[petsc-users] Parallel DM example for FEM

[Anthony Vergottis]

I compile ex12 but when I run the program I get this in the terminal.

adoni at Adoni:~/Desktop/petsc-lat/src/snes/examples/tutorials$ make ex12
/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/bin/mpicxx -o ex12.o -c
-Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g  -fPIC
 -I/home/adoni/Desktop/petsc-lat/include
-I/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/include
 /home/adoni/Desktop/petsc-lat/src/snes/examples/tutorials/ex12.c
/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/bin/mpicxx -Wall
-Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -g  -o ex12
ex12.o -Wl,-rpath,/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib
-L/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib  -lpetsc
-Wl,-rpath,/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib -lflapack
-lfblas -ltriangle -lX11 -lparmetis -lmetis -lpthread -lchaco -lctetgen -lm
-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.6
-L/usr/lib/gcc/x86_64-linux-gnu/4.6 -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 -lmpichf90 -lgfortran -lm -lgfortran -lm -lquadmath
-lm -lmpichcxx -lstdc++ -ldl -lmpich -lopa -lmpl -lrt -lpthread -lgcc_s
-ldl
/bin/rm -f ex12.o
adoni at Adoni:~/Desktop/petsc-lat/src/snes/examples/tutorials$ mpiexec -np 2
./ex12
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Invalid argument!
[0]PETSC ERROR: The section cell closure size 0 != dual space dimension 1!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development GIT revision: unknown  GIT Date: unknown
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./ex12 on a arch-linux2-c-debug named Adoni by adoni Mon
Nov 11 12:21:49 2013
[0]PETSC ERROR: Libraries linked from
/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib
[0]PETSC ERROR: Configure run at Fri Nov  8 20:03:26 2013
[0]PETSC ERROR: Configure options --with-clanguage=c++
--with-shared-libraries=1 --download-f-blas-lapack --download-mpich
--download-boost --download-triangle --download-ctetgen --download-chaco
--download-metis --download-parmetis
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: DMPlexProjectFunctionLocal() line 207 in
src/dm/impls/plex/plexfem.c
[0]PETSC ERROR: DMPlexProjectFunction() line 258 in
src/dm/impls/plex/plexfem.c
[0]PETSC ERROR: main() line 686 in
/home/adoni/Desktop/petsc-lat/src/snes/examples/tutorials/ex12.c
[0]PETSC ERROR: --------------------- Error Message
------------------------------------
[0]PETSC ERROR: Invalid argument!
[0]PETSC ERROR: The section cell closure size 0 != dual space dimension 1!
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Development GIT revision: unknown  GIT Date: unknown
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: ./ex12 on a arch-linux2-c-debug named Adoni by adoni Mon
Nov 11 12:21:49 2013
[0]PETSC ERROR: Libraries linked from
/home/adoni/Desktop/petsc-lat/arch-linux2-c-debug/lib
[0]PETSC ERROR: Configure run at Fri Nov  8 20:03:26 2013
[0]PETSC ERROR: Configure options --with-clanguage=c++
--with-shared-libraries=1 --download-f-blas-lapack --download-mpich
--download-boost --download-triangle --download-ctetgen --download-chaco
--download-metis --download-parmetis
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: DMPlexProjectFunctionLocal() line 207 in
src/dm/impls/plex/plexfem.c
[0]PETSC ERROR: DMPlexProjectFunction() line 258 in
src/dm/impls/plex/plexfem.c
[0]PETSC ERROR: main() line 686 in
/home/adoni/Desktop/petsc-lat/src/snes/examples/tutorials/ex12.c
application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0

This occurs for all process counts.

Thanks.

Adoni


On 11 November 2013 12:19, Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Nov 11, 2013 at 6:10 AM, Anthony Vergottis <a.vergottis at ucl.ac.uk>wrote:
>
>> Dear All,
>>
>> I am trying to find a good example within PETSc that examples with some
>> detail the use of DM objects within a parallel and FEM framework. I have
>> looked at most of the example and have not found anything like this. Is
>> there any other material available on the subject from any other source or
>> maybe I missed something within the PETSc full download file?
>>
>
> Did you look at SNES ex12? Is it not understandable?
>
>   Thanks,
>
>      Matt
>
>
>> Thanks in advance.
>>
>> Regards,
>> Adonis
>>
>
>
>
> --
> 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
>
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