[petsc-users] Error while building PETSc with MATLAB
INTURU SRINIVAS 20PHD0548
inturu.srinivas2020 at vitstudent.ac.in
Fri Sep 1 09:49:43 CDT 2023
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
>>> > > > >> >
>>> > > > >> >
>>> > > > >>
>>> > > > >>
>>> > > >
>>> > > >
>>> > >
>>> >
>>> >
>>>
>>
>>
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