[petsc-users] Error while building PETSc with MATLAB
Amneet Bhalla
mail2amneet at gmail.com
Tue Sep 5 13:02:32 CDT 2023
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
>>>>> > > > >>>> > > >>> > > for
>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I
>>>>> tried without
>>>>> > > > >>>> linking
>>>>> > > > >>>> > > >>> Matlab
>>>>> > > > >>>> > > >>> > > with
>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while
>>>>> configuring
>>>>> > > > >>>> libmesh 1.6.2
>>>>> > > > >>>> > > >>> that
>>>>> > > > >>>> > > >>> > > PETSc
>>>>> > > > >>>> > > >>> > > > > was not found but --enable-petsc-required is
>>>>> > > specified.
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for
>>>>> libmesh with
>>>>> > > > >>>> PETSc and
>>>>> > > > >>>> > > >>> Matlab
>>>>> > > > >>>> > > >>> > > is in
>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for complicated
>>>>> > > geometries
>>>>> > > > >>>> it is
>>>>> > > > >>>> > > >>> > > mentioned to
>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh construct.
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these
>>>>> various
>>>>> > > things
>>>>> > > > >>>> and ended
>>>>> > > > >>>> > > >>> up with
>>>>> > > > >>>> > > >>> > > > > errors.
>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further to
>>>>> do my
>>>>> > > > >>>> research work.
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as
>>>>> possible.
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > Thanks and Regards
>>>>> > > > >>>> > > >>> > > > > Srinivas
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla <
>>>>> > > > >>>> mail2amneet at gmail.com>
>>>>> > > > >>>> > > >>> > > wrote:
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas,
>>>>> > > > >>>> > > >>> > > > > >
>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don’t need
>>>>> libMesh for
>>>>> > > the
>>>>> > > > >>>> WEC
>>>>> > > > >>>> > > >>> application.
>>>>> > > > >>>> > > >>> > > You
>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that
>>>>> builds with
>>>>> > > > >>>> Matlab.
>>>>> > > > >>>> > > >>> > > > > >
>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for wanting
>>>>> to build
>>>>> > > > >>>> libMesh?
>>>>> > > > >>>> > > >>> > > > > >
>>>>> > > > >>>> > > >>> > > > > > Thanks,
>>>>> > > > >>>> > > >>> > > > > > —Amneet
>>>>> > > > >>>> > > >>> > > > > >
>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM INTURU
>>>>> SRINIVAS
>>>>> > > > >>>> 20PHD0548 via
>>>>> > > > >>>> > > >>> > > petsc-users
>>>>> > > > >>>> > > >>> > > > > > <petsc-users at mcs.anl.gov> wrote:
>>>>> > > > >>>> > > >>> > > > > >
>>>>> > > > >>>> > > >>> > > > > >> Hi,
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by
>>>>> removing all
>>>>> > > > >>>> occurrences
>>>>> > > > >>>> > > >>> of
>>>>> > > > >>>> > > >>> > > "-lut
>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I ran
>>>>> "make
>>>>> > > test"
>>>>> > > > >>>> got the
>>>>> > > > >>>> > > >>> > > following
>>>>> > > > >>>> > > >>> > > > > >> errors
>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug:
>>>>> > > > >>>> > > >>> > > > > >> TEST
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>> > > > >>>> > > >>> > > > > >> not ok
>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>> > > > >>>> > > >>> Error
>>>>> > > > >>>> > > >>> > > code: 124
>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ---------------------
>>>>> Error
>>>>> > > Message
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>>
>>>>> --------------------------------------------------------------
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external
>>>>> library
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB
>>>>> engine
>>>>> > > on
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>> > > > >>>> for
>>>>> > > > >>>> > > >>> trouble
>>>>> > > > >>>> > > >>> > > > > >> shooting.
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version
>>>>> 3.13.4,
>>>>> > > Aug
>>>>> > > > >>>> 01, 2020
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a
>>>>> > > linux-debug
>>>>> > > > >>>> named
>>>>> > > > >>>> > > >>> > > MB108SMEC028
>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>>> > > > >>>> > > >>> --with-debugging=1
>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1
>>>>> --download-fblaslapack=1
>>>>> > > > >>>> --with-x=0
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>>> > > > >>>> > > >>> --with-matlab-engine=1
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1
>>>>> PetscMatlabEngineCreate()
>>>>> > > line
>>>>> > > > >>>> 67 in
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>>
>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table
>>>>> entries:
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of
>>>>> Error
>>>>> > > > >>>> Message
>>>>> > > > >>>> > > >>> -------send
>>>>> > > > >>>> > > >>> > > entire
>>>>> > > > >>>> > > >>> > > > > >> error message to
>>>>> > > petsc-maint at mcs.anl.gov----------
>>>>> > > > >>>> > > >>> > > > > >> #
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> --------------------------------------------------------------------------
>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in
>>>>> communicator
>>>>> > > > >>>> > > >>> MPI_COMM_SELF
>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076.
>>>>> > > > >>>> > > >>> > > > > >> #
>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open
>>>>> MPI to
>>>>> > > kill
>>>>> > > > >>>> all MPI
>>>>> > > > >>>> > > >>> > > processes.
>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from
>>>>> other
>>>>> > > processes,
>>>>> > > > >>>> > > >>> depending on
>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them.
>>>>> > > > >>>> > > >>> > > > > >> #
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> --------------------------------------------------------------------------
>>>>> > > > >>>> > > >>> > > > > >> ok
>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>> > > > >>>> # SKIP
>>>>> > > > >>>> > > >>> Command
>>>>> > > > >>>> > > >>> > > > > >> failed so no diff
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt
>>>>> > > > >>>> > > >>> > > > > >> TEST
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>> > > > >>>> > > >>> > > > > >> not ok
>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>> > > > >>>> > > >>> Error
>>>>> > > > >>>> > > >>> > > code: 124
>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ---------------------
>>>>> Error
>>>>> > > Message
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>>
>>>>> --------------------------------------------------------------
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external
>>>>> library
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start MATLAB
>>>>> engine
>>>>> > > on
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>> > > > >>>> for
>>>>> > > > >>>> > > >>> trouble
>>>>> > > > >>>> > > >>> > > > > >> shooting.
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release Version
>>>>> 3.13.4,
>>>>> > > Aug
>>>>> > > > >>>> 01, 2020
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test on a
>>>>> > > linux-opt
>>>>> > > > >>>> named
>>>>> > > > >>>> > > >>> > > MB108SMEC028 by
>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3
>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3
>>>>> > > > >>>> --PETSC_ARCH=linux-opt
>>>>> > > > >>>> > > >>> > > --with-debugging=0
>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0
>>>>> > > > >>>> --download-fblaslapack=1
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>>> > > > >>>> > > >>> --with-matlab-engine=1
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1
>>>>> PetscMatlabEngineCreate()
>>>>> > > line
>>>>> > > > >>>> 67 in
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>>
>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126 in
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table
>>>>> entries:
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End of
>>>>> Error
>>>>> > > > >>>> Message
>>>>> > > > >>>> > > >>> -------send
>>>>> > > > >>>> > > >>> > > entire
>>>>> > > > >>>> > > >>> > > > > >> error message to
>>>>> > > petsc-maint at mcs.anl.gov----------
>>>>> > > > >>>> > > >>> > > > > >> #
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> --------------------------------------------------------------------------
>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in
>>>>> communicator
>>>>> > > > >>>> > > >>> MPI_COMM_SELF
>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076.
>>>>> > > > >>>> > > >>> > > > > >> #
>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes Open
>>>>> MPI to
>>>>> > > kill
>>>>> > > > >>>> all MPI
>>>>> > > > >>>> > > >>> > > processes.
>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from
>>>>> other
>>>>> > > processes,
>>>>> > > > >>>> > > >>> depending on
>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them.
>>>>> > > > >>>> > > >>> > > > > >> #
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> --------------------------------------------------------------------------
>>>>> > > > >>>> > > >>> > > > > >> ok
>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>> > > > >>>> # SKIP
>>>>> > > > >>>> > > >>> Command
>>>>> > > > >>>> > > >>> > > > > >> failed so no diff.
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc 3.17.5
>>>>> > > version. I
>>>>> > > > >>>> am
>>>>> > > > >>>> > > >>> sharing the
>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both petsc
>>>>> 3.13.4 and
>>>>> > > > >>>> petsc
>>>>> > > > >>>> > > >>> 3.17.5.
>>>>> > > > >>>> > > >>> > > Please find
>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful.
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards
>>>>> > > > >>>> > > >>> > > > > >> Srinivas
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56 PM Satish
>>>>> Balay <
>>>>> > > > >>>> > > >>> balay at mcs.anl.gov>
>>>>> > > > >>>> > > >>> > > wrote:
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not
>>>>> petsc's
>>>>> > > > >>>> > > >>> configure.log/make.log
>>>>> > > > >>>> > > >>> > > for
>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> >>>>
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> Matlab:
>>>>> > > > >>>> > > >>> > > > > >>> Includes:
>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include
>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b
>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine:
>>>>> > > > >>>> > > >>> > > > > >>> Library:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>> > > > >>>> > > >>> > > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>> > > -leng
>>>>> > > > >>>> -lmex
>>>>> > > > >>>> > > >>> -lmx
>>>>> > > > >>>> > > >>> > > -lmat -lut
>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc
>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C
>>>>> > > > >>>> > > >>> > > > > >>> <<<<<
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a) -
>>>>> we are
>>>>> > > seeing:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> >>>
>>>>> > > > >>>> > > >>> > > > > >>> Matlab:
>>>>> > > > >>>> > > >>> > > > > >>> Includes:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include
>>>>> > > > >>>> > > >>> > > > > >>> Libraries:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat
>>>>> > > > >>>> > > >>> > > > > >>> Executable:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>>
>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a
>>>>> > > > >>>> > > >>> > > > > >>> mex:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex
>>>>> > > > >>>> > > >>> > > > > >>> matlab:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab
>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64
>>>>> > > > >>>> > > >>> > > > > >>> <<<
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n -licuuc"
>>>>> are not
>>>>> > > > >>>> preset here.
>>>>> > > > >>>> > > >>> This
>>>>> > > > >>>> > > >>> > > might
>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab versions.
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> You can:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> - edit
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables
>>>>> > > > >>>> > > >>> > > and
>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut
>>>>> -licudata
>>>>> > > -licui18n
>>>>> > > > >>>> -licuuc"
>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in
>>>>> > > '/home/vit/sfw/petsc/3.13.4'
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now.
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> Satish
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS
>>>>> 20PHD0548
>>>>> > > via
>>>>> > > > >>>> > > >>> petsc-users
>>>>> > > > >>>> > > >>> > > wrote:
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while
>>>>> building
>>>>> > > > >>>> petsc3.13.4 with
>>>>> > > > >>>> > > >>> > > matlab and
>>>>> > > > >>>> > > >>> > > > > >>> also
>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building libmesh
>>>>> with
>>>>> > > > >>>> petsc3.17.5 and
>>>>> > > > >>>> > > >>> matlab.
>>>>> > > > >>>> > > >>> > > > > >>> Building
>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done
>>>>> > > successfully.
>>>>> > > > >>>> But
>>>>> > > > >>>> > > >>> libmesh is
>>>>> > > > >>>> > > >>> > > not
>>>>> > > > >>>> > > >>> > > > > >>> able to
>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc
>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments.
>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31 PM
>>>>> Satish Balay <
>>>>> > > > >>>> > > >>> balay at mcs.anl.gov>
>>>>> > > > >>>> > > >>> > > > > >>> wrote:
>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log from
>>>>> both
>>>>> > > > >>>> petsc-3.13 and
>>>>> > > > >>>> > > >>> 3.17 [or
>>>>> > > > >>>> > > >>> > > 3.19].
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the logs
>>>>> > > friendly to
>>>>> > > > >>>> mailing
>>>>> > > > >>>> > > >>> list -
>>>>> > > > >>>> > > >>> > > or
>>>>> > > > >>>> > > >>> > > > > >>> send
>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint]
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with 3.17?
>>>>> [or
>>>>> > > 3.19?]
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>> > > Satish
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU SRINIVAS
>>>>> > > 20PHD0548
>>>>> > > > >>>> via
>>>>> > > > >>>> > > >>> petsc-users
>>>>> > > > >>>> > > >>> > > wrote:
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file
>>>>> while
>>>>> > > building
>>>>> > > > >>>> > > >>> petsc-3.13.4
>>>>> > > > >>>> > > >>> > > with
>>>>> > > > >>>> > > >>> > > > > >>> Matlab.
>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and do
>>>>> the
>>>>> > > needful.
>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at 10:19 AM
>>>>> INTURU
>>>>> > > > >>>> SRINIVAS
>>>>> > > > >>>> > > >>> 20PHD0548 <
>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>> inturu.srinivas2020 at vitstudent.ac.in>
>>>>> > > wrote:
>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5.
>>>>> During
>>>>> > > building
>>>>> > > > >>>> of
>>>>> > > > >>>> > > >>> libmesh, the
>>>>> > > > >>>> > > >>> > > error
>>>>> > > > >>>> > > >>> > > > > >>> shows
>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found
>>>>> > > > >>>> > > >>> > > > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at 9:43 PM
>>>>> Satish
>>>>> > > > >>>> Balay <
>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov>
>>>>> > > > >>>> > > >>> > > > > >>> > > wrote:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> https://ibamr.github.io/linux
>>>>> says
>>>>> > > > >>>> petsc-3.17
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with
>>>>> petsc-3.17.5?
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU
>>>>> SRINIVAS
>>>>> > > > >>>> 20PHD0548 via
>>>>> > > > >>>> > > >>> > > petsc-users
>>>>> > > > >>>> > > >>> > > > > >>> wrote:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello,
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc with
>>>>> MATLAB for
>>>>> > > > >>>> working on
>>>>> > > > >>>> > > >>> the
>>>>> > > > >>>> > > >>> > > > > >>> simulation
>>>>> > > > >>>> > > >>> > > > > >>> > > using
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While
>>>>> building the
>>>>> > > PETSc,
>>>>> > > > >>>> using the
>>>>> > > > >>>> > > >>> > > following
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_ARCH=linux-debug
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-fblaslapack=1 \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateResidual':
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEnginePut'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGet'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `EvaluateJacobian':
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEnginePut'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGet'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders':
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGet'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main':
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineCreate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> > >
>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>> > > > >>>> `PetscMatlabEngineDestroy'
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld returned
>>>>> 1 exit
>>>>> > > > >>>> status
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: ***
>>>>> [gmakefile.test:185:
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>>
>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test]
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for
>>>>> unfinished
>>>>> > > jobs....
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve this
>>>>> issue
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>> > > > >>>> > > >>> > > > > >>>
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent from
>>>>> Vellore
>>>>> > > > >>>> Institute of
>>>>> > > > >>>> > > >>> > > Technology.
>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may contain
>>>>> legally
>>>>> > > > >>>> protected
>>>>> > > > >>>> > > >>> > > confidential or
>>>>> > > > >>>> > > >>> > > > > >> privileged information of “Vellore
>>>>> Institute of
>>>>> > > > >>>> Technology”.
>>>>> > > > >>>> > > >>> If
>>>>> > > > >>>> > > >>> > > you are
>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you should
>>>>> not
>>>>> > > > >>>> disseminate,
>>>>> > > > >>>> > > >>> distribute
>>>>> > > > >>>> > > >>> > > or copy
>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender
>>>>> immediately
>>>>> > > > >>>> and destroy
>>>>> > > > >>>> > > >>> all
>>>>> > > > >>>> > > >>> > > copies of
>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If you
>>>>> have
>>>>> > > > >>>> received this
>>>>> > > > >>>> > > >>> email
>>>>> > > > >>>> > > >>> > > in error,
>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by
>>>>> reply email
>>>>> > > and
>>>>> > > > >>>> delete
>>>>> > > > >>>> > > >>> the
>>>>> > > > >>>> > > >>> > > original
>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without
>>>>> reading
>>>>> > > them.*
>>>>> > > > >>>> > > >>> > > > > >>
>>>>> > > > >>>> > > >>> > > > > >
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > > >
>>>>> > > > >>>> > > >>> > > >
>>>>> > > > >>>> > > >>> > >
>>>>> > > > >>>> > > >>> >
>>>>> > > > >>>> > > >>> >
>>>>> > > > >>>> > > >>>
>>>>> > > > >>>> > > >>
>>>>> > > > >>>> > > >>
>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore
>>>>> Institute of
>>>>> > > > >>>> Technology.
>>>>> > > > >>>> > > >> The contents of this email may contain legally
>>>>> protected
>>>>> > > > >>>> confidential or
>>>>> > > > >>>> > > >> privileged information of “Vellore Institute of
>>>>> > > Technology”. If
>>>>> > > > >>>> you are
>>>>> > > > >>>> > > >> not the intended recipient, you should not
>>>>> disseminate,
>>>>> > > > >>>> distribute or copy
>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately
>>>>> and destroy
>>>>> > > > >>>> all copies of
>>>>> > > > >>>> > > >> this message and any attachments. If you have
>>>>> received this
>>>>> > > > >>>> email in error,
>>>>> > > > >>>> > > >> please promptly notify the sender by reply email and
>>>>> delete
>>>>> > > the
>>>>> > > > >>>> original
>>>>> > > > >>>> > > >> email and any backup copies without reading them.*
>>>>> > > > >>>> > > >>
>>>>> > > > >>>> > > >
>>>>> > > > >>>> > > >
>>>>> > > > >>>> > > > --
>>>>> > > > >>>> > > > --Amneet
>>>>> > > > >>>> > > >
>>>>> > > > >>>> > > >
>>>>> > > > >>>> > > >
>>>>> > > > >>>> > > >
>>>>> > > > >>>> > >
>>>>> > > > >>>> > >
>>>>> > > > >>>>
>>>>> > > > >>>
>>>>> > > > >>>
>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute of
>>>>> > > Technology.
>>>>> > > > >>> The contents of this email may contain legally protected
>>>>> > > confidential or
>>>>> > > > >>> privileged information of “Vellore Institute of
>>>>> Technology”. If you
>>>>> > > are
>>>>> > > > >>> not the intended recipient, you should not disseminate,
>>>>> distribute
>>>>> > > or copy
>>>>> > > > >>> this e-mail. Please notify the sender immediately and
>>>>> destroy all
>>>>> > > copies of
>>>>> > > > >>> this message and any attachments. If you have received this
>>>>> email in
>>>>> > > error,
>>>>> > > > >>> please promptly notify the sender by reply email and delete
>>>>> the
>>>>> > > original
>>>>> > > > >>> email and any backup copies without reading them.*
>>>>> > > > >>>
>>>>> > > > >>
>>>>> > > > >>
>>>>> > > > >> --
>>>>> > > > >> What most experimenters take for granted before they begin
>>>>> their
>>>>> > > > >> experiments is infinitely more interesting than any results
>>>>> to which
>>>>> > > their
>>>>> > > > >> experiments lead.
>>>>> > > > >> -- Norbert Wiener
>>>>> > > > >>
>>>>> > > > >> https://www.cse.buffalo.edu/~knepley/
>>>>> > > > >> <http://www.cse.buffalo.edu/~knepley/>
>>>>> > > > >>
>>>>> > > > >
>>>>> > > > >
>>>>> > > > > *Disclaimer:This message was sent from Vellore Institute of
>>>>> Technology.
>>>>> > > > > The contents of this email may contain legally protected
>>>>> confidential
>>>>> > > or
>>>>> > > > > privileged information of “Vellore Institute of Technology”.
>>>>> If you
>>>>> > > are
>>>>> > > > > not the intended recipient, you should not disseminate,
>>>>> distribute or
>>>>> > > copy
>>>>> > > > > this e-mail. Please notify the sender immediately and destroy
>>>>> all
>>>>> > > copies of
>>>>> > > > > this message and any attachments. If you have received this
>>>>> email in
>>>>> > > error,
>>>>> > > > > please promptly notify the sender by reply email and delete the
>>>>> > > original
>>>>> > > > > email and any backup copies without reading them.*
>>>>> > > > >
>>>>> > > >
>>>>> > > >
>>>>> > > >
>>>>> > >
>>>>> >
>>>>> >
>>>>
>>>>
>>>>
>>>> *Disclaimer:This message was sent from Vellore Institute of
>>>> Technology. The contents of this email may contain legally protected
>>>> confidential or privileged information of “Vellore Institute of
>>>> Technology”. If you are not the intended recipient, you should not
>>>> disseminate, distribute or copy this e-mail. Please notify the sender
>>>> immediately and destroy all copies of this message and any attachments. If
>>>> you have received this email in error, please promptly notify the sender by
>>>> reply email and delete the original email and any backup copies without
>>>> reading them.*
>>>>
>>>
>>>
>>> --
>>> --Amneet
>>>
>>>
>>>
>>>
>>
>> *Disclaimer:This message was sent from Vellore Institute of Technology.
>> The contents of this email may contain legally protected confidential or
>> privileged information of “Vellore Institute of Technology”. If you are
>> not the intended recipient, you should not disseminate, distribute or copy
>> this e-mail. Please notify the sender immediately and destroy all copies of
>> this message and any attachments. If you have received this email in error,
>> please promptly notify the sender by reply email and delete the original
>> email and any backup copies without reading them.*
>>
>>
>>
>
> *Disclaimer:This message was sent from Vellore Institute of Technology.
> The contents of this email may contain legally protected confidential or
> privileged information of “Vellore Institute of Technology”. If you are
> not the intended recipient, you should not disseminate, distribute or copy
> this e-mail. Please notify the sender immediately and destroy all copies of
> this message and any attachments. If you have received this email in error,
> please promptly notify the sender by reply email and delete the original
> email and any backup copies without reading them.*
>
>
>
--
--Amneet
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