[petsc-users] Error while building PETSc with MATLAB
INTURU SRINIVAS 20PHD0548
inturu.srinivas2020 at vitstudent.ac.in
Wed Sep 6 02:58:03 CDT 2023
Hi Amneet,
I repeated the same procedure again and this time it is working.
*$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L
/usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp2.cpp
-lMatlabDataArray -lMatlabEngine*
*$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64*
*$export LD_LIBRARY_PATH*
*$./a.out*
Square root of -2 is 0 + 1.41421i
Square root of 2 is 1.41421 + 0i
Square root of 6 is 2.44949 + 0i
Square root of 8 is 2.82843 + 0i
I don't know how it is working this time?
Thanks and regards
Srinivas
On Wed, Sep 6, 2023 at 12:17 PM INTURU SRINIVAS 20PHD0548 <
inturu.srinivas2020 at vitstudent.ac.in> wrote:
> Hi Amneet,
> I tried the following example to run a matlab engine.
>
> #include "MatlabDataArray.hpp"
> #include "MatlabEngine.hpp"
> #include <iostream>
> void callSQRT() {
>
> using namespace matlab::engine;
>
> // Start MATLAB engine synchronously
> std::unique_ptr<MATLABEngine> matlabPtr = startMATLAB();
>
> //Create MATLAB data array factory
> matlab::data::ArrayFactory factory;
>
> // Define a four-element typed array
> matlab::data::TypedArray<double> const argArray =
> factory.createArray({ 1,4 }, { -2.0, 2.0, 6.0, 8.0 });
>
> // Call MATLAB sqrt function on the data array
> matlab::data::Array const results = matlabPtr->feval(u"sqrt",
> argArray);
>
> // Display results
> for (int i = 0; i < results.getNumberOfElements(); i++) {
> double a = argArray[i];
> std::complex<double> v = results[i];
> double realPart = v.real();
> double imgPart = v.imag();
> std::cout << "Square root of " << a << " is " <<
> realPart << " + " << imgPart << "i" << std::endl;
> }
> }
>
> int main() {
> callSQRT();
> return 0;
> }
>
> *$g++ -std=c++11 -I /usr/local/MATLAB/R2020b/extern/include/ -L
> /usr/local/MATLAB/R2020b/extern/bin/glnxa64/ -pthread myEngineApp.cpp
> -lMatlabDataArray -lMatlabEngine*
>
> *$LD_LIBRARY_PATH=/usr/local/MATLAB/R2020b/extern/bin/glnxa64:/usr/local/MATLAB/R2020b/sys/os/glnxa64*
> *$export LD_LIBRARY_PATH*
> *$./a.out*
> Starting
> Error: The import statement 'import matlab.internal.engine.input' cannot
> be found or cannot be imported. Imported names must end with '.*' or be
> fully qualified.
>
> terminate called after throwing an instance of
> 'matlab::engine::EngineException'
> what(): MATLAB process cannot be created.
> Aborted (core dumped)
>
> I got the above error for Matlab R2020b. Please help me to sort out this.
>
> Thanks and regards
> Srinivas
>
> On Tue, Sep 5, 2023 at 11:39 PM Amneet Bhalla <mail2amneet at gmail.com>
> wrote:
>
>> BTW, what Barry is suggesting is the following:
>>
>> Compile a sample code with a command line this:
>>
>>
>> g++ -std=c++11 -I *matlabroot*/extern/include/ -L *matlabroot*/extern/bin/glnxa64/
>> -pthread myEngineApp.cpp -lMatlabDataArray -lMatlabEngine
>>
>>
>> This command is provided here:
>>
>> https://www.mathworks.com/help/matlab/matlab_external/build-c-engine-programs.html
>>
>>
>> A sample MATLAB code is here:
>>
>> https://www.mathworks.com/help/matlab/matlab_external/call-matlab-functions-from-c-1.html
>>
>>
>> (You can just pick a few lines of code from here to create a barebone example)
>>
>>
>> On Tue, Sep 5, 2023 at 11:02 AM Amneet Bhalla <mail2amneet at gmail.com>
>> wrote:
>>
>>> Srinivas --- Do you have a different version of MATLAB that you can
>>> install? If your organization has a MATLAB license, you can install recent
>>> versions of MATLAB from mathworks.com
>>>
>>> On Tue, Sep 5, 2023 at 10:37 AM Barry Smith <bsmith at petsc.dev> wrote:
>>>
>>>>
>>>> Ok, I have no suggestions. It seems to be more an issue with the
>>>> Matlab than PETSc. You could find a pure Matlab example of using the engine
>>>> (in the Matlab documentation) and try it to see if it works.
>>>>
>>>> Barry
>>>>
>>>>
>>>> On Sep 5, 2023, at 12:27 PM, INTURU SRINIVAS 20PHD0548 <
>>>> inturu.srinivas2020 at vitstudent.ac.in> wrote:
>>>>
>>>> I replaced e->ep = engOpen(buffer); with e->ep = engOpen("");
>>>> I got the same errors for petsc 3.17.5
>>>>
>>>>
>>>> *make all*
>>>> CC linux-opt/obj/sys/classes/matlabengine/matlab.o
>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5
>>>> BEGINNING TO COMPILE MATLAB INTERFACE
>>>> Building with 'gcc'.
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>> In function ‘PetscBinaryWrite’:
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>> warning: ‘err’ may be used uninitialized in this function
>>>> [-Wmaybe-uninitialized]
>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>> | ^
>>>>
>>>> MEX completed successfully.
>>>> Building with 'gcc'.
>>>> MEX completed successfully.
>>>> Building with 'gcc'.
>>>> MEX completed successfully.
>>>> Building with 'gcc'.
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>> In function ‘PetscBinaryWrite’:
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>> warning: ‘err’ may be used uninitialized in this function
>>>> [-Wmaybe-uninitialized]
>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>> | ^
>>>>
>>>> MEX completed successfully.
>>>> =========================================
>>>> =========================================
>>>> Now to check if the libraries are working do:
>>>> make PETSC_DIR=/home/vit/sfw/petsc/3.17.5 PETSC_ARCH=linux-opt check
>>>>
>>>> *make test query=requires queryval=matlab
>>>> DATAFILESPATH=/home/vit/datafiles/*
>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab
>>>> query=requires
>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85
>>>> # [0]PETSC ERROR: --------------------- Error Message
>>>> --------------------------------------------------------------
>>>> # [0]PETSC ERROR: Error in external library
>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with
>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>> shooting.
>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022
>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue
>>>> Sep 5 21:39:22 2023
>>>> # [0]PETSC ERROR: Configure options
>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0
>>>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>> --with-matlab-engine=1 -with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>> --known-64-bit-blas-indices=1
>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:83
>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:332
>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at
>>>> /home/vit/sfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:245
>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at
>>>> /home/vit/sfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144
>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at
>>>> /home/vit/sfw/petsc/3.17.5/src/mat/interface/matrix.c:3020
>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at
>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131
>>>> # [0]PETSC ERROR: #7 PCSetUp() at
>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990
>>>> # [0]PETSC ERROR: #8 KSPSetUp() at
>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407
>>>> # [0]PETSC ERROR: #9 main() at
>>>> /home/vit/sfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305
>>>> # [0]PETSC ERROR: PETSc Option Table entries:
>>>> # [0]PETSC ERROR: -check_pointer_intensity 0
>>>> # [0]PETSC ERROR: -error_output_stdout
>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1
>>>> # [0]PETSC ERROR: -malloc_dump
>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
>>>> # [0]PETSC ERROR: -pc_type lu
>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0
>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send
>>>> entire error message to petsc-maint at mcs.anl.gov----------
>>>> #
>>>> --------------------------------------------------------------------------
>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>>> # with errorcode 85.
>>>> #
>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>> # You may or may not see output from other processes, depending on
>>>> # exactly when Open MPI kills them.
>>>> #
>>>> --------------------------------------------------------------------------
>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
>>>>
>>>>
>>>> # FAILED ksp_ksp_tutorials-ex72_12
>>>> #
>>>> # To rerun failed tests:
>>>> # /usr/bin/make -f gmakefile test test-fail=1
>>>>
>>>> Thanks and regards
>>>> Srinivas
>>>>
>>>> On Tue, Sep 5, 2023 at 9:05 PM Barry Smith <bsmith at petsc.dev> wrote:
>>>>
>>>>>
>>>>> The error is occuring during
>>>>>
>>>>> e->ep = engOpen(buffer);
>>>>>
>>>>> Since the direct launch of /usr/local/MATLAB/R2020b/bin/matlab
>>>>> -glnxa64 -nodisplay -nosplash from your terminal shell worked we have to
>>>>> assume the problem is occuring when engOpen() is attempting to connect the
>>>>> stdout and stdin from the Matlab session that is launched to the
>>>>> executable.
>>>>>
>>>>> You can try the following. In 3.17.5 edit the
>>>>> file src/sys/classes/matlabengine/matlab.c and locate the line
>>>>>
>>>>> e->ep = engOpen(buffer);
>>>>>
>>>>> replace it with
>>>>>
>>>>> e->ep = engOpen("");
>>>>>
>>>>> Now in the PETSc directory do make all (it should recompile one file)
>>>>> and then run the
>>>>>
>>>>> make test query=requires queryval=matlab
>>>>> DATAFILESPATH=/home/vit/datafiles/
>>>>>
>>>>> again
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Sep 5, 2023, at 3:39 AM, INTURU SRINIVAS 20PHD0548 via petsc-users <
>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>
>>>>> Hi Amneeth,
>>>>>
>>>>> I think the errors are different with petsc 3.17.5
>>>>>
>>>>> *./configure --CC=/usr/bin/mpicc --CXX=/usr/bin/mpicxx
>>>>> --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>>>> PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0
>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1*
>>>>>
>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>> The version of PETSc you are using is out-of-date, we recommend
>>>>> updating to the new release
>>>>> Available Version: 3.19.5 Installed Version: 3.17.5
>>>>> https://petsc.org/release/download/
>>>>>
>>>>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>>
>>>>> =============================================================================================
>>>>> Configuring PETSc to compile on your system
>>>>>
>>>>>
>>>>> =============================================================================================
>>>>> Compilers:
>>>>>
>>>>> C Compiler: /usr/bin/mpicc -fPIC -Wall -Wwrite-strings
>>>>> -Wno-unknown-pragmas -Wno-lto-type-mismatch -fstack-protector
>>>>> -fvisibility=hidden -O3
>>>>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>> C++ Compiler: /usr/bin/mpicxx -Wall -Wwrite-strings
>>>>> -Wno-strict-aliasing -Wno-unknown-pragmas -Wno-lto-type-mismatch
>>>>> -fstack-protector -fvisibility=hidden -O3 -std=gnu++17 -fPIC
>>>>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0
>>>>> Fortran Compiler: /usr/bin/mpif90 -fPIC -Wall
>>>>> -ffree-line-length-0 -Wno-lto-type-mismatch -Wno-unused-dummy-argument -O3
>>>>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>> Linkers:
>>>>> Shared linker: /usr/bin/mpicc -shared -fPIC -Wall
>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch
>>>>> -fstack-protector -fvisibility=hidden -O3
>>>>> Dynamic linker: /usr/bin/mpicc -shared -fPIC -Wall
>>>>> -Wwrite-strings -Wno-unknown-pragmas -Wno-lto-type-mismatch
>>>>> -fstack-protector -fvisibility=hidden -O3
>>>>> Libraries linked against: -lquadmath -lstdc++ -ldl
>>>>> BlasLapack:
>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so -liomp5 -lpthread
>>>>> uses OpenMP; use export OMP_NUM_THREADS=<p> or -omp_num_threads <p>
>>>>> to control the number of threads
>>>>> uses 8 byte integers
>>>>> MPI:
>>>>> Version: 3
>>>>> mpiexec: /usr/bin/mpiexec
>>>>> Implementation: openmpi
>>>>> OMPI_VERSION: 4.0.3
>>>>> pthread:
>>>>> cmake:
>>>>> Version: 3.16.3
>>>>> /usr/bin/cmake
>>>>> regex:
>>>>> Matlab:
>>>>> Includes: -I/usr/local/MATLAB/R2020b/extern/include
>>>>> /usr/local/MATLAB/R2020b
>>>>> MatlabEngine:
>>>>> Library: -Wl,-rpath,/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex -lmx -lmat
>>>>> -lmwm_dispatcher -lmwopcmodel -lmwservices -lmwopcmodel -lmwm_dispatcher
>>>>> -lmwmpath -lmwopcmodel -lmwservices -lmwopcmodel -lmwservices -lxerces-c
>>>>> Language used to compile PETSc: C
>>>>> PETSc:
>>>>> PETSC_ARCH: linux-opt
>>>>> PETSC_DIR: /home/vit/ibamrsfw/petsc/3.17.5
>>>>> Prefix: <inplace installation>
>>>>> Scalar type: real
>>>>> Precision: double
>>>>> Support for __float128
>>>>> Integer size: 4 bytes
>>>>> Single library: yes
>>>>> Shared libraries: yes
>>>>> Memory alignment from malloc(): 16 bytes
>>>>> Using GNU make: /usr/bin/make
>>>>>
>>>>> xxx=========================================================================xxx
>>>>> Configure stage complete. Now build PETSc libraries with:
>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt
>>>>> all
>>>>>
>>>>> xxx=========================================================================xxx
>>>>>
>>>>> *$make*
>>>>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o
>>>>> CLINKER linux-opt/lib/libpetsc.so.3.17.5
>>>>> BEGINNING TO COMPILE MATLAB INTERFACE
>>>>> Building with 'gcc'.
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>> In function ‘PetscBinaryWrite’:
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>>> warning: ‘err’ may be used uninitialized in this function
>>>>> [-Wmaybe-uninitialized]
>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>>> | ^
>>>>>
>>>>> MEX completed successfully.
>>>>> Building with 'gcc'.
>>>>> MEX completed successfully.
>>>>> Building with 'gcc'.
>>>>> MEX completed successfully.
>>>>> Building with 'gcc'.
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>> In function ‘PetscBinaryWrite’:
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/viewer/impls/socket/matlab/bread.c:164:6:
>>>>> warning: ‘err’ may be used uninitialized in this function
>>>>> [-Wmaybe-uninitialized]
>>>>> 164 | if (err < 0) PETSC_MEX_ERROR("Error writing to socket\n");
>>>>> | ^
>>>>>
>>>>> MEX completed successfully.
>>>>> =========================================
>>>>> =========================================
>>>>> Now to check if the libraries are working do:
>>>>> make PETSC_DIR=/home/vit/ibamrsfw/petsc/3.17.5 PETSC_ARCH=linux-opt
>>>>> check
>>>>>
>>>>> *$make test query=requires queryval=matlab
>>>>> DATAFILESPATH=/home/vit/datafiles/*
>>>>> /usr/bin/python3
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/config/gmakegentest.py
>>>>> --petsc-dir=/home/vit/ibamrsfw/petsc/3.17.5 --petsc-arch=linux-opt
>>>>> --testdir=./linux-opt/tests
>>>>> Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/ queryval=matlab
>>>>> query=requires
>>>>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
>>>>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>>>> TEST linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 85
>>>>> # [0]PETSC ERROR: --------------------- Error Message
>>>>> --------------------------------------------------------------
>>>>> # [0]PETSC ERROR: Error in external library
>>>>> # [0]PETSC ERROR: Unable to start MATLAB engine with
>>>>> /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
>>>>> # [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>>> shooting.
>>>>> # [0]PETSC ERROR: Petsc Release Version 3.17.5, Sep 30, 2022
>>>>> # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by vit Tue
>>>>> Sep 5 10:15:57 2023
>>>>> # [0]PETSC ERROR: Configure options --CC=/usr/bin/mpicc
>>>>> --CXX=/usr/bin/mpicxx --FC=/usr/bin/mpif90 COPTFLAGS=-O3 CXXOPTFLAGS=-O3
>>>>> FOPTFLAGS=-O3 PETSC_ARCH=linux-opt --with-debugging=0 --with-x=0
>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:82
>>>>> # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:331
>>>>> # [0]PETSC ERROR: #3 PetscMatlabEnginePut() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/sys/classes/matlabengine/matlab.c:244
>>>>> # [0]PETSC ERROR: #4 MatLUFactorNumeric_Matlab() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/impls/aij/seq/matlab/aijmatlab.c:144
>>>>> # [0]PETSC ERROR: #5 MatLUFactorNumeric() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/mat/interface/matrix.c:3020
>>>>> # [0]PETSC ERROR: #6 PCSetUp_LU() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/impls/factor/lu/lu.c:131
>>>>> # [0]PETSC ERROR: #7 PCSetUp() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/pc/interface/precon.c:990
>>>>> # [0]PETSC ERROR: #8 KSPSetUp() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/interface/itfunc.c:407
>>>>> # [0]PETSC ERROR: #9 main() at
>>>>> /home/vit/ibamrsfw/petsc/3.17.5/src/ksp/ksp/tutorials/ex72.c:305
>>>>> # [0]PETSC ERROR: PETSc Option Table entries:
>>>>> # [0]PETSC ERROR: -check_pointer_intensity 0
>>>>> # [0]PETSC ERROR: -error_output_stdout
>>>>> # [0]PETSC ERROR: -f0 /home/vit/datafiles//matrices/arco1
>>>>> # [0]PETSC ERROR: -malloc_dump
>>>>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
>>>>> # [0]PETSC ERROR: -pc_type lu
>>>>> # [0]PETSC ERROR: -use_gpu_aware_mpi 0
>>>>> # [0]PETSC ERROR: ----------------End of Error Message -------send
>>>>> entire error message to petsc-maint at mcs.anl.gov----------
>>>>> #
>>>>> --------------------------------------------------------------------------
>>>>> # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>>>> # with errorcode 85.
>>>>> #
>>>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>>>> # You may or may not see output from other processes, depending on
>>>>> # exactly when Open MPI kills them.
>>>>> #
>>>>> --------------------------------------------------------------------------
>>>>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
>>>>>
>>>>>
>>>>> # FAILED ksp_ksp_tutorials-ex72_12
>>>>> #
>>>>> # To rerun failed tests:
>>>>> # /usr/bin/make -f gmakefile test test-fail=1
>>>>>
>>>>> To get the info of the error there is no specific probe id reported.
>>>>>
>>>>> How to check error info and proceed further?
>>>>>
>>>>> Thanks and regards
>>>>> Srinivas
>>>>>
>>>>> On Tue, Sep 5, 2023 at 1:08 AM Amneet Bhalla <mail2amneet at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Do you get similar errors with petsc 3.17.5 using the new configure
>>>>>> options that Satish mentioned?
>>>>>>
>>>>>> On Sun, Sep 3, 2023 at 10:19 PM INTURU SRINIVAS 20PHD0548 via
>>>>>> petsc-users <petsc-users at mcs.anl.gov> wrote:
>>>>>>
>>>>>>> Sorry for missing that.
>>>>>>> */usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash*
>>>>>>>
>>>>>>> < M A T L A B (R) >
>>>>>>> Copyright 1984-2020 The MathWorks, Inc.
>>>>>>> R2020b Update 3 (9.9.0.1538559) 64-bit (glnxa64)
>>>>>>> November 23, 2020
>>>>>>>
>>>>>>>
>>>>>>> To get started, type doc.
>>>>>>> For product information, visit www.mathworks.com.
>>>>>>>
>>>>>>> Thanks and regards
>>>>>>> Srinivas
>>>>>>>
>>>>>>> On Mon, Sep 4, 2023 at 10:19 AM Satish Balay <balay at mcs.anl.gov>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> You are missing one more step:
>>>>>>>>
>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028
>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with
>>>>>>>> command /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
>>>>>>>>
>>>>>>>> No run matlab manually on "MB108SMEC028" with the command
>>>>>>>> "/usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash"
>>>>>>>>
>>>>>>>> Does this work for you? As the message indicates this command is
>>>>>>>> invoked by "matlab_ls_test" - and that is failing.
>>>>>>>>
>>>>>>>> Satish
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, 4 Sep 2023, INTURU SRINIVAS 20PHD0548 via petsc-users wrote:
>>>>>>>>
>>>>>>>> > Hi Sathish,
>>>>>>>> >
>>>>>>>> > I tried the following procedure
>>>>>>>> >
>>>>>>>> > *$make *
>>>>>>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.4
>>>>>>>> > BEGINNING TO COMPILE MATLAB INTERFACE
>>>>>>>> > Building with 'gcc'.
>>>>>>>> >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>>> > In function ‘PetscBinaryWrite’:
>>>>>>>> >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>>>>>> > warning: ‘err’ may be used uninitialized in this function
>>>>>>>> > [-Wmaybe-uninitialized]
>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to
>>>>>>>> socket\n");
>>>>>>>> > | ^
>>>>>>>> >
>>>>>>>> > MEX completed successfully.
>>>>>>>> > Building with 'gcc'.
>>>>>>>> > MEX completed successfully.
>>>>>>>> > Building with 'gcc'.
>>>>>>>> > MEX completed successfully.
>>>>>>>> > Building with 'gcc'.
>>>>>>>> >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>>> > In function ‘PetscBinaryWrite’:
>>>>>>>> >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>>>>>> > warning: ‘err’ may be used uninitialized in this function
>>>>>>>> > [-Wmaybe-uninitialized]
>>>>>>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to
>>>>>>>> socket\n");
>>>>>>>> > | ^
>>>>>>>> >
>>>>>>>> > MEX completed successfully.
>>>>>>>> > =========================================
>>>>>>>> > Now to check if the libraries are working do:
>>>>>>>> > make PETSC_DIR=/home/vit/sfw/petsc/3.13.4 PETSC_ARCH=linux-opt
>>>>>>>> check
>>>>>>>> >
>>>>>>>> > *$make test query=requires queryval=matlab
>>>>>>>> > DATAFILESPATH=/home/vit/datafiles/*
>>>>>>>> > Using MAKEFLAGS: -- DATAFILESPATH=/home/vit/datafiles/
>>>>>>>> queryval=matlab
>>>>>>>> > query=requires
>>>>>>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
>>>>>>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>>>>>>> > TEST
>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>>>>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 139
>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > --------------------------------------------------------------
>>>>>>>> > # [0]PETSC ERROR: Error in external library
>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>>>>>> > # [0]PETSC ERROR: See
>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > for trouble shooting.
>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by
>>>>>>>> vit Mon Sep
>>>>>>>> > 4 10:02:32 2023
>>>>>>>> > # [0]PETSC ERROR: Configure options
>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > --------------------------------------------------------------
>>>>>>>> > # [0]PETSC ERROR: Petsc has generated inconsistent data
>>>>>>>> > # [0]PETSC ERROR:
>>>>>>>> > # [0]PETSC ERROR: See
>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > for trouble shooting.
>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by
>>>>>>>> vit Mon Sep
>>>>>>>> > 4 10:02:32 2023
>>>>>>>> > # [0]PETSC ERROR: Configure options
>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > # [0]PETSC ERROR: #2 PETSC_MATLAB_ENGINE_() line 316 in
>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > # [0]PETSC ERROR:
>>>>>>>> >
>>>>>>>> ------------------------------------------------------------------------
>>>>>>>> > # [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation
>>>>>>>> Violation,
>>>>>>>> > probably memory access out of range
>>>>>>>> > # [0]PETSC ERROR: Try option -start_in_debugger or
>>>>>>>> -on_error_attach_debugger
>>>>>>>> > # [0]PETSC ERROR: or see
>>>>>>>> > https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
>>>>>>>> > # [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and
>>>>>>>> Apple Mac OS
>>>>>>>> > X to find memory corruption errors
>>>>>>>> > # [0]PETSC ERROR: configure using --with-debugging=yes,
>>>>>>>> recompile, link,
>>>>>>>> > and run
>>>>>>>> > # [0]PETSC ERROR: to get more information on the crash.
>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > --------------------------------------------------------------
>>>>>>>> > # [0]PETSC ERROR: Signal received
>>>>>>>> > # [0]PETSC ERROR: See
>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > for trouble shooting.
>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>>>>>>> > # [0]PETSC ERROR: ../ex72 on a linux-opt named MB108SMEC028 by
>>>>>>>> vit Mon Sep
>>>>>>>> > 4 10:02:32 2023
>>>>>>>> > # [0]PETSC ERROR: Configure options
>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > # [0]PETSC ERROR: #3 User provided function() line 0 in unknown
>>>>>>>> file
>>>>>>>> > #
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
>>>>>>>> > # with errorcode 50162059.
>>>>>>>> > #
>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
>>>>>>>> processes.
>>>>>>>> > # You may or may not see output from other processes, depending on
>>>>>>>> > # exactly when Open MPI kills them.
>>>>>>>> > #
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no diff
>>>>>>>> > CC
>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
>>>>>>>> > CLINKER
>>>>>>>> > linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>>>>>> > TEST
>>>>>>>> >
>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>>>>> > not ok tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
>>>>>>>> code: 124
>>>>>>>> > # Running problem 5
>>>>>>>> > # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > --------------------------------------------------------------
>>>>>>>> > # [0]PETSC ERROR: Error in external library
>>>>>>>> > # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>>>>>> > # [0]PETSC ERROR: See
>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > for trouble shooting.
>>>>>>>> > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>>>>>>> > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named
>>>>>>>> MB108SMEC028 by
>>>>>>>> > vit Mon Sep 4 10:02:34 2023
>>>>>>>> > # [0]PETSC ERROR: Configure options
>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > # [0]PETSC ERROR: #2 main() line 126 in
>>>>>>>> >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>>>>> > # [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>>> > # [0]PETSC ERROR: -prob_id 5
>>>>>>>> > # [0]PETSC ERROR: -tao_smonitor
>>>>>>>> > # [0]PETSC ERROR: ----------------End of Error Message
>>>>>>>> -------send entire
>>>>>>>> > error message to petsc-maint at mcs.anl.gov----------
>>>>>>>> > #
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > # MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
>>>>>>>> > # with errorcode 126076.
>>>>>>>> > #
>>>>>>>> > # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
>>>>>>>> processes.
>>>>>>>> > # You may or may not see output from other processes, depending on
>>>>>>>> > # exactly when Open MPI kills them.
>>>>>>>> > #
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test # SKIP
>>>>>>>> Command failed
>>>>>>>> > so no diff
>>>>>>>> >
>>>>>>>> > # -------------
>>>>>>>> > # Summary
>>>>>>>> > # -------------
>>>>>>>> > # FAILED ksp_ksp_tutorials-ex72_12
>>>>>>>> > tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>>>>> > # success 0/2 tests (0.0%)
>>>>>>>> > # failed 2/2 tests (100.0%)
>>>>>>>> > # todo 0/2 tests (0.0%)
>>>>>>>> > # skip 0/2 tests (0.0%)
>>>>>>>> > #
>>>>>>>> > # Wall clock time for tests: 4 sec
>>>>>>>> > # Approximate CPU time (not incl. build time): 0.03 sec
>>>>>>>> > #
>>>>>>>> > # To rerun failed tests:
>>>>>>>> > # /usr/bin/make -f gmakefile test test-fail=1
>>>>>>>> > #
>>>>>>>> > # Timing summary (actual test time / total CPU time):
>>>>>>>> > # ksp_ksp_tutorials-ex72_12: 0.01 sec / 0.02 sec
>>>>>>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test: 0.01 sec /
>>>>>>>> 0.01 sec
>>>>>>>> >
>>>>>>>> > *$cd src/tao/leastsquares/tutorials/matlab/*
>>>>>>>> > *$make matlab_ls_test*
>>>>>>>> > /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall
>>>>>>>> -Wwrite-strings
>>>>>>>> > -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
>>>>>>>> > -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings
>>>>>>>> -Wno-strict-aliasing
>>>>>>>> > -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -O3
>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/include
>>>>>>>> > -I/home/vit/sfw/petsc/3.13.4/linux-opt/include
>>>>>>>> > -I/usr/local/MATLAB/R2020b/extern/include
>>>>>>>> > -I/home/vit/sfw/linux/openmpi/4.1.4/include matlab_ls_test.c
>>>>>>>> > -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib
>>>>>>>> > -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib
>>>>>>>> > /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
>>>>>>>> > -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> > -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> >
>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>>>>> > -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib
>>>>>>>> > -L/home/vit/sfw/linux/openmpi/4.1.4/lib
>>>>>>>> > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
>>>>>>>> > -L/usr/lib/gcc/x86_64-linux-gnu/9
>>>>>>>> -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>>>>>>>> > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu
>>>>>>>> > -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm -leng -lmex
>>>>>>>> -lmx
>>>>>>>> > -lmat -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr
>>>>>>>> -lmpi_mpifh
>>>>>>>> > -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread
>>>>>>>> -lquadmath
>>>>>>>> > -lstdc++ -ldl -o matlab_ls_test
>>>>>>>> >
>>>>>>>> > *$LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5
>>>>>>>> ./matlab_ls_test
>>>>>>>> > -tao_smonitor -prob_id 5 -info*
>>>>>>>> > [0] PetscInitialize(): PETSc successfully started: number of
>>>>>>>> processors = 1
>>>>>>>> > [0] PetscGetHostName(): Rejecting domainname, likely is NIS
>>>>>>>> > MB108SMEC028.(none)
>>>>>>>> > [0] PetscInitialize(): Running on machine: MB108SMEC028
>>>>>>>> > Running problem 5
>>>>>>>> > [0] PetscCommDuplicate(): Duplicating a communicator
>>>>>>>> 140155238476992
>>>>>>>> > 94202473157392 max tags = 2147483647
>>>>>>>> > [0] PetscMatlabEngineCreate(): Starting MATLAB engine with command
>>>>>>>> > /usr/local/MATLAB/R2020b/bin/matlab -glnxa64 -nodisplay -nosplash
>>>>>>>> > [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > --------------------------------------------------------------
>>>>>>>> > [0]PETSC ERROR: Error in external library
>>>>>>>> > [0]PETSC ERROR: Unable to start MATLAB engine on
>>>>>>>> > [0]PETSC ERROR: See
>>>>>>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > for trouble shooting.
>>>>>>>> > [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01, 2020
>>>>>>>> > [0]PETSC ERROR: ./matlab_ls_test on a linux-opt named
>>>>>>>> MB108SMEC028 by vit
>>>>>>>> > Mon Sep 4 10:09:56 2023
>>>>>>>> > [0]PETSC ERROR: Configure options
>>>>>>>> > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4 COPTFLAGS=-O3
>>>>>>>> > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
>>>>>>>> > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > [0]PETSC ERROR: #2 main() line 126 in matlab_ls_test.c
>>>>>>>> > [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>>> > [0]PETSC ERROR: -info
>>>>>>>> > [0]PETSC ERROR: -prob_id 5
>>>>>>>> > [0]PETSC ERROR: -tao_smonitor
>>>>>>>> > [0]PETSC ERROR: ----------------End of Error Message -------send
>>>>>>>> entire
>>>>>>>> > error message to petsc-maint at mcs.anl.gov----------
>>>>>>>> >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
>>>>>>>> > with errorcode 126076.
>>>>>>>> >
>>>>>>>> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI
>>>>>>>> processes.
>>>>>>>> > You may or may not see output from other processes, depending on
>>>>>>>> > exactly when Open MPI kills them.
>>>>>>>> >
>>>>>>>> > Please find the attachment for configure.log and make.log files
>>>>>>>> >
>>>>>>>> > On Sun, Sep 3, 2023 at 8:00 PM Satish Balay <balay at mcs.anl.gov>
>>>>>>>> wrote:
>>>>>>>> >
>>>>>>>> > > To use datafiles in the test suite:
>>>>>>>> > >
>>>>>>>> > > cd $HOME
>>>>>>>> > > git clone https://gitlab.com/petsc/datafiles
>>>>>>>> > > <configure should now pick up this location and set
>>>>>>>> DATAFILESPATH - or set
>>>>>>>> > > manually with make>
>>>>>>>> > >
>>>>>>>> > > make test query=requires queryval=matlab
>>>>>>>> DATAFILESPATH=$HOME/datafiles
>>>>>>>> > >
>>>>>>>> > > Satish
>>>>>>>> > >
>>>>>>>> > > On Sun, 3 Sep 2023, Matthew Knepley wrote:
>>>>>>>> > >
>>>>>>>> > > > On Sun, Sep 3, 2023 at 8:47 AM INTURU SRINIVAS 20PHD0548 <
>>>>>>>> > > > inturu.srinivas2020 at vitstudent.ac.in> wrote:
>>>>>>>> > > >
>>>>>>>> > > > > Hi Matthew,
>>>>>>>> > > > >
>>>>>>>> > > > > I am using PETSc to simulate the problems using IBAMR. I do
>>>>>>>> not have
>>>>>>>> > > any
>>>>>>>> > > > > separate test files to test PETSc alone. Can you please
>>>>>>>> help me how to
>>>>>>>> > > > > define this DATAFILESPATH?
>>>>>>>> > > > >
>>>>>>>> > > >
>>>>>>>> > > > That test you tried uses a certain matrix. On our machine, we
>>>>>>>> point to
>>>>>>>> > > this
>>>>>>>> > > > matrix using an environment variable, DATAFILESPATH. You
>>>>>>>> don't have those
>>>>>>>> > > > matrices, since they are just for testing here. That
>>>>>>>> > > > is why I suggested just using a different matrix, or running
>>>>>>>> a problem
>>>>>>>> > > you
>>>>>>>> > > > care about in IBAMR.
>>>>>>>> > > >
>>>>>>>> > > > Thanks,
>>>>>>>> > > >
>>>>>>>> > > > Matt
>>>>>>>> > > >
>>>>>>>> > > >
>>>>>>>> > > > > Thanks and regards
>>>>>>>> > > > > Srinivas.
>>>>>>>> > > > >
>>>>>>>> > > > > On Sun, Sep 3, 2023 at 6:06 PM Matthew Knepley <
>>>>>>>> knepley at gmail.com>
>>>>>>>> > > wrote:
>>>>>>>> > > > >
>>>>>>>> > > > >> On Sun, Sep 3, 2023 at 3:04 AM INTURU SRINIVAS 20PHD0548
>>>>>>>> via
>>>>>>>> > > petsc-users <
>>>>>>>> > > > >> petsc-users at mcs.anl.gov> wrote:
>>>>>>>> > > > >>
>>>>>>>> > > > >>> Hi Sathish,
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> Thank you so much for your efforts and the support you
>>>>>>>> are giving me
>>>>>>>> > > to
>>>>>>>> > > > >>> sort this out.
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> I tried to follow the same procedure which you followed
>>>>>>>> to build
>>>>>>>> > > Petsc
>>>>>>>> > > > >>> 3.13.4 with Matlab-R2020b on Ubuntu20.04.
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> *$./configure
>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>>>>>>> > > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>>>>>>> PETSC_ARCH=linux-opt
>>>>>>>> > > > >>> --with-debugging=0 --with-x=0
>>>>>>>> > > --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1*
>>>>>>>> > > > >>> Using python3 for Python
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> ===============================================================================
>>>>>>>> > > > >>> Configuring PETSc to compile on your system
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> ===============================================================================
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> ===============================================================================
>>>>>>>> > > > >>> It appears you do
>>>>>>>> not have
>>>>>>>> > > valgrind
>>>>>>>> > > > >>> installed on your system.
>>>>>>>> > > > >>> We HIGHLY recommend you install it from
>>>>>>>> www.valgrind.org
>>>>>>>> > > > >>> Or install
>>>>>>>> > > valgrind-devel or
>>>>>>>> > > > >>> equivalent using your package manager.
>>>>>>>> > > > >>> Then rerun ./configure
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> ===============================================================================
>>>>>>>> > > > >>> Compilers:
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> C Compiler:
>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>>>>> > > -fPIC
>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing
>>>>>>>> -Wno-unknown-pragmas
>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> > > > >>> Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>>>>> > > > >>> C++ Compiler:
>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>>>>>> > > > >>> -Wall -Wwrite-strings -Wno-strict-aliasing
>>>>>>>> -Wno-unknown-pragmas
>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3 -fPIC
>>>>>>>> > > > >>> Version: g++ (Ubuntu 11.4.0-2ubuntu1~20.04) 11.4.0
>>>>>>>> > > > >>> Fortran Compiler:
>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>>>>>> > > > >>> -fPIC -Wall -ffree-line-length-0
>>>>>>>> -Wno-unused-dummy-argument -O3
>>>>>>>> > > > >>> Version: GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2)
>>>>>>>> 9.4.0
>>>>>>>> > > > >>> Linkers:
>>>>>>>> > > > >>> Shared linker:
>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>>>>> > > -shared
>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
>>>>>>>> > > -Wno-unknown-pragmas
>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> > > > >>> Dynamic linker:
>>>>>>>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>>>>> > > -shared
>>>>>>>> > > > >>> -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
>>>>>>>> > > -Wno-unknown-pragmas
>>>>>>>> > > > >>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> > > > >>> Libraries linked against: -lquadmath -lstdc++ -ldl
>>>>>>>> > > > >>> make:
>>>>>>>> > > > >>> Version: 4.2
>>>>>>>> > > > >>> /usr/bin/make
>>>>>>>> > > > >>> BlasLapack:
>>>>>>>> > > > >>> Library: /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64 -liomp5
>>>>>>>> -lpthread
>>>>>>>> > > > >>> uses OpenMP; use export OMP_NUM_THREADS=<p> or
>>>>>>>> -omp_num_threads
>>>>>>>> > > <p> to
>>>>>>>> > > > >>> control the number of threads
>>>>>>>> > > > >>> uses 8 byte integers
>>>>>>>> > > > >>> MPI:
>>>>>>>> > > > >>> Version: 3
>>>>>>>> > > > >>> Includes: -I/home/vit/sfw/linux/openmpi/4.1.4/include
>>>>>>>> > > > >>> Mpiexec: /home/vit/sfw/linux/openmpi/4.1.4/bin/mpiexec
>>>>>>>> > > --oversubscribe
>>>>>>>> > > > >>> OMPI_VERSION: 4.1.4
>>>>>>>> > > > >>> pthread:
>>>>>>>> > > > >>> cmake:
>>>>>>>> > > > >>> Version: 3.16.3
>>>>>>>> > > > >>> /usr/bin/cmake
>>>>>>>> > > > >>> regex:
>>>>>>>> > > > >>> Matlab:
>>>>>>>> > > > >>> Includes: -I/usr/local/MATLAB/R2020b/extern/include
>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> MatlabEngine:
>>>>>>>> > > > >>> Library:
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64 -leng -lmex
>>>>>>>> -lmx -lmat
>>>>>>>> > > -lut
>>>>>>>> > > > >>> -licudata -licui18n -licuuc
>>>>>>>> > > > >>> Language used to compile PETSc: C
>>>>>>>> > > > >>> PETSc:
>>>>>>>> > > > >>> PETSC_ARCH: linux-opt
>>>>>>>> > > > >>> PETSC_DIR: /home/vit/sfw/petsc/3.13.4
>>>>>>>> > > > >>> Scalar type: real
>>>>>>>> > > > >>> Precision: double
>>>>>>>> > > > >>> Support for __float128
>>>>>>>> > > > >>> Integer size: 4 bytes
>>>>>>>> > > > >>> shared libraries: enabled
>>>>>>>> > > > >>> Memory alignment from malloc(): 16 bytes
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> xxx=========================================================================xxx
>>>>>>>> > > > >>> Configure stage complete. Now build PETSc libraries with:
>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4
>>>>>>>> PETSC_ARCH=linux-opt all
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> xxx=========================================================================xxx
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> Then I removed all occurrences of -lut -licudata
>>>>>>>> -licui18n -licuuc as
>>>>>>>> > > > >>> you suggested earlier.
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> *$make*
>>>>>>>> > > > >>> FC linux-opt/obj/tao/f90-mod/petsctaomod.o
>>>>>>>> > > > >>> CLINKER linux-opt/lib/libpetsc.so.3.13.4
>>>>>>>> > > > >>> BEGINNING TO COMPILE MATLAB INTERFACE
>>>>>>>> > > > >>> Building with 'gcc'.
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>>> > > > >>> In function ‘PetscBinaryWrite’:
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>>>>>> > > > >>> warning: ‘err’ may be used uninitialized in this function
>>>>>>>> > > > >>> [-Wmaybe-uninitialized]
>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to
>>>>>>>> socket\n");
>>>>>>>> > > > >>> | ^
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> MEX completed successfully.
>>>>>>>> > > > >>> Building with 'gcc'.
>>>>>>>> > > > >>> MEX completed successfully.
>>>>>>>> > > > >>> Building with 'gcc'.
>>>>>>>> > > > >>> MEX completed successfully.
>>>>>>>> > > > >>> Building with 'gcc'.
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:
>>>>>>>> > > > >>> In function ‘PetscBinaryWrite’:
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>>>>>> > > > >>> warning: ‘err’ may be used uninitialized in this function
>>>>>>>> > > > >>> [-Wmaybe-uninitialized]
>>>>>>>> > > > >>> 167 | if (err < 0) PETSC_MEX_ERROR("Error writing to
>>>>>>>> socket\n");
>>>>>>>> > > > >>> | ^
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> MEX completed successfully.
>>>>>>>> > > > >>> =========================================
>>>>>>>> > > > >>> Now to check if the libraries are working do:
>>>>>>>> > > > >>> make PETSC_DIR=/home/vit/sfw/petsc/3.13.4
>>>>>>>> PETSC_ARCH=linux-opt check
>>>>>>>> > > > >>> ===============================================
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> *$make test query=requires queryval=matlab*
>>>>>>>> > > > >>> Using MAKEFLAGS: -- queryval=matlab query=requires
>>>>>>>> > > > >>> CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
>>>>>>>> > > > >>> CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>>>>>>> > > > >>> TEST
>>>>>>>> linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>>>>>> > > > >>> not ok ksp_ksp_tutorials-ex72_12 # Error code: 169
>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > > > >>>
>>>>>>>> --------------------------------------------------------------
>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to open file
>>>>>>>> > > > >>> # [0]PETSC ERROR: Cannot locate file: /matrices/arco1
>>>>>>>> > > > >>>
>>>>>>>> > > > >>
>>>>>>>> > > > >> No, the problem is that you do not have DATAFILESPATH
>>>>>>>> defined, so it
>>>>>>>> > > > >> cannot find the matrix to test. Try running some test of
>>>>>>>> yours.
>>>>>>>> > > > >>
>>>>>>>> > > > >> Thanks,
>>>>>>>> > > > >>
>>>>>>>> > > > >> Matt
>>>>>>>> > > > >>
>>>>>>>> > > > >>
>>>>>>>> > > > >>> # [0]PETSC ERROR: See
>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for
>>>>>>>> trouble
>>>>>>>> > > > >>> shooting.
>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01,
>>>>>>>> 2020
>>>>>>>> > > > >>> # [0]PETSC ERROR: ../ex72 on a linux-opt named
>>>>>>>> MB108SMEC028 by vit
>>>>>>>> > > Sun
>>>>>>>> > > > >>> Sep 3 11:51:03 2023
>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options
>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>>>>>>> COPTFLAGS=-O3
>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscViewerFileSetUp_BinarySTDIO()
>>>>>>>> line 1444 in
>>>>>>>> > > > >>>
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 PetscViewerSetUp_Binary() line 1511
>>>>>>>> in
>>>>>>>> > > > >>>
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/impls/binary/binv.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: #3 PetscViewerSetUp() line 328 in
>>>>>>>> > > > >>>
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/viewer/interface/view.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: #4 MatLoad_SeqAIJ() line 4563 in
>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/impls/aij/seq/aij.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: #5 MatLoad() line 1225 in
>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/mat/interface/matrix.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: #6 main() line 113 in
>>>>>>>> > > > >>> /home/vit/sfw/petsc/3.13.4/src/ksp/ksp/tutorials/ex72.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>>> > > > >>> # [0]PETSC ERROR: -f0 /matrices/arco1
>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_factor_mat_solver_type matlab
>>>>>>>> > > > >>> # [0]PETSC ERROR: -pc_type lu
>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message
>>>>>>>> -------send
>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov----------
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator
>>>>>>>> MPI_COMM_SELF
>>>>>>>> > > > >>> # with errorcode 113065.
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all
>>>>>>>> MPI processes.
>>>>>>>> > > > >>> # You may or may not see output from other processes,
>>>>>>>> depending on
>>>>>>>> > > > >>> # exactly when Open MPI kills them.
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>> ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so no
>>>>>>>> diff
>>>>>>>> > > > >>> CC
>>>>>>>> > > > >>>
>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
>>>>>>>> > > > >>> CLINKER
>>>>>>>> > > > >>>
>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>>>>>> > > > >>> TEST
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>>>>> > > > >>> not ok tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>>>>> Error
>>>>>>>> > > code: 124
>>>>>>>> > > > >>> # Running problem 5
>>>>>>>> > > > >>> # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > > > >>>
>>>>>>>> --------------------------------------------------------------
>>>>>>>> > > > >>> # [0]PETSC ERROR: Error in external library
>>>>>>>> > > > >>> # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>>>>>> > > > >>> # [0]PETSC ERROR: See
>>>>>>>> > > > >>> https://www.mcs.anl.gov/petsc/documentation/faq.html for
>>>>>>>> trouble
>>>>>>>> > > > >>> shooting.
>>>>>>>> > > > >>> # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug 01,
>>>>>>>> 2020
>>>>>>>> > > > >>> # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt named
>>>>>>>> > > MB108SMEC028 by
>>>>>>>> > > > >>> vit Sun Sep 3 11:51:05 2023
>>>>>>>> > > > >>> # [0]PETSC ERROR: Configure options
>>>>>>>> > > > >>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>>>>>>> COPTFLAGS=-O3
>>>>>>>> > > > >>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> --with-debugging=0
>>>>>>>> > > > >>> --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > > > >>> # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line 67 in
>>>>>>>> > > > >>>
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: #2 main() line 126 in
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>>>>> > > > >>> # [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>>> > > > >>> # [0]PETSC ERROR: -prob_id 5
>>>>>>>> > > > >>> # [0]PETSC ERROR: -tao_smonitor
>>>>>>>> > > > >>> # [0]PETSC ERROR: ----------------End of Error Message
>>>>>>>> -------send
>>>>>>>> > > > >>> entire error message to petsc-maint at mcs.anl.gov----------
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>> # MPI_ABORT was invoked on rank 0 in communicator
>>>>>>>> MPI_COMM_SELF
>>>>>>>> > > > >>> # with errorcode 126076.
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all
>>>>>>>> MPI processes.
>>>>>>>> > > > >>> # You may or may not see output from other processes,
>>>>>>>> depending on
>>>>>>>> > > > >>> # exactly when Open MPI kills them.
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>> ok tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>>>>> SKIP Command
>>>>>>>> > > > >>> failed so no diff
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> # -------------
>>>>>>>> > > > >>> # Summary
>>>>>>>> > > > >>> # -------------
>>>>>>>> > > > >>> # FAILED ksp_ksp_tutorials-ex72_12
>>>>>>>> > > > >>> tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>>>>> > > > >>> # success 0/2 tests (0.0%)
>>>>>>>> > > > >>> # failed 2/2 tests (100.0%)
>>>>>>>> > > > >>> # todo 0/2 tests (0.0%)
>>>>>>>> > > > >>> # skip 0/2 tests (0.0%)
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>> # Wall clock time for tests: 3 sec
>>>>>>>> > > > >>> # Approximate CPU time (not incl. build time): 0.05 sec
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>> # To rerun failed tests:
>>>>>>>> > > > >>> # /usr/bin/make -f gmakefile test test-fail=1
>>>>>>>> > > > >>> #
>>>>>>>> > > > >>> # Timing summary (actual test time / total CPU time):
>>>>>>>> > > > >>> # ksp_ksp_tutorials-ex72_12: 0.02 sec / 0.03 sec
>>>>>>>> > > > >>> # tao_leastsquares_tutorials_matlab-matlab_ls_test:
>>>>>>>> 0.02 sec /
>>>>>>>> > > 0.02 sec
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> *How to sort out this error?*
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> *$cd src/tao/leastsquares/tutorials/matlab/*
>>>>>>>> > > > >>> *$make matlab_ls_test*
>>>>>>>> > > > >>> /home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc -fPIC -Wall
>>>>>>>> > > -Wwrite-strings
>>>>>>>> > > > >>> -Wno-strict-aliasing -Wno-unknown-pragmas
>>>>>>>> -fstack-protector
>>>>>>>> > > > >>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings
>>>>>>>> > > -Wno-strict-aliasing
>>>>>>>> > > > >>> -Wno-unknown-pragmas -fstack-protector
>>>>>>>> -fvisibility=hidden -O3
>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/include
>>>>>>>> > > > >>> -I/home/vit/sfw/petsc/3.13.4/linux-opt/include
>>>>>>>> > > > >>> -I/usr/local/MATLAB/R2020b/extern/include
>>>>>>>> > > > >>> -I/home/vit/sfw/linux/openmpi/4.1.4/include
>>>>>>>> matlab_ls_test.c
>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/petsc/3.13.4/linux-opt/lib
>>>>>>>> > > > >>> -L/home/vit/sfw/petsc/3.13.4/linux-opt/lib
>>>>>>>> > > > >>> /usr/local/MATLAB/R2020b/bin/glnxa64/mkl.so
>>>>>>>> > > > >>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/sys/os/glnxa64
>>>>>>>> > > > >>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>>>>> > > > >>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > > > >>> -Wl,-rpath,/home/vit/sfw/linux/openmpi/4.1.4/lib
>>>>>>>> > > > >>> -L/home/vit/sfw/linux/openmpi/4.1.4/lib
>>>>>>>> > > > >>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
>>>>>>>> > > > >>> -L/usr/lib/gcc/x86_64-linux-gnu/9
>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>>>>>>>> > > > >>> -L/usr/lib/x86_64-linux-gnu
>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu
>>>>>>>> > > > >>> -L/lib/x86_64-linux-gnu -lpetsc -liomp5 -lpthread -lm
>>>>>>>> -leng -lmex
>>>>>>>> > > -lmx
>>>>>>>> > > > >>> -lmat -lstdc++ -ldl -lmpi_usempif08
>>>>>>>> -lmpi_usempi_ignore_tkr
>>>>>>>> > > -lmpi_mpifh
>>>>>>>> > > > >>> -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath
>>>>>>>> -lpthread
>>>>>>>> > > -lquadmath
>>>>>>>> > > > >>> -lstdc++ -ldl -o matlab_ls_test
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> I think there is a problem with the Matlab-R2020b version.
>>>>>>>> > > > >>> I am sharing the configure.log and make.log files. Please
>>>>>>>> find the
>>>>>>>> > > > >>> attachment and do the needful.
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> Thanks and regards
>>>>>>>> > > > >>> Srinivas
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> On Sat, Sep 2, 2023 at 11:15 PM Satish Balay <
>>>>>>>> balay at mcs.anl.gov>
>>>>>>>> > > wrote:
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>> Perhaps you can try the following to get additional info
>>>>>>>> - and debug
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> Satish
>>>>>>>> > > > >>>> ----------
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> balay at compute-386-07:/scratch/balay/petsc$ cd
>>>>>>>> > > > >>>> src/tao/leastsquares/tutorials/matlab/
>>>>>>>> > > > >>>> balay at compute-386-07
>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
>>>>>>>> > > > >>>> make matlab_ls_test
>>>>>>>> > > > >>>>
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC
>>>>>>>> > > -Wall
>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>>>>>>> > > -fstack-protector
>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC -Wall -Wwrite-strings
>>>>>>>> > > -Wno-strict-aliasing
>>>>>>>> > > > >>>> -Wno-unknown-pragmas -fstack-protector
>>>>>>>> -fvisibility=hidden -O3
>>>>>>>> > > > >>>> -I/scratch/balay/petsc/include
>>>>>>>> > > -I/scratch/balay/petsc/linux-opt/include
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include
>>>>>>>> > > > >>>> -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include
>>>>>>>> > > > >>>> matlab_ls_test.c
>>>>>>>> -Wl,-rpath,/scratch/balay/petsc/linux-opt/lib
>>>>>>>> > > > >>>> -L/scratch/balay/petsc/linux-opt/lib
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>>>>>> > > > >>>>
>>>>>>>> -Wl,-rpath,/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib
>>>>>>>> > > > >>>> -L/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib
>>>>>>>> > > > >>>> -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/9
>>>>>>>> > > > >>>> -L/usr/lib/gcc/x86_64-linux-gnu/9
>>>>>>>> > > -Wl,-rpath,/usr/lib/x86_64-linux-gnu
>>>>>>>> > > > >>>> -L/usr/lib/x86_64-linux-gnu
>>>>>>>> -Wl,-rpath,/lib/x86_64-linux-gnu
>>>>>>>> > > > >>>> -L/lib/x86_64-linux-gnu -lpetsc -llapack -lblas
>>>>>>>> -lpthread -lm -leng
>>>>>>>> > > -lmex
>>>>>>>> > > > >>>> -lmx -lmat -lut -licudata -licui18n -licuuc -lstdc++
>>>>>>>> -ldl -lmpifort
>>>>>>>> > > -lmpi
>>>>>>>> > > > >>>> -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath
>>>>>>>> -lstdc++ -ldl -o
>>>>>>>> > > > >>>> matlab_ls_test
>>>>>>>> > > > >>>> balay at compute-386-07
>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5
>>>>>>>> ./matlab_ls_test
>>>>>>>> > > > >>>> -tao_smonitor -prob_id 5 -info
>>>>>>>> > > > >>>> [0] PetscInitialize(): PETSc successfully started:
>>>>>>>> number of
>>>>>>>> > > processors
>>>>>>>> > > > >>>> = 1
>>>>>>>> > > > >>>> [0] PetscGetHostName(): Rejecting domainname, likely is
>>>>>>>> NIS
>>>>>>>> > > > >>>> compute-386-07.(none)
>>>>>>>> > > > >>>> [0] PetscInitialize(): Running on machine: compute-386-07
>>>>>>>> > > > >>>> Running problem 5
>>>>>>>> > > > >>>> [0] PetscCommDuplicate(): Duplicating a communicator
>>>>>>>> 1140850689
>>>>>>>> > > > >>>> -2080374784 max tags = 268435455
>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Starting MATLAB engine
>>>>>>>> with command
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash
>>>>>>>> > > > >>>> [0] PetscMatlabEngineCreate(): Started MATLAB engine
>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Evaluating MATLAB
>>>>>>>> string:
>>>>>>>> > > > >>>> TestingInitialize
>>>>>>>> > > > >>>> [0] PetscMatlabEngineEvaluate(): Done evaluating Matlab
>>>>>>>> string:
>>>>>>>> > > > >>>> TestingInitialize
>>>>>>>> > > > >>>> 5
>>>>>>>> > > > >>>> <snip>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> <<<< Now verify if the above matlab command actually
>>>>>>>> works for you
>>>>>>>> > > - on
>>>>>>>> > > > >>>> this machine..>>>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> balay at compute-386-07
>>>>>>>> > > :/scratch/balay/petsc/src/tao/leastsquares/tutorials/matlab$
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
>>>>>>>> > > > >>>> -glnxa64 -nodisplay -nosplash
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> < M A T L A B (R) >
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> Copyright 1984-2021 The
>>>>>>>> MathWorks, Inc.
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> R2021a (9.10.0.1602886) 64-bit
>>>>>>>> (glnxa64)
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> February 17, 2021
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> To get started, type doc.
>>>>>>>> > > > >>>> For product information, visit www.mathworks.com.
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> >>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> On Sat, 2 Sep 2023, Satish Balay via petsc-users wrote:
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> > Please don't cc: both petsc-users and petsc-maint
>>>>>>>> [reverting
>>>>>>>> > > thread
>>>>>>>> > > > >>>> to petsc-users only]
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > I'm not sure what is happening here. Can you send the
>>>>>>>> > > corresponding
>>>>>>>> > > > >>>> configure.log, make.log [compressed]?
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > Here is my attempt to reproduce (with petsc-3.13) on
>>>>>>>> Ubuntu-20.04,
>>>>>>>> > > > >>>> with Matlab-R2021a - and that works:
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ git branch
>>>>>>>> > > > >>>> > main
>>>>>>>> > > > >>>> > release
>>>>>>>> > > > >>>> > * release-3.13
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ module load
>>>>>>>> > > matlab/R2021a
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ which
>>>>>>>> matlab
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/matlab
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ ./configure
>>>>>>>> > > > >>>>
>>>>>>>> --with-mpi-dir=/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/
>>>>>>>> > > > >>>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>>>>>>> PETSC_ARCH=linux-opt
>>>>>>>> > > > >>>> --with-debugging=0 --with-x=0
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --with-matlab-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --with-blaslapack-dir=/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1 --with-matlab-engine=1
>>>>>>>> > > > >>>> > <snip>
>>>>>>>> > > > >>>> > Compilers:
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> > C Compiler:
>>>>>>>> > > > >>>>
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc -fPIC
>>>>>>>> > > -Wall
>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>>>>>>> > > -fstack-protector
>>>>>>>> > > > >>>> -fvisibility=hidden -O3
>>>>>>>> > > > >>>> > Version: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>>>>> > > > >>>> > C++ Compiler:
>>>>>>>> > > > >>>>
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicxx -Wall
>>>>>>>> > > > >>>> -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas
>>>>>>>> > > -fstack-protector
>>>>>>>> > > > >>>> -fvisibility=hidden -O3 -fPIC
>>>>>>>> > > > >>>> > Version: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>>>>> > > > >>>> > Fortran Compiler:
>>>>>>>> > > > >>>>
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpif90 -fPIC
>>>>>>>> > > -Wall
>>>>>>>> > > > >>>> -ffree-line-length-0 -Wno-unused-dummy-argument -O3
>>>>>>>> > > > >>>> > Version: GNU Fortran (Ubuntu
>>>>>>>> 9.4.0-1ubuntu1~20.04.2) 9.4.0
>>>>>>>> > > > >>>> > Linkers:
>>>>>>>> > > > >>>> > Shared linker:
>>>>>>>> > > > >>>>
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc
>>>>>>>> > > -shared -fPIC
>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing
>>>>>>>> -Wno-unknown-pragmas
>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> > > > >>>> > Dynamic linker:
>>>>>>>> > > > >>>>
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpicc
>>>>>>>> > > -shared -fPIC
>>>>>>>> > > > >>>> -Wall -Wwrite-strings -Wno-strict-aliasing
>>>>>>>> -Wno-unknown-pragmas
>>>>>>>> > > > >>>> -fstack-protector -fvisibility=hidden -O3
>>>>>>>> > > > >>>> > Libraries linked against: -lquadmath -lstdc++ -ldl
>>>>>>>> > > > >>>> > make:
>>>>>>>> > > > >>>> > Version: 4.2
>>>>>>>> > > > >>>> > /usr/bin/make
>>>>>>>> > > > >>>> > BlasLapack:
>>>>>>>> > > > >>>> > Library:
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64/mkl.so
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64
>>>>>>>> > > > >>>> -liomp5 -lpthread
>>>>>>>> > > > >>>> > uses OpenMP; use export OMP_NUM_THREADS=<p> or
>>>>>>>> -omp_num_threads
>>>>>>>> > > <p>
>>>>>>>> > > > >>>> to control the number of threads
>>>>>>>> > > > >>>> > uses 8 byte integers
>>>>>>>> > > > >>>> > MPI:
>>>>>>>> > > > >>>> > Version: 4
>>>>>>>> > > > >>>> > Includes:
>>>>>>>> > > -I/nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/include
>>>>>>>> > > > >>>> > Mpiexec:
>>>>>>>> > > /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/bin/mpiexec
>>>>>>>> > > > >>>> > MPICH_NUMVERSION: 40002300
>>>>>>>> > > > >>>> > pthread:
>>>>>>>> > > > >>>> > Library: -lpthread
>>>>>>>> > > > >>>> > cmake:
>>>>>>>> > > > >>>> > Version: 3.16.3
>>>>>>>> > > > >>>> > /usr/bin/cmake
>>>>>>>> > > > >>>> > regex:
>>>>>>>> > > > >>>> > Matlab:
>>>>>>>> > > > >>>> > Includes:
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/include
>>>>>>>> > > > >>>> >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a
>>>>>>>> > > > >>>> > MatlabEngine:
>>>>>>>> > > > >>>> > Library:
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64:/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/bin/glnxa64
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/extern/lib/glnxa64
>>>>>>>> > > > >>>> -leng -lmex -lmx -lmat -lut -licudata -licui18n -licuuc
>>>>>>>> > > > >>>> > sowing:
>>>>>>>> > > > >>>> > Version: 1.1.25
>>>>>>>> > > > >>>> > /scratch/balay/petsc/linux-opt/bin/bfort
>>>>>>>> > > > >>>> > valgrind:
>>>>>>>> > > > >>>> > Language used to compile PETSc: C
>>>>>>>> > > > >>>> > PETSc:
>>>>>>>> > > > >>>> > PETSC_ARCH: linux-opt
>>>>>>>> > > > >>>> > PETSC_DIR: /scratch/balay/petsc
>>>>>>>> > > > >>>> > Scalar type: real
>>>>>>>> > > > >>>> > Precision: double
>>>>>>>> > > > >>>> > Support for __float128
>>>>>>>> > > > >>>> > Integer size: 4 bytes
>>>>>>>> > > > >>>> > shared libraries: enabled
>>>>>>>> > > > >>>> > Memory alignment from malloc(): 16 bytes
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> xxx=========================================================================xxx
>>>>>>>> > > > >>>> > Configure stage complete. Now build PETSc libraries
>>>>>>>> with:
>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc
>>>>>>>> PETSC_ARCH=linux-opt all
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> xxx=========================================================================xxx
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > <snip>
>>>>>>>> > > > >>>> > FC linux-opt/obj/tao/f90-mod/petsctaomod.o
>>>>>>>> > > > >>>> > CLINKER linux-opt/lib/libpetsc.so.3.13.6
>>>>>>>> > > > >>>> > BEGINNING TO COMPILE MATLAB INTERFACE
>>>>>>>> > > > >>>> > Building with 'gcc'.
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In
>>>>>>>> > > > >>>> function ‘PetscBinaryWrite’:
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>>>>>> > > > >>>> warning: ‘err’ may be used uninitialized in this function
>>>>>>>> > > > >>>> [-Wmaybe-uninitialized]
>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing
>>>>>>>> to
>>>>>>>> > > socket\n");
>>>>>>>> > > > >>>> > | ^
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > MEX completed successfully.
>>>>>>>> > > > >>>> > Building with 'gcc'.
>>>>>>>> > > > >>>> > MEX completed successfully.
>>>>>>>> > > > >>>> > Building with 'gcc'.
>>>>>>>> > > > >>>> > MEX completed successfully.
>>>>>>>> > > > >>>> > Building with 'gcc'.
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c: In
>>>>>>>> > > > >>>> function ‘PetscBinaryWrite’:
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /scratch/balay/petsc/src/sys/classes/viewer/impls/socket/matlab/bread.c:167:6:
>>>>>>>> > > > >>>> warning: ‘err’ may be used uninitialized in this function
>>>>>>>> > > > >>>> [-Wmaybe-uninitialized]
>>>>>>>> > > > >>>> > 167 | if (err < 0) PETSC_MEX_ERROR("Error writing
>>>>>>>> to
>>>>>>>> > > socket\n");
>>>>>>>> > > > >>>> > | ^
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > MEX completed successfully.
>>>>>>>> > > > >>>> > =========================================
>>>>>>>> > > > >>>> > Now to check if the libraries are working do:
>>>>>>>> > > > >>>> > make PETSC_DIR=/scratch/balay/petsc
>>>>>>>> PETSC_ARCH=linux-opt check
>>>>>>>> > > > >>>> > =========================================
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$ make test
>>>>>>>> > > query=requires
>>>>>>>> > > > >>>> queryval=matlab
>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires
>>>>>>>> > > > >>>> > CC linux-opt/tests/ksp/ksp/tutorials/ex72.o
>>>>>>>> > > > >>>> > CLINKER linux-opt/tests/ksp/ksp/tutorials/ex72
>>>>>>>> > > > >>>> > TEST
>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>>>>>> > > > >>>> > not ok ksp_ksp_tutorials-ex72_12 # Error code: 1
>>>>>>>> > > > >>>> > # ../ex72:
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5:
>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12)
>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12 # SKIP Command failed so
>>>>>>>> no diff
>>>>>>>> > > > >>>> > CC
>>>>>>>> > > > >>>>
>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o
>>>>>>>> > > > >>>> > CLINKER
>>>>>>>> > > > >>>>
>>>>>>>> linux-opt/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>>>>>> > > > >>>> > TEST
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>>>>> > > > >>>> > not ok
>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
>>>>>>>> > > code:
>>>>>>>> > > > >>>> 1
>>>>>>>> > > > >>>> > # ../matlab_ls_test:
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu20.04-x86_64/matlab/R2021a/sys/os/glnxa64/libgfortran.so.5:
>>>>>>>> > > > >>>> version `GFORTRAN_9' not found (required by
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/projects/petsc/soft/u20.04/mpich-4.0.2/lib/libmpifort.so.12)
>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>>>>> SKIP
>>>>>>>> > > Command
>>>>>>>> > > > >>>> failed so no diff
>>>>>>>> > > > >>>> > <snip>
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$
>>>>>>>> > > > >>>> LD_PRELOAD=/lib/x86_64-linux-gnu/libgfortran.so.5 make
>>>>>>>> test
>>>>>>>> > > query=requires
>>>>>>>> > > > >>>> queryval=matlab
>>>>>>>> > > > >>>> > Using MAKEFLAGS: -- queryval=matlab query=requires
>>>>>>>> > > > >>>> > TEST
>>>>>>>> > > linux-opt/tests/counts/ksp_ksp_tutorials-ex72_12.counts
>>>>>>>> > > > >>>> > ok ksp_ksp_tutorials-ex72_12
>>>>>>>> > > > >>>> > ok diff-ksp_ksp_tutorials-ex72_12
>>>>>>>> > > > >>>> > TEST
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>>>>> > > > >>>> > ok tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>>>>> > > > >>>> > ok
>>>>>>>> diff-tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > # -------------
>>>>>>>> > > > >>>> > # Summary
>>>>>>>> > > > >>>> > # -------------
>>>>>>>> > > > >>>> > # success 4/4 tests (100.0%)
>>>>>>>> > > > >>>> > # failed 0/4 tests (0.0%)
>>>>>>>> > > > >>>> > # todo 0/4 tests (0.0%)
>>>>>>>> > > > >>>> > # skip 0/4 tests (0.0%)
>>>>>>>> > > > >>>> > #
>>>>>>>> > > > >>>> > # Wall clock time for tests: 27 sec
>>>>>>>> > > > >>>> > # Approximate CPU time (not incl. build time):
>>>>>>>> 15.190000000000001
>>>>>>>> > > sec
>>>>>>>> > > > >>>> > #
>>>>>>>> > > > >>>> > # Timing summary (actual test time / total CPU time):
>>>>>>>> > > > >>>> > # tao_leastsquares_tutorials_matlab-matlab_ls_test:
>>>>>>>> 6.47 sec /
>>>>>>>> > > 7.54
>>>>>>>> > > > >>>> sec
>>>>>>>> > > > >>>> > # ksp_ksp_tutorials-ex72_12: 6.46 sec / 7.65 sec
>>>>>>>> > > > >>>> > balay at compute-386-07:/scratch/balay/petsc$
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > On Sat, 2 Sep 2023, INTURU SRINIVAS 20PHD0548 wrote:
>>>>>>>> > > > >>>> >
>>>>>>>> > > > >>>> > > Based on the suggestions given by Sathish, I have
>>>>>>>> tried to
>>>>>>>> > > > >>>> configure petsc
>>>>>>>> > > > >>>> > > 3.13.4 with Matlab-R2020b. But, it was not
>>>>>>>> successful. After
>>>>>>>> > > > >>>> running make
>>>>>>>> > > > >>>> > > -j 10 test command I have got the following error
>>>>>>>> message.
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > > not ok
>>>>>>>> tao_leastsquares_tutorials_matlab-matlab_ls_test # Error
>>>>>>>> > > > >>>> code: 124
>>>>>>>> > > > >>>> > > # Running problem 5
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: --------------------- Error Message
>>>>>>>> > > > >>>> > >
>>>>>>>> --------------------------------------------------------------
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Error in external library
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Unable to start MATLAB engine on
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: See
>>>>>>>> > > > >>>> https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > > > >>>> > > for trouble shooting.
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Petsc Release Version 3.13.4, Aug
>>>>>>>> 01, 2020
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ../matlab_ls_test on a linux-opt
>>>>>>>> named
>>>>>>>> > > > >>>> MB108SMEC028 by
>>>>>>>> > > > >>>> > > vit Sat Sep 2 12:27:22 2023
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: Configure options
>>>>>>>> > > > >>>> > > --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>>>>>>> COPTFLAGS=-O3
>>>>>>>> > > > >>>> > > CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 PETSC_ARCH=linux-opt
>>>>>>>> > > > >>>> --with-debugging=0
>>>>>>>> > > > >>>> > > --with-x=0 --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> > > --with-matlab-engine=1
>>>>>>>> > > > >>>> --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> > > --known-64-bit-blas-indices=1
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #1 PetscMatlabEngineCreate() line
>>>>>>>> 67 in
>>>>>>>> > > > >>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: #2 main() line 126 in
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: PETSc Option Table entries:
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -prob_id 5
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: -tao_smonitor
>>>>>>>> > > > >>>> > > # [0]PETSC ERROR: ----------------End of Error
>>>>>>>> Message
>>>>>>>> > > -------send
>>>>>>>> > > > >>>> entire
>>>>>>>> > > > >>>> > > error message to petsc-maint at mcs.anl.gov----------
>>>>>>>> > > > >>>> > > #
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>>> > > # MPI_ABORT was invoked on rank 0 in communicator
>>>>>>>> MPI_COMM_SELF
>>>>>>>> > > > >>>> > > # with errorcode 126076.
>>>>>>>> > > > >>>> > > #
>>>>>>>> > > > >>>> > > # NOTE: invoking MPI_ABORT causes Open MPI to kill
>>>>>>>> all MPI
>>>>>>>> > > > >>>> processes.
>>>>>>>> > > > >>>> > > # You may or may not see output from other
>>>>>>>> processes, depending
>>>>>>>> > > on
>>>>>>>> > > > >>>> > > # exactly when Open MPI kills them.
>>>>>>>> > > > >>>> > > #
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > > I request you to help me to sort out this error.
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > > Thanks
>>>>>>>> > > > >>>> > > Srinivas
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > > On Fri, Sep 1, 2023 at 11:42 PM Amneet Bhalla <
>>>>>>>> > > > >>>> mail2amneet at gmail.com> wrote:
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > > > I think there should be two hyphens in
>>>>>>>> > > > >>>> > > > -with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > > i.e.:
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > > --with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > > On Fri, Sep 1, 2023 at 10:25 AM INTURU SRINIVAS
>>>>>>>> 20PHD0548 via
>>>>>>>> > > > >>>> petsc-users <
>>>>>>>> > > > >>>> > > > petsc-users at mcs.anl.gov> wrote:
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > >> Thank you Sathish.I will try this
>>>>>>>> > > > >>>> > > >>
>>>>>>>> > > > >>>> > > >> On Fri, Sep 1, 2023, 22:53 Satish Balay <
>>>>>>>> balay at mcs.anl.gov>
>>>>>>>> > > > >>>> wrote:
>>>>>>>> > > > >>>> > > >>
>>>>>>>> > > > >>>> > > >>> yes [and remove fblaslapack. don't know if hypre
>>>>>>>> will work
>>>>>>>> > > > >>>> here].
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>> > > >>> i.e:
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>> > > >>> ./configure
>>>>>>>> --with-mpi-dir=/home/vit/sfw/linux/openmpi/4.1.4
>>>>>>>> > > > >>>> > > >>> COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>>>>>>> > > PETSC_ARCH=linux-opt
>>>>>>>> > > > >>>> > > >>> --with-debugging=0 --with-x=0 \
>>>>>>>> > > > >>>> > > >>> --with-matlab-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> --with-matlab-engine=1
>>>>>>>> > > > >>>> > > >>> -with-blaslapack-dir=/usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> --known-64-bit-blas-indices=1
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>> > > >>> Satish
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>> > > >>> On Fri, 1 Sep 2023, INTURU SRINIVAS 20PHD0548 via
>>>>>>>> > > petsc-users
>>>>>>>> > > > >>>> wrote:
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>> > > >>> > Hi Satish,
>>>>>>>> > > > >>>> > > >>> >
>>>>>>>> > > > >>>> > > >>> > -with-blaslapack-dir=/path/to/matlab_dir
>>>>>>>> > > > >>>> > > >>> > --known-64-bit-blas-indices=1
>>>>>>>> > > > >>>> > > >>> >
>>>>>>>> > > > >>>> > > >>> > Is this what you are suggesting?
>>>>>>>> > > > >>>> > > >>> >
>>>>>>>> > > > >>>> > > >>> > On Fri, Sep 1, 2023, 20:42 Satish Balay <
>>>>>>>> > > balay at mcs.anl.gov>
>>>>>>>> > > > >>>> wrote:
>>>>>>>> > > > >>>> > > >>> >
>>>>>>>> > > > >>>> > > >>> > > Also:
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > '-known-64-bit-blas-indices=1',
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > Note: most externalpackages might not work
>>>>>>>> in this mode.
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > [we can't really over come such
>>>>>>>> dependency/conflicts
>>>>>>>> > > across
>>>>>>>> > > > >>>> packages]
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > Satish
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > On Fri, 1 Sep 2023, Satish Balay via
>>>>>>>> petsc-users wrote:
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > Here is the matlab test that runs in CI
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> https://gitlab.com/petsc/petsc/-/jobs/4904566768
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> config/examples/arch-ci-linux-matlab-ilp64.py
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > # Note: regular BLAS [with 32-bit
>>>>>>>> integers] conflict
>>>>>>>> > > with
>>>>>>>> > > > >>>> > > >>> > > > # MATLAB BLAS - hence requiring
>>>>>>>> > > > >>>> -known-64-bit-blas-indices=1
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > Ah - so you need to use the ilp64
>>>>>>>> blas/lapack with
>>>>>>>> > > > >>>> matlab - to
>>>>>>>> > > > >>>> > > >>> have a
>>>>>>>> > > > >>>> > > >>> > > compatible build
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > '--with-blaslapack-dir='+matlab_dir,
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > Satish
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > On Fri, 1 Sep 2023, INTURU SRINIVAS
>>>>>>>> 20PHD0548 via
>>>>>>>> > > > >>>> petsc-users
>>>>>>>> > > > >>>> > > >>> wrote:
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > > Hi Amneet,
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > Without libmesh, even for PETSc with
>>>>>>>> MATLAB is not
>>>>>>>> > > > >>>> working. It is
>>>>>>>> > > > >>>> > > >>> > > showing
>>>>>>>> > > > >>>> > > >>> > > > > error for both 3.13.4 and 3.17.5
>>>>>>>> versions.
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > I am trying to install IBAMR in HPC
>>>>>>>> cluster with
>>>>>>>> > > > >>>> libmesh and
>>>>>>>> > > > >>>> > > >>> this is
>>>>>>>> > > > >>>> > > >>> > > for
>>>>>>>> > > > >>>> > > >>> > > > > general usage not only for WEC. This I
>>>>>>>> tried without
>>>>>>>> > > > >>>> linking
>>>>>>>> > > > >>>> > > >>> Matlab
>>>>>>>> > > > >>>> > > >>> > > with
>>>>>>>> > > > >>>> > > >>> > > > > PETSc. Here also I got the error while
>>>>>>>> configuring
>>>>>>>> > > > >>>> libmesh 1.6.2
>>>>>>>> > > > >>>> > > >>> that
>>>>>>>> > > > >>>> > > >>> > > PETSc
>>>>>>>> > > > >>>> > > >>> > > > > was not found but
>>>>>>>> --enable-petsc-required is
>>>>>>>> > > specified.
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > The reason for specifically asking for
>>>>>>>> libmesh with
>>>>>>>> > > > >>>> PETSc and
>>>>>>>> > > > >>>> > > >>> Matlab
>>>>>>>> > > > >>>> > > >>> > > is in
>>>>>>>> > > > >>>> > > >>> > > > > the cfd-mpc-wecs application for
>>>>>>>> complicated
>>>>>>>> > > geometries
>>>>>>>> > > > >>>> it is
>>>>>>>> > > > >>>> > > >>> > > mentioned to
>>>>>>>> > > > >>>> > > >>> > > > > build cfd-mpc-wecs with libmesh
>>>>>>>> construct.
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > For the past 10 days I am trying these
>>>>>>>> various
>>>>>>>> > > things
>>>>>>>> > > > >>>> and ended
>>>>>>>> > > > >>>> > > >>> up with
>>>>>>>> > > > >>>> > > >>> > > > > errors.
>>>>>>>> > > > >>>> > > >>> > > > > I want to solve this and proceed further
>>>>>>>> to do my
>>>>>>>> > > > >>>> research work.
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > Please help me to solve this as soon as
>>>>>>>> possible.
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > Thanks and Regards
>>>>>>>> > > > >>>> > > >>> > > > > Srinivas
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > On Fri, Sep 1, 2023, 19:48 Amneet Bhalla
>>>>>>>> <
>>>>>>>> > > > >>>> mail2amneet at gmail.com>
>>>>>>>> > > > >>>> > > >>> > > wrote:
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > > Hi Srinivas,
>>>>>>>> > > > >>>> > > >>> > > > > >
>>>>>>>> > > > >>>> > > >>> > > > > > As discussed earlier you don’t need
>>>>>>>> libMesh for
>>>>>>>> > > the
>>>>>>>> > > > >>>> WEC
>>>>>>>> > > > >>>> > > >>> application.
>>>>>>>> > > > >>>> > > >>> > > You
>>>>>>>> > > > >>>> > > >>> > > > > > can just work with PETSc 3.17.5 that
>>>>>>>> builds with
>>>>>>>> > > > >>>> Matlab.
>>>>>>>> > > > >>>> > > >>> > > > > >
>>>>>>>> > > > >>>> > > >>> > > > > > Do you have a specific reason for
>>>>>>>> wanting to build
>>>>>>>> > > > >>>> libMesh?
>>>>>>>> > > > >>>> > > >>> > > > > >
>>>>>>>> > > > >>>> > > >>> > > > > > Thanks,
>>>>>>>> > > > >>>> > > >>> > > > > > —Amneet
>>>>>>>> > > > >>>> > > >>> > > > > >
>>>>>>>> > > > >>>> > > >>> > > > > > On Thu, Aug 31, 2023 at 10:16 PM
>>>>>>>> INTURU SRINIVAS
>>>>>>>> > > > >>>> 20PHD0548 via
>>>>>>>> > > > >>>> > > >>> > > petsc-users
>>>>>>>> > > > >>>> > > >>> > > > > > <petsc-users at mcs.anl.gov> wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >
>>>>>>>> > > > >>>> > > >>> > > > > >> Hi,
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >> I ran "make all" for petsc 3.13.4 by
>>>>>>>> removing all
>>>>>>>> > > > >>>> occurrences
>>>>>>>> > > > >>>> > > >>> of
>>>>>>>> > > > >>>> > > >>> > > "-lut
>>>>>>>> > > > >>>> > > >>> > > > > >> -licudata -licui18n -licuuc". When I
>>>>>>>> ran "make
>>>>>>>> > > test"
>>>>>>>> > > > >>>> got the
>>>>>>>> > > > >>>> > > >>> > > following
>>>>>>>> > > > >>>> > > >>> > > > > >> errors
>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-debug:
>>>>>>>> > > > >>>> > > >>> > > > > >> TEST
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-debug/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>>>>> > > > >>>> > > >>> > > > > >> not ok
>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>>>>> > > > >>>> > > >>> Error
>>>>>>>> > > > >>>> > > >>> > > code: 124
>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR:
>>>>>>>> --------------------- Error
>>>>>>>> > > Message
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>>
>>>>>>>> --------------------------------------------------------------
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external
>>>>>>>> library
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start
>>>>>>>> MATLAB engine
>>>>>>>> > > on
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > > > >>>> for
>>>>>>>> > > > >>>> > > >>> trouble
>>>>>>>> > > > >>>> > > >>> > > > > >> shooting.
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release
>>>>>>>> Version 3.13.4,
>>>>>>>> > > Aug
>>>>>>>> > > > >>>> 01, 2020
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test
>>>>>>>> on a
>>>>>>>> > > linux-debug
>>>>>>>> > > > >>>> named
>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028
>>>>>>>> > > > >>>> > > >>> > > > > >> by vit Fri Sep 1 10:01:11 2023
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>>>>>> > > > >>>> > > >>> --with-debugging=1
>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1
>>>>>>>> --download-fblaslapack=1
>>>>>>>> > > > >>>> --with-x=0
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1
>>>>>>>> PetscMatlabEngineCreate()
>>>>>>>> > > line
>>>>>>>> > > > >>>> 67 in
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126
>>>>>>>> in
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table
>>>>>>>> entries:
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End
>>>>>>>> of Error
>>>>>>>> > > > >>>> Message
>>>>>>>> > > > >>>> > > >>> -------send
>>>>>>>> > > > >>>> > > >>> > > entire
>>>>>>>> > > > >>>> > > >>> > > > > >> error message to
>>>>>>>> > > petsc-maint at mcs.anl.gov----------
>>>>>>>> > > > >>>> > > >>> > > > > >> #
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in
>>>>>>>> communicator
>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF
>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076.
>>>>>>>> > > > >>>> > > >>> > > > > >> #
>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes
>>>>>>>> Open MPI to
>>>>>>>> > > kill
>>>>>>>> > > > >>>> all MPI
>>>>>>>> > > > >>>> > > >>> > > processes.
>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from
>>>>>>>> other
>>>>>>>> > > processes,
>>>>>>>> > > > >>>> > > >>> depending on
>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them.
>>>>>>>> > > > >>>> > > >>> > > > > >> #
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>>> > > >>> > > > > >> ok
>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>>>>> > > > >>>> # SKIP
>>>>>>>> > > > >>>> > > >>> Command
>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >> in petsc/3.13.4/linux-opt
>>>>>>>> > > > >>>> > > >>> > > > > >> TEST
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-opt/tests/counts/tao_leastsquares_tutorials_matlab-matlab_ls_test.counts
>>>>>>>> > > > >>>> > > >>> > > > > >> not ok
>>>>>>>> > > > >>>> tao_leastsquares_tutorials_matlab-matlab_ls_test #
>>>>>>>> > > > >>>> > > >>> Error
>>>>>>>> > > > >>>> > > >>> > > code: 124
>>>>>>>> > > > >>>> > > >>> > > > > >> # Running problem 5
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR:
>>>>>>>> --------------------- Error
>>>>>>>> > > Message
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>>
>>>>>>>> --------------------------------------------------------------
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Error in external
>>>>>>>> library
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Unable to start
>>>>>>>> MATLAB engine
>>>>>>>> > > on
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: See
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > https://www.mcs.anl.gov/petsc/documentation/faq.html
>>>>>>>> > > > >>>> for
>>>>>>>> > > > >>>> > > >>> trouble
>>>>>>>> > > > >>>> > > >>> > > > > >> shooting.
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Petsc Release
>>>>>>>> Version 3.13.4,
>>>>>>>> > > Aug
>>>>>>>> > > > >>>> 01, 2020
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ../matlab_ls_test
>>>>>>>> on a
>>>>>>>> > > linux-opt
>>>>>>>> > > > >>>> named
>>>>>>>> > > > >>>> > > >>> > > MB108SMEC028 by
>>>>>>>> > > > >>>> > > >>> > > > > >> vit Fri Sep 1 10:34:12 2023
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: Configure options
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> --CC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicc
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > --CXX=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpicxx
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> --FC=/home/vit/sfw/linux/openmpi/4.1.4/bin/mpif90
>>>>>>>> > > > >>>> > > >>> --COPTFLAGS=-O3
>>>>>>>> > > > >>>> > > >>> > > > > >> --CXXOPTFLAGS=-O3 --FOPTFLAGS=-O3
>>>>>>>> > > > >>>> --PETSC_ARCH=linux-opt
>>>>>>>> > > > >>>> > > >>> > > --with-debugging=0
>>>>>>>> > > > >>>> > > >>> > > > > >> --download-hypre=1 --with-x=0
>>>>>>>> > > > >>>> --download-fblaslapack=1
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>>>>>> > > > >>>> > > >>> --with-matlab-engine=1
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #1
>>>>>>>> PetscMatlabEngineCreate()
>>>>>>>> > > line
>>>>>>>> > > > >>>> 67 in
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > /home/vit/sfw/petsc/3.13.4/src/sys/classes/matlabengine/matlab.c
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: #2 main() line 126
>>>>>>>> in
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: PETSc Option Table
>>>>>>>> entries:
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -prob_id 5
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: -tao_smonitor
>>>>>>>> > > > >>>> > > >>> > > > > >> # [0]PETSC ERROR: ----------------End
>>>>>>>> of Error
>>>>>>>> > > > >>>> Message
>>>>>>>> > > > >>>> > > >>> -------send
>>>>>>>> > > > >>>> > > >>> > > entire
>>>>>>>> > > > >>>> > > >>> > > > > >> error message to
>>>>>>>> > > petsc-maint at mcs.anl.gov----------
>>>>>>>> > > > >>>> > > >>> > > > > >> #
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>>> > > >>> > > > > >> # MPI_ABORT was invoked on rank 0 in
>>>>>>>> communicator
>>>>>>>> > > > >>>> > > >>> MPI_COMM_SELF
>>>>>>>> > > > >>>> > > >>> > > > > >> # with errorcode 126076.
>>>>>>>> > > > >>>> > > >>> > > > > >> #
>>>>>>>> > > > >>>> > > >>> > > > > >> # NOTE: invoking MPI_ABORT causes
>>>>>>>> Open MPI to
>>>>>>>> > > kill
>>>>>>>> > > > >>>> all MPI
>>>>>>>> > > > >>>> > > >>> > > processes.
>>>>>>>> > > > >>>> > > >>> > > > > >> # You may or may not see output from
>>>>>>>> other
>>>>>>>> > > processes,
>>>>>>>> > > > >>>> > > >>> depending on
>>>>>>>> > > > >>>> > > >>> > > > > >> # exactly when Open MPI kills them.
>>>>>>>> > > > >>>> > > >>> > > > > >> #
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> --------------------------------------------------------------------------
>>>>>>>> > > > >>>> > > >>> > > > > >> ok
>>>>>>>> > > tao_leastsquares_tutorials_matlab-matlab_ls_test
>>>>>>>> > > > >>>> # SKIP
>>>>>>>> > > > >>>> > > >>> Command
>>>>>>>> > > > >>>> > > >>> > > > > >> failed so no diff.
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >> The same errors occurred for petsc
>>>>>>>> 3.17.5
>>>>>>>> > > version. I
>>>>>>>> > > > >>>> am
>>>>>>>> > > > >>>> > > >>> sharing the
>>>>>>>> > > > >>>> > > >>> > > > > >> config.log and make.log for both
>>>>>>>> petsc 3.13.4 and
>>>>>>>> > > > >>>> petsc
>>>>>>>> > > > >>>> > > >>> 3.17.5.
>>>>>>>> > > > >>>> > > >>> > > Please find
>>>>>>>> > > > >>>> > > >>> > > > > >> the attachment and do the needful.
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >> Thanks and regards
>>>>>>>> > > > >>>> > > >>> > > > > >> Srinivas
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >> On Tue, Aug 29, 2023 at 10:56 PM
>>>>>>>> Satish Balay <
>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov>
>>>>>>>> > > > >>>> > > >>> > > wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> Well - you sent in libmesh log not
>>>>>>>> petsc's
>>>>>>>> > > > >>>> > > >>> configure.log/make.log
>>>>>>>> > > > >>>> > > >>> > > for
>>>>>>>> > > > >>>> > > >>> > > > > >>> petsc-3.17
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> Anyway - with petsc-3.13 - you have:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>>
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab:
>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes:
>>>>>>>> > > > >>>> -I/usr/local/MATLAB/R2020b/extern/include
>>>>>>>> > > > >>>> > > >>> > > > > >>> /usr/local/MATLAB/R2020b
>>>>>>>> > > > >>>> > > >>> > > > > >>> MatlabEngine:
>>>>>>>> > > > >>>> > > >>> > > > > >>> Library:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/usr/local/MATLAB/R2020b/sys/os/glnxa64:/usr/local/MATLAB/R2020b/bin/glnxa64:/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> -L/usr/local/MATLAB/R2020b/bin/glnxa64
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> -L/usr/local/MATLAB/R2020b/extern/lib/glnxa64
>>>>>>>> > > -leng
>>>>>>>> > > > >>>> -lmex
>>>>>>>> > > > >>>> > > >>> -lmx
>>>>>>>> > > > >>>> > > >>> > > -lmat -lut
>>>>>>>> > > > >>>> > > >>> > > > > >>> -licudata -licui18n -licuuc
>>>>>>>> > > > >>>> > > >>> > > > > >>> Language used to compile PETSc: C
>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<<<
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> With petsc-3.19 (and matlab-R2022a)
>>>>>>>> - we are
>>>>>>>> > > seeing:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > https://gitlab.com/petsc/petsc/-/jobs/4904566768
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab:
>>>>>>>> > > > >>>> > > >>> > > > > >>> Includes:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -I/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/extern/include
>>>>>>>> > > > >>>> > > >>> > > > > >>> Libraries:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -Wl,-rpath,/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> -L/nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/glnxa64
>>>>>>>> > > > >>>> > > >>> > > > > >>> -leng -lmex -lmx -lmat
>>>>>>>> > > > >>>> > > >>> > > > > >>> Executable:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a
>>>>>>>> > > > >>>> > > >>> > > > > >>> mex:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/mex
>>>>>>>> > > > >>>> > > >>> > > > > >>> matlab:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /nfs/gce/software/custom/linux-ubuntu22.04-x86_64/matlab/R2022a/bin/matlab
>>>>>>>> > > > >>>> > > >>> > > > > >>> -glnxa64
>>>>>>>> > > > >>>> > > >>> > > > > >>> <<<
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> I.e "-lut -licudata -licui18n
>>>>>>>> -licuuc" are not
>>>>>>>> > > > >>>> preset here.
>>>>>>>> > > > >>>> > > >>> This
>>>>>>>> > > > >>>> > > >>> > > might
>>>>>>>> > > > >>>> > > >>> > > > > >>> be a change wrt newer matlab
>>>>>>>> versions.
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> You can:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> - edit
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> /home/vit/sfw/petsc/3.13.4/linux-opt/lib/petsc/conf/petscvariables
>>>>>>>> > > > >>>> > > >>> > > and
>>>>>>>> > > > >>>> > > >>> > > > > >>> remove all occurrences of "-lut
>>>>>>>> -licudata
>>>>>>>> > > -licui18n
>>>>>>>> > > > >>>> -licuuc"
>>>>>>>> > > > >>>> > > >>> > > > > >>> - now run 'make all' in
>>>>>>>> > > '/home/vit/sfw/petsc/3.13.4'
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> And see if the build works now.
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> Satish
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> On Tue, 29 Aug 2023, INTURU SRINIVAS
>>>>>>>> 20PHD0548
>>>>>>>> > > via
>>>>>>>> > > > >>>> > > >>> petsc-users
>>>>>>>> > > > >>>> > > >>> > > wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > I am sharing the log files while
>>>>>>>> building
>>>>>>>> > > > >>>> petsc3.13.4 with
>>>>>>>> > > > >>>> > > >>> > > matlab and
>>>>>>>> > > > >>>> > > >>> > > > > >>> also
>>>>>>>> > > > >>>> > > >>> > > > > >>> > the log file while building
>>>>>>>> libmesh with
>>>>>>>> > > > >>>> petsc3.17.5 and
>>>>>>>> > > > >>>> > > >>> matlab.
>>>>>>>> > > > >>>> > > >>> > > > > >>> Building
>>>>>>>> > > > >>>> > > >>> > > > > >>> > petsc 3.17.5 with matlab was done
>>>>>>>> > > successfully.
>>>>>>>> > > > >>>> But
>>>>>>>> > > > >>>> > > >>> libmesh is
>>>>>>>> > > > >>>> > > >>> > > not
>>>>>>>> > > > >>>> > > >>> > > > > >>> able to
>>>>>>>> > > > >>>> > > >>> > > > > >>> > find the petsc
>>>>>>>> > > > >>>> > > >>> > > > > >>> > Please find the attachments.
>>>>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > On Tue, Aug 29, 2023 at 7:31 PM
>>>>>>>> Satish Balay <
>>>>>>>> > > > >>>> > > >>> balay at mcs.anl.gov>
>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Send configure.log, make.log
>>>>>>>> from both
>>>>>>>> > > > >>>> petsc-3.13 and
>>>>>>>> > > > >>>> > > >>> 3.17 [or
>>>>>>>> > > > >>>> > > >>> > > 3.19].
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > [you can gzip them to make the
>>>>>>>> logs
>>>>>>>> > > friendly to
>>>>>>>> > > > >>>> mailing
>>>>>>>> > > > >>>> > > >>> list -
>>>>>>>> > > > >>>> > > >>> > > or
>>>>>>>> > > > >>>> > > >>> > > > > >>> send
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > them to petsc-maint]
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > And does test suite work with
>>>>>>>> 3.17? [or
>>>>>>>> > > 3.19?]
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > Satish
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > On Tue, 29 Aug 2023, INTURU
>>>>>>>> SRINIVAS
>>>>>>>> > > 20PHD0548
>>>>>>>> > > > >>>> via
>>>>>>>> > > > >>>> > > >>> petsc-users
>>>>>>>> > > > >>>> > > >>> > > wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > I am sharing the make.log file
>>>>>>>> while
>>>>>>>> > > building
>>>>>>>> > > > >>>> > > >>> petsc-3.13.4
>>>>>>>> > > > >>>> > > >>> > > with
>>>>>>>> > > > >>>> > > >>> > > > > >>> Matlab.
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > Please find the attachment and
>>>>>>>> do the
>>>>>>>> > > needful.
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > On Tue, Aug 29, 2023 at
>>>>>>>> 10:19 AM INTURU
>>>>>>>> > > > >>>> SRINIVAS
>>>>>>>> > > > >>>> > > >>> 20PHD0548 <
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>>>>> inturu.srinivas2020 at vitstudent.ac.in>
>>>>>>>> > > wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > I tried with petsc-3.17.5.
>>>>>>>> During
>>>>>>>> > > building
>>>>>>>> > > > >>>> of
>>>>>>>> > > > >>>> > > >>> libmesh, the
>>>>>>>> > > > >>>> > > >>> > > error
>>>>>>>> > > > >>>> > > >>> > > > > >>> shows
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > petsc was not found
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > > On Mon, Aug 28, 2023 at
>>>>>>>> 9:43 PM Satish
>>>>>>>> > > > >>>> Balay <
>>>>>>>> > > > >>>> > > >>> > > balay at mcs.anl.gov>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> https://ibamr.github.io/linux says
>>>>>>>> > > > >>>> petsc-3.17
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Here you are using 3.13
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Can you retry with
>>>>>>>> petsc-3.17.5?
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Satish
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> On Mon, 28 Aug 2023, INTURU
>>>>>>>> SRINIVAS
>>>>>>>> > > > >>>> 20PHD0548 via
>>>>>>>> > > > >>>> > > >>> > > petsc-users
>>>>>>>> > > > >>>> > > >>> > > > > >>> wrote:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Hello,
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I want to build PETSc
>>>>>>>> with MATLAB for
>>>>>>>> > > > >>>> working on
>>>>>>>> > > > >>>> > > >>> the
>>>>>>>> > > > >>>> > > >>> > > > > >>> simulation
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > using
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> IBAMR
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > open software. While
>>>>>>>> building the
>>>>>>>> > > PETSc,
>>>>>>>> > > > >>>> using the
>>>>>>>> > > > >>>> > > >>> > > following
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export PETSC_DIR=$PWD
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > export
>>>>>>>> PETSC_ARCH=linux-debug
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > ./configure \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> --CC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicc \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> --CXX=$HOME/sfw/linux/openmpi/4.1.4/bin/mpicxx \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> --FC=$HOME/sfw/linux/openmpi/4.1.4/bin/mpif90 \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-debugging=1 \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --download-hypre=1 \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> --download-fblaslapack=1 \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-x=0 \
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> --with-matlab-dir=/usr/local/MATLAB/R2020b/
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > --with-matlab-engine=1
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> --with-matlab-engine-dir=/usr/local/MATLAB/R2020b/extern/engines/
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make -j4 test
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > I got the following error
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > CLINKER
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function
>>>>>>>> `EvaluateResidual':
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:32:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEnginePut'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:33:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:35:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGet'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function
>>>>>>>> `EvaluateJacobian':
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:46:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEnginePut'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:47:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:49:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGet'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `TaoPounders':
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:75:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGet'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test.o: in
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > function `main':
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:126:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineCreate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:127:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:139:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:140:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:142:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:144:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:146:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:148:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineGetArray'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:154:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:157:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineEvaluate'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > /usr/bin/ld:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> > >
>>>>>>>> /home/vit/sfw/petsc/3.13.4/src/tao/leastsquares/tutorials/matlab/matlab_ls_test.c:158:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > undefined reference to
>>>>>>>> > > > >>>> `PetscMatlabEngineDestroy'
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > collect2: error: ld
>>>>>>>> returned 1 exit
>>>>>>>> > > > >>>> status
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: ***
>>>>>>>> [gmakefile.test:185:
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>>
>>>>>>>> linux-debug/tests/tao/leastsquares/tutorials/matlab/matlab_ls_test]
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> Error 1
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > make: *** Waiting for
>>>>>>>> unfinished
>>>>>>>> > > jobs....
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Please help me to solve
>>>>>>>> this issue
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Thank you
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> > Srinivas
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> > >
>>>>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>>>>> > > > >>>> > > >>> > > > > >>> >
>>>>>>>> > > > >>>> > > >>> > > > > >>>
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >> *Disclaimer:This message was sent
>>>>>>>> from Vellore
>>>>>>>> > > > >>>> Institute of
>>>>>>>> > > > >>>> > > >>> > > Technology.
>>>>>>>> > > > >>>> > > >>> > > > > >> The contents of this email may
>>>>>>>> contain legally
>>>>>>>> > > > >>>> protected
>>>>>>>> > > > >>>> > > >>> > > confidential or
>>>>>>>> > > > >>>> > > >>> > > > > >> privileged information of “Vellore
>>>>>>>> Institute of
>>>>>>>> > > > >>>> Technology”.
>>>>>>>> > > > >>>> > > >>> If
>>>>>>>> > > > >>>> > > >>> > > you are
>>>>>>>> > > > >>>> > > >>> > > > > >> not the intended recipient, you
>>>>>>>> should not
>>>>>>>> > > > >>>> disseminate,
>>>>>>>> > > > >>>> > > >>> distribute
>>>>>>>> > > > >>>> > > >>> > > or copy
>>>>>>>> > > > >>>> > > >>> > > > > >> this e-mail. Please notify the sender
>>>>>>>> immediately
>>>>>>>> > > > >>>> and destroy
>>>>>>>> > > > >>>> > > >>> all
>>>>>>>> > > > >>>> > > >>> > > copies of
>>>>>>>> > > > >>>> > > >>> > > > > >> this message and any attachments. If
>>>>>>>> you have
>>>>>>>> > > > >>>> received this
>>>>>>>> > > > >>>> > > >>> email
>>>>>>>> > > > >>>> > > >>> > > in error,
>>>>>>>> > > > >>>> > > >>> > > > > >> please promptly notify the sender by
>>>>>>>> reply email
>>>>>>>> > > and
>>>>>>>> > > > >>>> delete
>>>>>>>> > > > >>>> > > >>> the
>>>>>>>> > > > >>>> > > >>> > > original
>>>>>>>> > > > >>>> > > >>> > > > > >> email and any backup copies without
>>>>>>>> reading
>>>>>>>> > > them.*
>>>>>>>> > > > >>>> > > >>> > > > > >>
>>>>>>>> > > > >>>> > > >>> > > > > >
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > > >
>>>>>>>> > > > >>>> > > >>> > > >
>>>>>>>> > > > >>>> > > >>> > >
>>>>>>>> > > > >>>> > > >>> >
>>>>>>>> > > > >>>> > > >>> >
>>>>>>>> > > > >>>> > > >>>
>>>>>>>> > > > >>>> > > >>
>>>>>>>> > > > >>>> > > >>
>>>>>>>> > > > >>>> > > >> *Disclaimer:This message was sent from Vellore
>>>>>>>> Institute of
>>>>>>>> > > > >>>> Technology.
>>>>>>>> > > > >>>> > > >> The contents of this email may contain legally
>>>>>>>> protected
>>>>>>>> > > > >>>> confidential or
>>>>>>>> > > > >>>> > > >> privileged information of “Vellore Institute of
>>>>>>>> > > Technology”. If
>>>>>>>> > > > >>>> you are
>>>>>>>> > > > >>>> > > >> not the intended recipient, you should not
>>>>>>>> disseminate,
>>>>>>>> > > > >>>> distribute or copy
>>>>>>>> > > > >>>> > > >> this e-mail. Please notify the sender immediately
>>>>>>>> and destroy
>>>>>>>> > > > >>>> all copies of
>>>>>>>> > > > >>>> > > >> this message and any attachments. If you have
>>>>>>>> received this
>>>>>>>> > > > >>>> email in error,
>>>>>>>> > > > >>>> > > >> please promptly notify the sender by reply email
>>>>>>>> and delete
>>>>>>>> > > the
>>>>>>>> > > > >>>> original
>>>>>>>> > > > >>>> > > >> email and any backup copies without reading them.*
>>>>>>>> > > > >>>> > > >>
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > > --
>>>>>>>> > > > >>>> > > > --Amneet
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > > >
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>> > >
>>>>>>>> > > > >>>>
>>>>>>>> > > > >>>
>>>>>>>> > > > >>>
>>>>>>>> > > > >>> *Disclaimer:This message was sent from Vellore Institute
>>>>>>>> of
>>>>>>>> > > Technology.
>>>>>>>> > > > >>> The contents of this email may contain legally protected
>>>>>>>> > > confidential or
>>>>>>>> > > > >>> privileged information of “Vellore Institute of
>>>>>>>> Technology”. If you
>>>>>>>> > > are
>>>>>>>> > > > >>> not the intended recipient, you should not disseminate,
>>>>>>>> distribute
>>>>>>>> > > or copy
>>>>>>>> > > > >>> this e-mail. Please notify the sender immediately and
>>>>>>>> destroy all
>>>>>>>> > > copies of
>>>>>>>> > > > >>> this message and any attachments. If you have received
>>>>>>>> this email in
>>>>>>>> > > error,
>>>>>>>> > > > >>> please promptly notify the sender by reply email and
>>>>>>>> delete the
>>>>>>>> > > original
>>>>>>>> > > > >>> email and any backup copies without reading them.*
>>>>>>>> > > > >>>
>>>>>>>> > > > >>
>>>>>>>> > > > >>
>>>>>>>> > > > >> --
>>>>>>>> > > > >> What most experimenters take for granted before they begin
>>>>>>>> their
>>>>>>>> > > > >> experiments is infinitely more interesting than any
>>>>>>>> results to which
>>>>>>>> > > their
>>>>>>>> > > > >> experiments lead.
>>>>>>>> > > > >> -- Norbert Wiener
>>>>>>>> > > > >>
>>>>>>>> > > > >> https://www.cse.buffalo.edu/~knepley/
>>>>>>>> > > > >> <http://www.cse.buffalo.edu/~knepley/>
>>>>>>>> > > > >>
>>>>>>>> > > > >
>>>>>>>> > > > >
>>>>>>>> > > > > *Disclaimer:This message was sent from Vellore Institute of
>>>>>>>> Technology.
>>>>>>>> > > > > The contents of this email may contain legally protected
>>>>>>>> confidential
>>>>>>>> > > or
>>>>>>>> > > > > privileged information of “Vellore Institute of
>>>>>>>> Technology”. If you
>>>>>>>> > > are
>>>>>>>> > > > > not the intended recipient, you should not disseminate,
>>>>>>>> distribute or
>>>>>>>> > > copy
>>>>>>>> > > > > this e-mail. Please notify the sender immediately and
>>>>>>>> destroy all
>>>>>>>> > > copies of
>>>>>>>> > > > > this message and any attachments. If you have received this
>>>>>>>> email in
>>>>>>>> > > error,
>>>>>>>> > > > > please promptly notify the sender by reply email and delete
>>>>>>>> the
>>>>>>>> > > original
>>>>>>>> > > > > email and any backup copies without reading them.*
>>>>>>>> > > > >
>>>>>>>> > > >
>>>>>>>> > > >
>>>>>>>> > > >
>>>>>>>> > >
>>>>>>>> >
>>>>>>>> >
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> *Disclaimer:This message was sent from Vellore Institute of
>>>>>>> Technology. The contents of this email may contain legally protected
>>>>>>> confidential or privileged information of “Vellore Institute of
>>>>>>> Technology”. If you are not the intended recipient, you should not
>>>>>>> disseminate, distribute or copy this e-mail. Please notify the sender
>>>>>>> immediately and destroy all copies of this message and any attachments. If
>>>>>>> you have received this email in error, please promptly notify the sender by
>>>>>>> reply email and delete the original email and any backup copies without
>>>>>>> reading them.*
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> --Amneet
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> *Disclaimer:This message was sent from Vellore Institute of
>>>>> Technology. The contents of this email may contain legally protected
>>>>> confidential or privileged information of “Vellore Institute of
>>>>> Technology”. If you are not the intended recipient, you should not
>>>>> disseminate, distribute or copy this e-mail. Please notify the sender
>>>>> immediately and destroy all copies of this message and any attachments. If
>>>>> you have received this email in error, please promptly notify the sender by
>>>>> reply email and delete the original email and any backup copies without
>>>>> reading them.*
>>>>>
>>>>>
>>>>>
>>>>
>>>> *Disclaimer:This message was sent from Vellore Institute of
>>>> Technology. The contents of this email may contain legally protected
>>>> confidential or privileged information of “Vellore Institute of
>>>> Technology”. If you are not the intended recipient, you should not
>>>> disseminate, distribute or copy this e-mail. Please notify the sender
>>>> immediately and destroy all copies of this message and any attachments. If
>>>> you have received this email in error, please promptly notify the sender by
>>>> reply email and delete the original email and any backup copies without
>>>> reading them.*
>>>>
>>>>
>>>>
>>>
>>> --
>>> --Amneet
>>>
>>>
>>>
>>>
>>
>> --
>> --Amneet
>>
>>
>>
>>
--
**Disclaimer:*
This message was sent from Vellore Institute of Technology.
The contents of this email may contain legally protected confidential or
privileged information of “Vellore Institute of Technology”. If you are
not the intended recipient, you should not disseminate, distribute or copy
this e-mail. Please notify the sender immediately and destroy all copies of
this message and any attachments. If you have received this email in error,
please promptly notify the sender by reply email and delete the original
email and any backup copies without reading them.*
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