[petsc-users] Error while building PETSc with MATLAB

Tue Aug 29 12:07:46 CDT 2023

On Tue, Aug 29, 2023 at 9:08 AM Satish Balay via petsc-users <
petsc-users 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?]
>

David Wells is working on this. The change is that petscversion.h now
includes petscconf.h which means you need all the include flags, but
Libmesh does not get the flags right.

  Thanks,

    Matt

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

-- 
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/>
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