[petsc-users] Parallel DM example for FEM

Mon Nov 11 06:52:17 CST 2013

Ok thank you very much yet again!

Adoni

On 11 November 2013 12:49, Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Nov 11, 2013 at 6:47 AM, Anthony Vergottis <a.vergottis at ucl.ac.uk>wrote:
>
>> I would also like to ask as I have some confusion. Are the DM objects
>> capable of handling all aspects of the parallel computations within a given
>> problem?
>>
>> Let me elaborate - for example if I am passing a mesh structure
>> (triangular 3 node elements) as the following:
>>
>> Elem 0: N1 N5 N6
>> etc.....
>> where N# is the node tag.
>>
>> into a DM object and then perform a decomposition for as many processes I
>> required. When the mesh partitions are distributed to their processes do I
>> then have the ability by using DM objects or something else built into
>> PETSc to compute specific calculations on each process without the need to
>> hardcode any MPI?
>>
>
> I believe the answer is yes. I could be more specific with a concrete
> example. For instance, the DM can
> calculate a parallel residual without the user ever seeing MPI.
>
>    Matt
>
>
>> I hope I have explained this well.
>>
>> Thanks again.
>> Adoni
>>
>>
>> On 11 November 2013 12:33, Anthony Vergottis <a.vergottis at ucl.ac.uk>wrote:
>>
>>> Thanks mate that worked!
>>>
>>> Thanks.
>>> Adoni
>>>
>>>
>>>
>>> On 11 November 2013 12:29, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>>> On Mon, Nov 11, 2013 at 6:25 AM, Anthony Vergottis <
>>>> a.vergottis at ucl.ac.uk> wrote:
>>>>
>>>>> I compile ex12 but when I run the program I get this in the terminal.
>>>>>
>>>>
>>>> I guess I should make better defaults. Here are the runs I use for ex12:
>>>>
>>>>
>>>> https://bitbucket.org/petsc/petsc/src/a965ca046084fa53248a41da989a0a62cb6266ea/config/builder.py?at=master#cl-180
>>>>
>>>> You can see that the problem here is that the -petscspace_order has not
>>>> been set. So to test P_1 I use
>>>>
>>>>   -run_type test -refinement_limit 0.0 -bc_type dirichlet -interpolate
>>>> 0 -petscspace_order 1 -show_initial -dm_plex_print_fem 1
>>>>
>>>> and then take away run_type (or use full) to solve the problem. SNES
>>>> ex62 is the Stokes problem, and run parameters are
>>>> in the same place.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
>>>>
>>>
>>>
>>
>
>
> --
> 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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