[petsc-users] Error while building PETSc with MATLAB
INTURU SRINIVAS 20PHD0548
inturu.srinivas2020 at vitstudent.ac.in
Tue Sep 5 13:07:05 CDT 2023
I will try with new version of MATLAB and let you know the status.
Thanks and regards
Srinivas
On Tue, Sep 5, 2023, 23:33 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
>>>>>> > > > >>>> > > # [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
>>>>>> > > >
>>>>>
>>>>>
--
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