[petsc-users] Error while building PETSc with MATLAB
Amneet Bhalla
mail2amneet at gmail.com
Wed Sep 6 14:30:14 CDT 2023
Sorry there was an extra : towards the end. It should be
export
LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$LD_LIBRARY_PATH
On Wed, Sep 6, 2023 at 12:25 PM Amneet Bhalla <mail2amneet at gmail.com> wrote:
> Can you also logout and log back in and see if it still works? It is best
> to put LD_LIBRARY_PATH in your .bashrc file
>
> *export LD_LIBRARY_PATH=*
> */usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64:$*
> *LD_LIBRARY_PATH:*
>
>
> On Wed, Sep 6, 2023 at 12:02 PM INTURU SRINIVAS 20PHD0548 <
> inturu.srinivas2020 at vitstudent.ac.in> wrote:
>
>> I will try and let you know.
>>
>> Thanks and regards
>> Srinivas
>>
>> On Wed, Sep 6, 2023, 23:47 Barry Smith <bsmith at petsc.dev> wrote:
>>
>>>
>>> Ok, so the C++ binding for Matlab engine is working on your machine.
>>> PETSc uses the C binding which links against different libraries but, one
>>> would think the C binding would work for sure if the C++ binding works. Can
>>> you try a Matlab Engine C example provided by Matlab?
>>>
>>>
>>>
>>>
>>> On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 <
>>> inturu.srinivas2020 at vitstudent.ac.in> wrote:
>>>
>>> Hi Amneet,
>>>
>>> I repeated the same procedure again and this time it is working.
>>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L
>>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp
>>> -lMatlabDataArray -lMatlabEngine*
>>>
>>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64*
>>> *$export LD_LIBRARY_PATH*
>>> *$./a.out*
>>> Square root of -2 is 0 + 1.41421i
>>> Square root of 2 is 1.41421 + 0i
>>> Square root of 6 is 2.44949 + 0i
>>> Square root of 8 is 2.82843 + 0i
>>> I don't know how it is working this time?
>>>
>>> Thanks and regards
>>> Srinivas
>>>
>>>
>>> On Wed, Sep 6, 2023 at 12:17 PM INTURU SRINIVAS 20PHD0548 <
>>> inturu.srinivas2020 at vitstudent.ac.in> wrote:
>>>
>>>> Hi Amneet,
>>>> I tried the following example to run a matlab engine.
>>>>
>>>> #include "MatlabDataArray.hpp"
>>>> #include "MatlabEngine.hpp"
>>>> #include <iostream>
>>>> void callSQRT() {
>>>>
>>>> using namespace matlab::engine;
>>>>
>>>> // Start MATLAB engine synchronously
>>>> std::unique_ptr<MATLABEngine> matlabPtr = startMATLAB();
>>>>
>>>> //Create MATLAB data array factory
>>>> matlab::data::ArrayFactory factory;
>>>>
>>>> // Define a four-element typed array
>>>> matlab::data::TypedArray<double> const argArray =
>>>> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 });
>>>>
>>>> // Call MATLAB sqrt function on the data array
>>>> matlab::data::Array const results = matlabPtr->feval(u"sqrt",
>>>> argArray);
>>>>
>>>> // Display results
>>>> for (int i = 0; i < results.getNumberOfElements(); i++) {
>>>> double a = argArray[i];
>>>> std::complex<double> v = results[i];
>>>> double realPart = v.real();
>>>> double imgPart = v.imag();
>>>> std::cout << "Square root of " << a << " is " <<
>>>> realPart << " + " << imgPart << "i" << std::endl;
>>>> }
>>>> }
>>>>
>>>> int main() {
>>>> callSQRT();
>>>> return 0;
>>>> }
>>>>
>>>> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L
>>>> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp
>>>> -lMatlabDataArray -lMatlabEngine*
>>>>
>>>> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64*
>>>> *$export LD_LIBRARY_PATH*
>>>> *$./a.out*
>>>> Starting
>>>> Error: The import statement 'import matlab.internal.engine.input'
>>>> cannot be found or cannot be imported. Imported names must end with '.*' or
>>>> be fully qualified.
>>>>
>>>> terminate called after throwing an instance of
>>>> 'matlab::engine::EngineException'
>>>> what(): MATLAB process cannot be created.
>>>> Aborted (core dumped)
>>>>
>>>> I got the above error for Matlab R2020b. Please help me to sort out
>>>> this.
>>>>
>>>> Thanks and regards
>>>> Srinivas
>>>>
>>>> On Tue, Sep 5, 2023 at 11:39 PM Amneet Bhalla <mail2amneet at gmail.com>
>>>> wrote:
>>>>
>>>>> BTW, what Barry is suggesting is the following:
>>>>>
>>>>> Compile a sample code with a command line this:
>>>>>
>>>>>
>>>>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/
>>>>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine
>>>>>
>>>>>
>>>>> This command is provided here:
>>>>>
>>>>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html
>>>>>
>>>>>
>>>>> A sample MATLAB code is here:
>>>>>
>>>>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html
>>>>>
>>>>>
>>>>> (You can just pick a few lines of code from here to create a barebone example)
>>>>>
>>>>>
>>>>> On Tue, Sep 5, 2023 at 11:02 AM Amneet Bhalla <mail2amneet at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Srinivas --- Do you have a different version of MATLAB that you can
>>>>>> install? If your organization has a MATLAB license, you can install recent
>>>>>> versions of MATLAB from mathworks.com
>>>>>>
>>>>>> On Tue, Sep 5, 2023 at 10:37 AM Barry Smith <bsmith at petsc.dev> wrote:
>>>>>>
>>>>>>>
>>>>>>> Ok, I have no suggestions. It seems to be more an issue with the
>>>>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine
>>>>>>> (in the Matlab documentation) and try it to see if it works.
>>>>>>>
>>>>>>> Barry
>>>>>>>
>>>>>>>
>>>>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 <
>>>>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote:
>>>>>>>
>>>>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen("");
>>>>>>> I got the same errors for petsc 3.17.5
>>>>>>>
>>>>>>>
>>>>>>> *make all*
>>>>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o
>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5
>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE
>>>>>>> Building with 'gcc'.
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>> In function ‘PetscBinaryWrite’:
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>>>>> warning: ‘err’ may be used uninitialized in this function
>>>>>>> [-Wmaybe-uninitialized]
>>>>>>> 164 | 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/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>> In function ‘PetscBinaryWrite’:
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>>>>> warning: ‘err’ may be used uninitialized in this function
>>>>>>> [-Wmaybe-uninitialized]
>>>>>>> 164 | 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/3.17.5 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
>>>>>>> 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: 85
>>>>>>> # [0]PETSC ERROR: --------------------- Error Message
>>>>>>> --------------------------------------------------------------
>>>>>>> # [0]PETSC ERROR: Error in external library
>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with
>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>>>>> shooting.
>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022
>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit
>>>>>>> Tue Sep 5 21:39:22 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() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83
>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332
>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245
>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144
>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020
>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131
>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990
>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407
>>>>>>> # [0]PETSC ERROR: #9 main() at
>>>>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305
>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0
>>>>>>> # [0]PETSC ERROR: -error_output_stdout
>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1
>>>>>>> # [0]PETSC ERROR: -malloc_dump
>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
>>>>>>> # [0]PETSC ERROR: -pc_type lu
>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0
>>>>>>> # [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_WORLD
>>>>>>> # with errorcode 85.
>>>>>>> #
>>>>>>> # 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
>>>>>>>
>>>>>>>
>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12
>>>>>>> #
>>>>>>> # To rerun failed tests:
>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1
>>>>>>>
>>>>>>> Thanks and regards
>>>>>>> Srinivas
>>>>>>>
>>>>>>> On Tue, Sep 5, 2023 at 9:05 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>>>>>
>>>>>>>>
>>>>>>>> The error is occuring during
>>>>>>>>
>>>>>>>> e->ep = engOpen(buffer);
>>>>>>>>
>>>>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab
>>>>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to
>>>>>>>> assume the problem is occuring when engOpen() is attempting to connect the
>>>>>>>> stdout and stdin from the Matlab session that is launched to the
>>>>>>>> executable.
>>>>>>>>
>>>>>>>> You can try the following. In 3.17.5 edit the
>>>>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line
>>>>>>>>
>>>>>>>> e->ep = engOpen(buffer);
>>>>>>>>
>>>>>>>> replace it with
>>>>>>>>
>>>>>>>> e->ep = engOpen("");
>>>>>>>>
>>>>>>>> Now in the PETSc directory do make all (it should recompile one
>>>>>>>> file) and then run the
>>>>>>>>
>>>>>>>> make test query=requires queryval=matlab
>>>>>>>> DATAFILESPATH=/home/vit/datafiles/
>>>>>>>>
>>>>>>>> again
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via
>>>>>>>> petsc-users <petsc-users at mcs.anl.gov> wrote:
>>>>>>>>
>>>>>>>> Hi Amneeth,
>>>>>>>>
>>>>>>>> I think the errors are different with petsc 3.17.5
>>>>>>>>
>>>>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx
>>>>>>>> --FC=/usr/bin/mpif90 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*
>>>>>>>>
>>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>>>>> The version of PETSc you are using is out-of-date, we recommend
>>>>>>>> updating to the new release
>>>>>>>> Available Version: 3.19.5 Installed Version: 3.17.5
>>>>>>>> https://petsc.org/release/download/
>>>>>>>>
>>>>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>>>>>
>>>>>>>> =============================================================================================
>>>>>>>> Configuring PETSc to compile on your
>>>>>>>> system
>>>>>>>>
>>>>>>>> =============================================================================================
>>>>>>>> Compilers:
>>>>>>>>
>>>>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings
>>>>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector
>>>>>>>> -fvisibility=hidden -O3
>>>>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings
>>>>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch
>>>>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC
>>>>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0
>>>>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall
>>>>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3
>>>>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>>>>> Linkers:
>>>>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall
>>>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch
>>>>>>>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall
>>>>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch
>>>>>>>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl
>>>>>>>> BlasLapack:
>>>>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -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
>>>>>>>> mpiexec: /usr/bin/mpiexec
>>>>>>>> Implementation: openmpi
>>>>>>>> OMPI_VERSION: 4.0.3
>>>>>>>> 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/bin/glnxa64
>>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat
>>>>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher
>>>>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c
>>>>>>>> Language used to compile PETSc: C
>>>>>>>> PETSc:
>>>>>>>> PETSC_ARCH: linux-opt
>>>>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5
>>>>>>>> Prefix: <inplace installation>
>>>>>>>> Scalar type: real
>>>>>>>> Precision: double
>>>>>>>> Support for __float128
>>>>>>>> Integer size: 4 bytes
>>>>>>>> Single library: yes
>>>>>>>> Shared libraries: yes
>>>>>>>> Memory alignment from malloc(): 16 bytes
>>>>>>>> Using GNU make: /usr/bin/make
>>>>>>>>
>>>>>>>> xxx=========================================================================xxx
>>>>>>>> Configure stage complete. Now build PETSc libraries with:
>>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5
>>>>>>>> PETSC_ARCH=linux-opt all
>>>>>>>>
>>>>>>>> xxx=========================================================================xxx
>>>>>>>>
>>>>>>>> *$make*
>>>>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o
>>>>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5
>>>>>>>> BEGINNING TO COMPILE MATLAB INTERFACE
>>>>>>>> Building with 'gcc'.
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>>> In function ‘PetscBinaryWrite’:
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>>>>>> warning: ‘err’ may be used uninitialized in this function
>>>>>>>> [-Wmaybe-uninitialized]
>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>>>>>> | ^
>>>>>>>>
>>>>>>>> MEX completed successfully.
>>>>>>>> Building with 'gcc'.
>>>>>>>> MEX completed successfully.
>>>>>>>> Building with 'gcc'.
>>>>>>>> MEX completed successfully.
>>>>>>>> Building with 'gcc'.
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>>> In function ‘PetscBinaryWrite’:
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>>>>>> warning: ‘err’ may be used uninitialized in this function
>>>>>>>> [-Wmaybe-uninitialized]
>>>>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>>>>>> | ^
>>>>>>>>
>>>>>>>> MEX completed successfully.
>>>>>>>> =========================================
>>>>>>>> =========================================
>>>>>>>> Now to check if the libraries are working do:
>>>>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt
>>>>>>>> check
>>>>>>>>
>>>>>>>> *$make test query=requires queryval=matlab
>>>>>>>> DATAFILESPATH=/home/vit/datafiles/*
>>>>>>>> /usr/bin/python3
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py
>>>>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt
>>>>>>>> --testdir=./linux-opt/tests
>>>>>>>> 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: 85
>>>>>>>> # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> --------------------------------------------------------------
>>>>>>>> # [0]PETSC ERROR: Error in external library
>>>>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with
>>>>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
>>>>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>>>>>> shooting.
>>>>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022
>>>>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit
>>>>>>>> Tue Sep 5 10:15:57 2023
>>>>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc
>>>>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 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() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82
>>>>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331
>>>>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244
>>>>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144
>>>>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020
>>>>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131
>>>>>>>> # [0]PETSC ERROR: #7 PCSetUp() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990
>>>>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407
>>>>>>>> # [0]PETSC ERROR: #9 main() at
>>>>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305
>>>>>>>> # [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0
>>>>>>>> # [0]PETSC ERROR: -error_output_stdout
>>>>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1
>>>>>>>> # [0]PETSC ERROR: -malloc_dump
>>>>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
>>>>>>>> # [0]PETSC ERROR: -pc_type lu
>>>>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0
>>>>>>>> # [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_WORLD
>>>>>>>> # with errorcode 85.
>>>>>>>> #
>>>>>>>> # 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
>>>>>>>>
>>>>>>>>
>>>>>>>> # FAILED ksp_ksp_tutorials-ex72_12
>>>>>>>> #
>>>>>>>> # To rerun failed tests:
>>>>>>>> # /usr/bin/make -f gmakefile test test-fail=1
>>>>>>>>
>>>>>>>> To get the info of the error there is no specific probe id reported.
>>>>>>>>
>>>>>>>> How to check error info and proceed further?
>>>>>>>>
>>>>>>>> Thanks and regards
>>>>>>>> Srinivas
>>>>>>>>
>>>>>>>> On Tue, Sep 5, 2023 at 1:08 AM Amneet Bhalla <mail2amneet at gmail.com>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Do you get similar errors with petsc 3.17.5 using the new
>>>>>>>>> configure options that Satish mentioned?
>>>>>>>>>
>>>>>>>>> On Sun, Sep 3, 2023 at 10:19 PM INTURU SRINIVAS 20PHD0548 via
>>>>>>>>> petsc-users <petsc-users at mcs.anl.gov> wrote:
>>>>>>>>>
>>>>>>>>>> Sorry for missing that.
>>>>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay
>>>>>>>>>> -nosplash*
>>>>>>>>>>
>>>>>>>>>> < M A T L A B (R) >
>>>>>>>>>> Copyright 1984-2020 The MathWorks, Inc.
>>>>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64)
>>>>>>>>>> November 23, 2020
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> To get started, type doc.
>>>>>>>>>> For product information, visit www.mathworks.com.
>>>>>>>>>>
>>>>>>>>>> Thanks and regards
>>>>>>>>>> Srinivas
>>>>>>>>>>
>>>>>>>>>> On Mon, Sep 4, 2023 at 10:19 AM Satish Balay <balay at mcs.anl.gov>
>>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>>> 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
>>>>>>>>>>> > > > >>>> >
>>>>>>>>>>
>>>>>>>>>>
>>
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> --
> --Amneet
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--
--Amneet
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