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 <[email protected]> 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 < > > [email protected]> 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 < > > [email protected] <mailto: > > [email protected]>> 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 <[email protected] > > <mailto:[email protected]>> 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 <[email protected] > > <mailto:[email protected]>> 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 <[email protected] > > <mailto:[email protected]>> 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 < > > [email protected] <mailto: > > [email protected]>> 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 [email protected] > > > >>>>>> # > > -------------------------------------------------------------------------- > > > >>>>>> # 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 <[email protected] > > <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> > > 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 [email protected] > > > >>>>>>>> # > > -------------------------------------------------------------------------- > > > >>>>>>>> # 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 < > > [email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> > > 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 < > > [email protected] <mailto:[email protected]>> 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 [email protected] > > > >>>>>>>>>>> > # > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > # 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 [email protected] > > > >>>>>>>>>>> > > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > 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 < > > [email protected] <mailto:[email protected]>> 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 < > > > >>>>>>>>>>> > > > [email protected] <mailto: > > [email protected]>> 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 < > > [email protected] <mailto:[email protected]>> > > > >>>>>>>>>>> > > wrote: > > > >>>>>>>>>>> > > > > > > > >>>>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04 AM INTURU SRINIVAS > > 20PHD0548 via > > > >>>>>>>>>>> > > petsc-users < > > > >>>>>>>>>>> > > > >> [email protected] <mailto: > > [email protected]>> 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 > > [email protected] > > > >>>>>>>>>>> > > > >>> # > > > >>>>>>>>>>> > > > >>> > > > >>>>>>>>>>> > > > > -------------------------------------------------------------------------- > > > >>>>>>>>>>> > > > >>> # 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 > > > >>>>>>>>>>> > > > >>> > > -------------------------------------------------------------- > > > >>>>>>> > >
