>> 3.17 [or
>>>> > > >>> > > 3.19].
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>> > > [you can gzip them to make the logs friendly to
>>>> mailing
>>>> > > >>> list -
>>>> > > >>> > > or
>>>> > > >>> > > > > >>> send
>>>> > > >>> > > > > >>> > > them to petsc-maint]
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>> > > And does test suite work with 3.17? [or 3.19?]
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>> > > Satish
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS 20PHD0548
>>>> via
>>>> > > >>> petsc-users
>>>> > > >>> > > wrote:
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>> > > > I am sharing the make.log file while building
>>>> > > >>> petsc-3.13.4
>>>> > > >>> > > with
>>>> > > >>> > > > > >>> Matlab.
>>>> > > >>> > > > > >>> > > > Please find the attachment and do the needful.
>>>> > > >>> > > > > >>> > > >
>>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19 AM INTURU
>>>> SRINIVAS
>>>> > > >>> 20PHD0548 <
>>>> > > >>> > > > > >>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote:
>>>> > > >>> > > > > >>> > > >
>>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5. During building
>>>> of
>>>> > > >>> libmesh, the
>>>> > > >>> > > error
>>>> > > >>> > > > > >>> shows
>>>> > > >>> > > > > >>> > > > > petsc was not found
>>>> > > >>> > > > > >>> > > > >
>>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43 PM Satish
>>>> Balay <
>>>> > > >>> > > balay at mcs.anl.gov>
>>>> > > >>> > > > > >>> > > wrote:
>>>> > > >>> > > > > >>> > > > >
>>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux says
>>>> petsc-3.17
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > > >> Here you are using 3.13
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > > >> Can you retry with petsc-3.17.5?
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > > >> Satish
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU SRINIVAS
>>>> 20PHD0548 via
>>>> > > >>> > > petsc-users
>>>> > > >>> > > > > >>> wrote:
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > > >> > Hello,
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with MATLAB for
>>>> working on
>>>> > > >>> the
>>>> > > >>> > > > > >>> simulation
>>>> > > >>> > > > > >>> > > using
>>>> > > >>> > > > > >>> > > > >> IBAMR
>>>> > > >>> > > > > >>> > > > >> > open software. While building the PETSc,
>>>> using the
>>>> > > >>> > > following
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD
>>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug
>>>> > > >>> > > > > >>> > > > >> > ./configure \
>>>> > > >>> > > > > >>> > > > >> >
>>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \
>>>> > > >>> > > > > >>> > > > >> >
>>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \
>>>> > > >>> > > > > >>> > > > >> >
>>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \
>>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \
>>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \
>>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \
>>>> > > >>> > > > > >>> > > > >> > --with-x=0 \
>>>> > > >>> > > > > >>> > > > >> >
>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>>
>>>> > > >>>
>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > make -j4
>>>> > > >>> > > > > >>> > > > >> > make -j4 test
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > I got the following error
>>>> > > >>> > > > > >>> > > > >> > CLINKER
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>>
>>>> > > >>>
>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual':
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEnginePut'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineEvaluate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGet'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian':
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEnginePut'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineEvaluate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGet'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>> > > >>> > > > > >>> > > > >> > function `TaoPounders':
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGet'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>> > > >>> > > > > >>> > > > >> > function `main':
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineCreate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineEvaluate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineEvaluate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGetArray'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGetArray'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGetArray'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGetArray'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineGetArray'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineEvaluate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineEvaluate'
>>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>>
>>>> > > >>> > >
>>>> > > >>>
>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158:
>>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>> `PetscMatlabEngineDestroy'
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned 1 exit
>>>> status
>>>> > > >>> > > > > >>> > > > >> > make: *** [gmakefile.test:185:
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>>
>>>> > > >>>
>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test]
>>>> > > >>> > > > > >>> > > > >> Error 1
>>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for unfinished jobs....
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > Please help me to solve this issue
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> > Thank you
>>>> > > >>> > > > > >>> > > > >> > Srinivas
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >> >
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > > >>
>>>> > > >>> > > > > >>> > > >
>>>> > > >>> > > > > >>> > > >
>>>> > > >>> > > > > >>> > >
>>>> > > >>> > > > > >>> >
>>>> > > >>> > > > > >>> >
>>>> > > >>> > > > > >>>
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >> *Disclaimer:This message was sent from Vellore
>>>> Institute of
>>>> > > >>> > > Technology.
>>>> > > >>> > > > > >> The contents of this email may contain legally
>>>> protected
>>>> > > >>> > > confidential or
>>>> > > >>> > > > > >> privileged information of “Vellore Institute of
>>>> Technology”.
>>>> > > >>> If
>>>> > > >>> > > you are
>>>> > > >>> > > > > >> not the intended recipient, you should not
>>>> disseminate,
>>>> > > >>> distribute
>>>> > > >>> > > or copy
>>>> > > >>> > > > > >> this e-mail. Please notify the sender immediately
>>>> and destroy
>>>> > > >>> all
>>>> > > >>> > > copies of
>>>> > > >>> > > > > >> this message and any attachments. If you have
>>>> received this
>>>> > > >>> email
>>>> > > >>> > > in error,
>>>> > > >>> > > > > >> please promptly notify the sender by reply email and
>>>> delete
>>>> > > >>> the
>>>> > > >>> > > original
>>>> > > >>> > > > > >> email and any backup copies without reading them.*
>>>> > > >>> > > > > >>
>>>> > > >>> > > > > >
>>>> > > >>> > > > >
>>>> > > >>> > > > >
>>>> > > >>> > > >
>>>> > > >>> > >
>>>> > > >>> >
>>>> > > >>> >
>>>> > > >>>
>>>> > > >>
>>>> > > >>
>>>> > > >> *Disclaimer:This message was sent from Vellore Institute of
>>>> Technology.
>>>> > > >> The contents of this email may contain legally protected
>>>> confidential or
>>>> > > >> privileged information of “Vellore Institute of Technology”. If
>>>> you are
>>>> > > >> not the intended recipient, you should not disseminate,
>>>> distribute or copy
>>>> > > >> this e-mail. Please notify the sender immediately and destroy
>>>> all copies of
>>>> > > >> this message and any attachments. If you have received this
>>>> email in error,
>>>> > > >> please promptly notify the sender by reply email and delete the
>>>> original
>>>> > > >> email and any backup copies without reading them.*
>>>> > > >>
>>>> > > >
>>>> > > >
>>>> > > > --
>>>> > > > --Amneet
>>>> > > >
>>>> > > >
>>>> > > >
>>>> > > >
>>>> > >
>>>> > >
>>>>
>>>
>>>
>>> *Disclaimer:This message was sent from Vellore Institute of Technology.
>>> The contents of this email may contain legally protected confidential or
>>> privileged information of “Vellore Institute of Technology”. If you are
>>> not the intended recipient, you should not disseminate, distribute or copy
>>> this e-mail. Please notify the sender immediately and destroy all copies of
>>> this message and any attachments. If you have received this email in error,
>>> please promptly notify the sender by reply email and delete the original
>>> email and any backup copies without reading them.*
>>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
>
> *Disclaimer:This message was sent from Vellore Institute of Technology.
> The contents of this email may contain legally protected confidential or
> privileged information of “Vellore Institute of Technology”. If you are
> not the intended recipient, you should not disseminate, distribute or copy
> this e-mail. Please notify the sender immediately and destroy all copies of
> this message and any attachments. If you have received this email in error,
> please promptly notify the sender by reply email and delete the original
> email and any backup copies without reading them.*
>
--
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/>
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