[petsc-users] Error while building PETSc with MATLAB
Satish Balay
balay at mcs.anl.gov
Wed Sep 6 15:34:40 CDT 2023
BTW: Stepping back and looking that the error message:
> > > >> Error: The import statement 'import matlab.internal.engine.input'
> > cannot be found or cannot be imported. Imported names must end with '.*' or
> > be fully qualified.
Google suggests:
https://www.mathworks.com/matlabcentral/answers/494387-python-engineerror-import-argument-matlab-internal-engine-input-cannot-be-found-or-cannot-be-impo
i.e a wrong "input.m" file is loaded - that's causing grief?
But its not clear to me how one would track this file. MATLABPATH? some default matlab config files?
And is this conflicting file coming from matlab install or $HOME?
Or the conflict is due to a different ".m" file - then input.m?
Assuming this is indeed the issue (a- I would suggest trying this out in
a fresh user account - and see if things work [both basic matlab only
test - and the petsc+matlab]
Satish
On Thu, 7 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote:
> I tried with different examples and all are working later.
> As you said there may be a license issue.
> I will try with latest matlab version.
>
> Thanks and regards
> Srinivas
>
> On Thu, Sep 7, 2023, 00:24 Satish Balay <balay at mcs.anl.gov> wrote:
>
> > I'm still curios why the first [c++] attempt failed but the second one
> > succeeded.
> >
> > The only difference I can spot is myEngineApp.cpp vs myEngineApp2.cpp.
> > What is the difference here between these 2 source files?
> >
> > Or is it some random error [the same source code worked failed before -
> > but works now - and might fail again later?]
> >
> > Maybe there is some issue with matlab license here - that prevents some
> > usages (or usage patterns) to fail?
> >
> > Satish
> >
> > On Wed, 6 Sep 2023, Barry Smith wrote:
> >
> > >
> > > Ok, so the C++ binding for Matlab engine is working on your machine.
> > PETSc uses the C binding which links against different libraries but, one
> > would think the C binding would work for sure if the C++ binding works. Can
> > you try a Matlab Engine C example provided by Matlab?
> > >
> > >
> > >
> > >
> > > > On Sep 6, 2023, at 3:58 AM, INTURU SRINIVAS 20PHD0548 <
> > inturu.srinivas2020 at vitstudent.ac.in> wrote:
> > > >
> > > > Hi Amneet,
> > > >
> > > > I repeated the same procedure again and this time it is working.
> > > > $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L
> > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp
> > -lMatlabDataArray -lMatlabEngine
> > > >
> > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64
> > > > $export LD_LIBRARY_PATH
> > > > $./a.out
> > > > Square root of -2 is 0 + 1.41421i
> > > > Square root of 2 is 1.41421 + 0i
> > > > Square root of 6 is 2.44949 + 0i
> > > > Square root of 8 is 2.82843 + 0i
> > > > I don't know how it is working this time?
> > > >
> > > > Thanks and regards
> > > > Srinivas
> > > >
> > > >
> > > > On Wed, Sep 6, 2023 at 12:17 PM INTURU SRINIVAS 20PHD0548 <
> > inturu.srinivas2020 at vitstudent.ac.in <mailto:
> > inturu.srinivas2020 at vitstudent.ac.in>> wrote:
> > > >> Hi Amneet,
> > > >> I tried the following example to run a matlab engine.
> > > >>
> > > >> #include "MatlabDataArray.hpp"
> > > >> #include "MatlabEngine.hpp"
> > > >> #include <iostream>
> > > >> void callSQRT() {
> > > >>
> > > >> using namespace matlab::engine;
> > > >>
> > > >> // Start MATLAB engine synchronously
> > > >> std::unique_ptr<MATLABEngine> matlabPtr = startMATLAB();
> > > >>
> > > >> //Create MATLAB data array factory
> > > >> matlab::data::ArrayFactory factory;
> > > >>
> > > >> // Define a four-element typed array
> > > >> matlab::data::TypedArray<double> const argArray =
> > > >> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 });
> > > >>
> > > >> // Call MATLAB sqrt function on the data array
> > > >> matlab::data::Array const results = matlabPtr->feval(u"sqrt",
> > argArray);
> > > >>
> > > >> // Display results
> > > >> for (int i = 0; i < results.getNumberOfElements(); i++) {
> > > >> double a = argArray[i];
> > > >> std::complex<double> v = results[i];
> > > >> double realPart = v.real();
> > > >> double imgPart = v.imag();
> > > >> std::cout << "Square root of " << a << " is " <<
> > > >> realPart << " + " << imgPart << "i" << std::endl;
> > > >> }
> > > >> }
> > > >>
> > > >> int main() {
> > > >> callSQRT();
> > > >> return 0;
> > > >> }
> > > >>
> > > >> $g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L
> > /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp
> > -lMatlabDataArray -lMatlabEngine
> > > >>
> > $LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64
> > > >> $export LD_LIBRARY_PATH
> > > >> $./a.out
> > > >> Starting
> > > >> Error: The import statement 'import matlab.internal.engine.input'
> > cannot be found or cannot be imported. Imported names must end with '.*' or
> > be fully qualified.
> > > >>
> > > >> terminate called after throwing an instance of
> > 'matlab::engine::EngineException'
> > > >> what(): MATLAB process cannot be created.
> > > >> Aborted (core dumped)
> > > >>
> > > >> I got the above error for Matlab R2020b. Please help me to sort out
> > this.
> > > >>
> > > >> Thanks and regards
> > > >> Srinivas
> > > >>
> > > >> On Tue, Sep 5, 2023 at 11:39 PM Amneet Bhalla <mail2amneet at gmail.com
> > <mailto:mail2amneet at gmail.com>> wrote:
> > > >>> BTW, what Barry is suggesting is the following:
> > > >>>
> > > >>> Compile a sample code with a command line this:
> > > >>>
> > > >>> g++ -std=c++11 -I matlabroot/extern/include/ -L
> > matlabroot/extern/bin/glnxa64/
> > > >>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine
> > > >>>
> > > >>> This command is provided here:
> > > >>>
> > https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html
> > > >>>
> > > >>> A sample MATLAB code is here:
> > > >>>
> > https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html
> > > >>>
> > > >>> (You can just pick a few lines of code from here to create a
> > barebone example)
> > > >>>
> > > >>> On Tue, Sep 5, 2023 at 11:02 AM Amneet Bhalla <mail2amneet at gmail.com
> > <mailto:mail2amneet at gmail.com>> wrote:
> > > >>>> Srinivas --- Do you have a different version of MATLAB that you can
> > install? If your organization has a MATLAB license, you can install recent
> > versions of MATLAB from mathworks.com <http://mathworks.com/>
> > > >>>> On Tue, Sep 5, 2023 at 10:37 AM Barry Smith <bsmith at petsc.dev
> > <mailto: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 <mailto:
> > 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
> > <mailto: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 <mailto: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 <mailto: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 <mailto: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 <
> > http://www.mathworks.com/>.
> > > >>>>>>>>>>
> > > >>>>>>>>>> Thanks and regards
> > > >>>>>>>>>> Srinivas
> > > >>>>>>>>>>
> > > >>>>>>>>>> On Mon, Sep 4, 2023 at 10:19 AM Satish Balay <
> > balay at mcs.anl.gov <mailto: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 <
> > 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 <mailto: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 <mailto:
> > 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 <mailto: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 <mailto:
> > 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 <http://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
> > > >>>>>>>>>>> > > > >>>
> > --------------------------------------------------------------
> > > >>>>>>>
>
>
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