[petsc-users] Error while building PETSc with MATLAB

Fri Sep 1 09:18:46 CDT 2023

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
>> > > > >> >
>> > > > >> >
>> > > > >>
>> > > > >>
>> > > >
>> > > >
>> > >
>> >
>> >
>>
>
>
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