[petsc-users] How to combine different element types into a single DMPlex?

[Hapla Vaclav]

Note there will soon be a generalization of DMPlexBuildFromCellListParallel() around, as a side product of our current collaborative efforts with Firedrake guys. It will take a PetscSection instead of relying on the blocksize [which is indeed always constant for the given dataset]. Stay tuned.

https://gitlab.com/petsc/petsc/-/merge_requests/4350

Thanks,

Vaclav

On 23 Sep 2021, at 16:53, Eric Chamberland <Eric.Chamberland at giref.ulaval.ca<mailto:Eric.Chamberland at giref.ulaval.ca>> wrote:


Hi,

oh, that's a great news!

In our case we have our home-made file-format, invariant to the number of processes (thanks to MPI_File_set_view), that uses collective, asynchronous MPI I/O native calls for unstructured hybrid meshes and fields .

So our needs are not for reading meshes but only to fill an hybrid DMPlex with DMPlexBuildFromCellListParallel (or something else to come?)... to exploit petsc partitioners and parallel overlap computation...

Thanks for the follow-up! :)

Eric


On 2021-09-22 7:20 a.m., Matthew Knepley wrote:
On Wed, Sep 22, 2021 at 3:04 AM Karin&NiKo <niko.karin at gmail.com<mailto:niko.karin at gmail.com>> wrote:
Dear Matthew,

This is great news!
For my part, I would be mostly interested in the parallel input interface. Sorry for that...
Indeed, in our application,  we already have a parallel mesh data structure that supports hybrid meshes with parallel I/O and distribution (based on the MED format). We would like to use a DMPlex to make parallel mesh adaptation.
 As a matter of fact, all our meshes are in the MED format. We could also contribute to extend the interface of DMPlex with MED (if you consider it could be usefull).

An MED interface does exist. I stopped using it for two reasons:

  1) The code was not portable and the build was failing on different architectures. I had to manually fix it.

  2) The boundary markers did not provide global information, so that parallel reading was much harder.

Feel free to update my MED reader to a better design.

  Thanks,

     Matt

Best regards,
Nicolas


Le mar. 21 sept. 2021 à 21:56, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> a écrit :
On Tue, Sep 21, 2021 at 10:31 AM Karin&NiKo <niko.karin at gmail.com<mailto:niko.karin at gmail.com>> wrote:
Dear Eric, dear Matthew,

I share Eric's desire to be able to manipulate meshes composed of different types of elements in a PETSc's DMPlex.
Since this discussion, is there anything new on this feature for the DMPlex object or am I missing something?

Thanks for finding this!

Okay, I did a rewrite of the Plex internals this summer. It should now be possible to interpolate a mesh with any
number of cell types, partition it, redistribute it, and many other manipulations.

You can read in some formats that support hybrid meshes. If you let me know how you plan to read it in, we can make it work.
Right now, I don't want to make input interfaces that no one will ever use. We have a project, joint with Firedrake, to finalize
parallel I/O. This will make parallel reading and writing for checkpointing possible, supporting topology, geometry, fields and
layouts, for many meshes in one HDF5 file. I think we will finish in November.

  Thanks,

     Matt

Thanks,
Nicolas

Le mer. 21 juil. 2021 à 04:25, Eric Chamberland <Eric.Chamberland at giref.ulaval.ca<mailto:Eric.Chamberland at giref.ulaval.ca>> a écrit :

Hi,

On 2021-07-14 3:14 p.m., Matthew Knepley wrote:
On Wed, Jul 14, 2021 at 1:25 PM Eric Chamberland <Eric.Chamberland at giref.ulaval.ca<mailto:Eric.Chamberland at giref.ulaval.ca>> wrote:
Hi,

while playing with DMPlexBuildFromCellListParallel, I noticed we have to
specify "numCorners" which is a fixed value, then gives a fixed number
of nodes for a series of elements.

How can I then add, for example, triangles and quadrangles into a DMPlex?

You can't with that function. It would be much mich more complicated if you could, and I am not sure
it is worth it for that function. The reason is that you would need index information to offset into the
connectivity list, and that would need to be replicated to some extent so that all processes know what
the others are doing. Possible, but complicated.

Maybe I can help suggest something for what you are trying to do?

Yes: we are trying to partition our parallel mesh with PETSc functions.  The mesh has been read in parallel so each process owns a part of it, but we have to manage mixed elements types.

When we directly use ParMETIS_V3_PartMeshKway, we give two arrays to describe the elements which allows mixed elements.

So, how would I read my mixed mesh in parallel and give it to PETSc DMPlex so I can use a PetscPartitioner with DMPlexDistribute ?

A second goal we have is to use PETSc to compute the overlap, which is something I can't find in PARMetis (and any other partitionning library?)

Thanks,

Eric


  Thanks,

      Matt


Thanks,

Eric

--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42



--
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/>

--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42


--
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/>


--
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/>

--
Eric Chamberland, ing., M. Ing
Professionnel de recherche
GIREF/Université Laval
(418) 656-2131 poste 41 22 42

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