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

Matthew Knepley knepley at gmail.com
Wed Jul 31 21:09:52 CDT 2024 

On Wed, Jul 31, 2024 at 4:16 PM Eric Chamberland <
Eric.Chamberland at giref.ulaval.ca> wrote:

> Hi Vaclav,
>
> Okay, I am coming back with this question after some time... ;)
>
> I am just wondering if it is now possible to call
> DMPlexBuildFromCellListParallel or something else, to build a mesh that
> combine different element types into a single DMPlex (in parallel of
> course) ?
>
1) Meshes with different cell types are fully functional, and some
applications have been using them for a while now.

2) The Firedrake I/O methods support these hybrid meshes.

3) You can, for example, read in a GMsh or ExodusII file with different
cell types.

However, there is no direct interface like
DMPlexBuildFromCellListParallel(). If you plan on creating meshes by hand,
I can build that for you.
No one so far has wanted that. Rather they want to read in a mesh in some
format, or alter a base mesh by inserting other cell types.

So, what is the motivating use case?

  Thanks,

     Matt

> Thanks,
>
> Eric
> On 2021-09-23 11:30, Hapla Vaclav wrote:
>
> 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://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/4350__;!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oBuRbcJg$ 
>
> Thanks,
>
> Vaclav
>
> On 23 Sep 2021, at 16:53, Eric Chamberland <
> 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> 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> a
>> écrit :
>>
>>> On Tue, Sep 21, 2021 at 10:31 AM Karin&NiKo <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> 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> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oP6W0x8e$ 
>>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oMwy-ztx$ >
>>>>>
>>>>> --
>>>>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oP6W0x8e$ 
>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oMwy-ztx$ >
>>>
>>
>
> --
> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oP6W0x8e$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!a7Z4JG-PH0CquDikXpywg-JEECEGlEIcXI5LzffVcIr4qqITdSAQJibbguyeQOCvW6DkzTDDbP58oMwy-ztx$ >
>
> --
> Eric Chamberland, ing., M. Ing
> Professionnel de recherche
> GIREF/Université Laval
> (418) 656-2131 poste 41 22 42
>
>
> --
> 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

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