[petsc-users] Question regarding DMPlex reordering

[Matthew Knepley]

On Tue, Oct 26, 2021 at 10:17 AM Pierre Seize <pierre.seize at onera.fr> wrote:

> Hi, I had the idea to try and renumber my mesh cells, as I've heard it's
> better: "neighbouring cells are stored next to one another, and memory
> access are faster".
> Right now, I load the mesh then I distribute it over the processes. I
> thought I'd try to permute the numbering between those two steps :
>
> DMPlexCreateFromFile
> DMPlexGetOrdering
> DMPlexPermute
> DMPlexDistribute
>
> but that gives me an error when it runs on more than one process:
>
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: No support for this operation for this object type
> [0]PETSC ERROR: Number of dofs for point 0 in the local section should be
> positive
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.16.0, unknown
> [0]PETSC ERROR: ./build/bin/yanss on a  named ldmpe202z.onera by pseize
> Tue Oct 26 16:03:33 2021
> [0]PETSC ERROR: Configure options --PETSC_ARCH=arch-ld-gcc
> --download-metis --download-parmetis --prefix=~/.local --with-cgns
> [0]PETSC ERROR: #1 PetscPartitionerDMPlexPartition() at
> /stck/pseize/softwares/petsc/src/dm/impls/plex/plexpartition.c:720
> [0]PETSC ERROR: #2 DMPlexDistribute() at
> /stck/pseize/softwares/petsc/src/dm/impls/plex/plexdistribute.c:1630
> [0]PETSC ERROR: #3 MeshLoadFromFile() at src/spatial.c:689
> [0]PETSC ERROR: #4 main() at src/main.c:22
> [0]PETSC ERROR: PETSc Option Table entries:
> [0]PETSC ERROR: -draw_comp 0
> [0]PETSC ERROR: -mesh data/box.msh
> [0]PETSC ERROR: -mesh_view draw
> [0]PETSC ERROR: -riemann anrs
> [0]PETSC ERROR: -ts_max_steps 100
> [0]PETSC ERROR: -vec_view_partition
> [0]PETSC ERROR: ----------------End of Error Message -------send entire
> error message to petsc-maint at mcs.anl.gov----------
>
> I checked and before I tried to reorder the mesh, the dm->localSection
> was NULL before entering DMPlexDistribute, and I was able to fix the
> error with DMSetLocalSection(dm, NULL) after DMPlexPermute, but it
> doesn't seems it's the right way to do what I want. Does someone have any
> advice ?
>
> Oh, this is probably me trying to be too clever. If a local section is
defined, then I try to use the number of dofs in it to load balance better.
There should never be a negative number of dofs in the local section (a
global section uses this to indicate a dof owned by another process).
So eliminating the local section will definitely fix that error.

Now the question of how you got a local section. DMPlexPermute()  does not
create one, so it seems like you had one ahead of time, and that
the values were not valid.

Note that you can probably get rid of some of the loading code using

  DMCreate(comm, &dm);
  DMSetType(dm, DMPLEX);
  DMSetFromOptions(dm);
  DMViewFromOptions(dm, NULL, "-mesh_view");

and use

  -dm_plex_filename databox,msh -mesh_view

  Thanks,

     Matt

> Thanks in advance
>
> Pierre Seize
>


-- 
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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