[petsc-users] strange error by changing the number of cells.

Yann JOBIC yann.jobic at univ-amu.fr
Tue Dec 18 07:52:17 CST 2018


Le 18/12/2018 à 14:26, Matthew Knepley a écrit :
> On Tue, Dec 18, 2018 at 5:23 AM Yann JOBIC via petsc-users 
> <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>> wrote:
>
>     Le 18/12/2018 à 03:01, Matthew Knepley a écrit :
>>     On Mon, Dec 17, 2018 at 4:24 PM Yann Jobic via petsc-users
>>     <petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov>> wrote:
>>
>>         Dear petsc users,
>>
>>         I'm using petsc FEM framework, with p4est. I'm getting a
>>         strange error,
>>         when changing the number of point in DMPlexCreateBoxMesh()
>>         (2D, 20x20 is
>>         ok, 22x22 is not) :
>>
>>         [0]PETSC ERROR: Nonconforming object sizes
>>         [0]PETSC ERROR: The section point closure size 20 != dual
>>         space dimension 18
>>
>>
>>     Okay, here is what the nomenclature means. The closure size is
>>     the size I get from the Section
>>     when I take the closure of the given point. So for example, if we
>>     have quads and Q2 elements,
>>     that would have a closure size of
>>
>>       3 x 3 = 9
>>
>>     per component. So a 2-component Q2 element would have closure
>>     size 18. The dual space
>>     dimension is the number of dual space basis vectors. If we use a
>>     Lagrange element, there
>>     would be 1 dof per vertex, 1 per edge and 1 per cell for
>>     quadratic fields, so on a quad that is
>>     9 dofs, and for 2 component fields that is 18. This is why the
>>     two numbers are designed to match.
>>     Could you give
>>
>>       -petscds_view
>>
>>     so I can see the element you are using, and also
>>     PetscSectionView() on the DM section (or use
>>     -petscsection_view although that catches all sections, so it hard
>>     to find the right one).
>>
>>       Thanks,
>     The problem arise in parallel, and for a 6x6 grid size. I'm doing
>     something wrong, but i don't know where. It's working fine in
>     older petsc version.
>     You will find in attachment the log files.
>
>     The code for the section is the following :
>         ierr = DMGetSection(dmAux,&section);CHKERRQ(ierr);
>         PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);
>
>     Thanks for the help !
>
>
> On 1 proc, you have 120 cells, but on 2 procs you have 126? Can you 
> also send the output with -dm_view?
> I can't see what is going on with the parallelization. Are you 
> specfiying some overlap in the partition?
I don't have an overlap. My DM is created by :

     ierr = DMPlexCreateBoxMesh(comm, dim, user->simplex, user->cells, 
DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE, interpolate, 
dm);CHKERRQ(ierr);

I then distribute the DM :

     ierr = DMPlexDistribute(*dm, 0, NULL, &distributedMesh);CHKERRQ(ierr);

And finally i convert to DMP4EST the resulting DM.
I copy this mesh to create the auxiliary one, for the auxiliary velocity 
field.

Is that right ?

Thanks,

PS : sorry for multiple sends, i forgot to send this email to the list.
>
>   Thanks,
>
>     Matt
>
>     Yann
>
>>
>>         Matt
>>
>>         [0]PETSC ERROR: See
>>         http://www.mcs.anl.gov/petsc/documentation/faq.html
>>         for trouble shooting.
>>         [0]PETSC ERROR: Petsc Release Version 3.10.2, Oct, 09, 2018
>>         [0]PETSC ERROR: ./gauss on a  named crabe by yann Mon Dec 17
>>         22:17:38 2018
>>         [0]PETSC ERROR: Configure options
>>         --prefix=/local/lib/petsc/3.10/p2/gcc/openmpi_gcc_all
>>         --with-single-library=0 --with-debugging=1
>>         --download-scalapack=1
>>         --download-metis=1 --download-parmetis=1 --download-ptscotch=1
>>         --download-mumps=1 --download-hypre=1 --download-superlu=1
>>         --download-superlu_dist=1 --download-fblaslapack=1
>>         --download-metis=1
>>         --download-ml=1 --download-p4est=1 --download-netcdf=1
>>         --download-pragmatic=1 --with-cxx-dialect=C++11
>>         --download-eigen=1
>>         --download-parms=1 --download-triangle=1 --download-hdf5=1
>>         --with-zlib=1
>>         --download-szlib=1 --download-suitesparse=1
>>         --with-shared-libraries=0
>>         PETSC_ARCH=openmpi_gcc_all
>>         [0]PETSC ERROR: #1 DMProjectLocal_Generic_Plex() line 400 in
>>         /local/yann/petsc-3.10.2/src/dm/impls/plex/plexproject.c
>>         [0]PETSC ERROR: #2 DMProjectFunctionLocal_Plex() line 530 in
>>         /local/yann/petsc-3.10.2/src/dm/impls/plex/plexproject.c
>>         [0]PETSC ERROR: #3 DMProjectFunctionLocal() line 6320 in
>>         /local/yann/petsc-3.10.2/src/dm/interface/dm.c
>>         [0]PETSC ERROR: #4 DMProjectFunctionLocal_p4est() line 4393 in
>>         /local/yann/petsc-3.10.2/src/dm/impls/forest/p4est/pforest.c
>>         [0]PETSC ERROR: #5 DMProjectFunctionLocal() line 6320 in
>>         /local/yann/petsc-3.10.2/src/dm/interface/dm.c
>>         [0]PETSC ERROR: #6 SetupVelocity() line 332 in
>>         /local/yann/fe-utils/petsc/3.10/gauss.c
>>         [0]PETSC ERROR: #7 SetupVelBC() line 359 in
>>         /local/yann/fe-utils/petsc/3.10/gauss.c
>>         [0]PETSC ERROR: #8 main() line 652 in
>>         /local/yann/fe-utils/petsc/3.10/gauss.c
>>
>>         I'm using petscspace_degree == 2 for the primary field, and
>>         also for the
>>         auxiliary one (velocity). The error occurs when i project the
>>         velocity
>>         function into the auxiliary field.
>>
>>         Do you see where the problem could come from ?
>>
>>         Best regards,
>>
>>         Yann
>>
>
>
>
> -- 
> 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/%7Eknepley/>


-- 
___________________________

Yann JOBIC
HPC engineer
Polytech Marseille DME
IUSTI-CNRS UMR 6595
Technopôle de Château Gombert
5 rue Enrico Fermi
13453 Marseille cedex 13
Tel : (33) 4 91 10 69 39
   ou  (33) 4 91 10 69 43
Fax : (33) 4 91 10 69 69

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