[petsc-dev] DMPlex + P_1 FE interpolation

[Dave May]

On Mon 10. Feb 2020 at 14:17, Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Feb 10, 2020 at 5:08 AM Dave May <dave.mayhem23 at gmail.com> wrote:
>
>>
>>
>> On Mon 10. Feb 2020 at 13:09, Matthew Knepley <knepley at gmail.com> wrote:
>>
>>> On Sun, Feb 9, 2020 at 11:11 PM Pierre Jolivet <
>>> pierre.jolivet at enseeiht.fr> wrote:
>>>
>>>>
>>>>
>>>> On 10 Feb 2020, at 6:20 AM, Matthew Knepley <knepley at gmail.com> wrote:
>>>>
>>>> On Sun, Feb 9, 2020 at 3:23 PM Pierre Jolivet <
>>>> pierre.jolivet at enseeiht.fr> wrote:
>>>>
>>>>> Hello,
>>>>> I’ve a hard time answering the following DMPlex questions by just
>>>>> looking at some of the examples and manual.
>>>>> Considering two DMPlex dm and dma, as in
>>>>> petsc/src/dm/impls/plex/examples/tests/ex19.c, I’d like to interpolate a
>>>>> simple P_1 FE function from dm to dma.
>>>>> The DMCreateInterpolation call gives me:
>>>>> [0]PETSC ERROR: Invalid argument
>>>>> [0]PETSC ERROR: Number of fine indices 0 != 4 dual basis vecs
>>>>> […]
>>>>>
>>>>
>>>> It looks like your fine grid has no discretization, since 0 is
>>>> numFIndices from
>>>>
>>>>   ierr = DMPlexGetClosureIndices(dmf, fsection, globalFSection, cell,
>>>> &numFIndices, &findices, NULL);CHKERRQ(ierr);
>>>>
>>>>
>>>>> [0]PETSC ERROR: #1 DMPlexComputeInterpolatorGeneral() line 2508 in
>>>>> petsc/src/dm/impls/plex/plexfem.c
>>>>> [0]PETSC ERROR: #2 DMCreateInterpolation_Plex() line 7688 in
>>>>> petsc/src/dm/impls/plex/plex.c
>>>>> [0]PETSC ERROR: #3 DMCreateInterpolation() line 1139 in
>>>>> petsc/src/dm/interface/dm.c
>>>>> But the DMs look OK, don’t they, cf. below?
>>>>> So I have three simple questions:
>>>>> 1) are all tests at the bottom of ex19.c broken because of PRAgMaTIc
>>>>> or because of DMPlex currently not supporting some operations? (I’m not
>>>>> using PRAgMaTIc to do mesh adaptation, so I was hoping to not run into an
>>>>> error)
>>>>>
>>>>
>>>> I don't think its broken.
>>>>
>>>>
>>>> Oh, OK. Could you help me figure out what’s the problem then, e.g.,
>>>> with a slight (command line) variation of test #6, please?
>>>>
>>>
>>> Sure. I am at SIAM this week, but as soon as I can I will get you the
>>> fix.
>>>
>>>
>>>> $ cd src/dm/impls/plex/examples/tests
>>>> $ git diff ex19.c
>>>> $ make ex19
>>>> $ mpirun ./ex19 -dim 3 -nbrVerEdge 10 -dm_plex_separate_marker 0 -met 0
>>>> -hmin 0.1 -hmax 0.3 -init_dm_view -adapt_dm_view -do_L2 -petscspace_degree
>>>> 1 -petscfe_default_quadrature_order 1 -dm_plex_hash_location
>>>> [0]PETSC ERROR: Nonconforming object sizes
>>>> [0]PETSC ERROR: The section point closure size 0 != dual space
>>>> dimension 4
>>>> […]
>>>> [0]PETSC ERROR: #1 DMProjectLocal_Generic_Plex() line 633 in
>>>> src/dm/impls/plex/plexproject.c
>>>> [0]PETSC ERROR: #2 DMProjectFunctionLocal_Plex() line 771 in
>>>> src/dm/impls/plex/plexproject.c
>>>> [0]PETSC ERROR: #3 DMProjectFunctionLocal() line 7809 in
>>>> src/dm/interface/dm.c
>>>> [0]PETSC ERROR: #4 DMProjectFunction() line 7766 in
>>>> src/dm/interface/dm.c
>>>>
>>>> If I comment the DMProjectFunction() call, I end up with the same error
>>>> as in my first message in DMCreateInterpolation().
>>>>
>>>> 2) is DMCreateInterpolation + MatInterpolate the correct way of
>>>>> transferring one Vec from a DMPlex onto another?
>>>>>
>>>>
>>>> That is the intent.
>>>>
>>>>
>>>>> 3) if yes, by looking at the names of the arguments in
>>>>> DMPlexComputeInterpolatorGeneral, dmc and dmf, could you comment on the
>>>>> performance of this function for unrelated meshes, e.g., if both DMs are
>>>>> “fine” and not one coarse and the other fine (albeit non-nested), for
>>>>> simple P_k spaces.
>>>>>
>>>>
>>>> In general, it is going to be horrible. Here is what it does: locate
>>>> the fine quadrature points in the coarse grid and interpolate to them. This
>>>> quadrature can have huge errors if it falls across multiple cells. This is
>>>> why the nested version works perfectly, and also why Patrick Farrell and
>>>> James Maddison have the Supermesh library, which makes a refinement of the
>>>> mesh until the quadrature is accurate everywhere. That way they guarantee
>>>> that at least the zeroth moment is preserved.
>>>>
>>>>
>>>> Two subquestions if I may:
>>>> 1) are there any plans to have this integrated through an external
>>>> package?
>>>>
>>>
>>> In the absence of a plan, there is a hope. I would really like it to
>>> happen.
>>>
>>>
>>>> 2) if I understand you correctly, you answered about the numerical
>>>> performance of the function. I can live with high interpolation errors if
>>>> both meshes are “far" from each other. I was mostly interested in the
>>>> parallel performance of the function.
>>>>
>>>
>>> Everything is purely local except for point location. Since it has never
>>> really been tested in this mode, I am sure the
>>> scaling can be bad. I believe the default is to extrapolate if the point
>>> is not covered, which makes sense for mostly
>>> matching meshes. There is parallel point location, but it is intended
>>> for a few points where we are sampling the solution,
>>> rather than lots of points everywhere which you would get for
>>> non-matching meshes with different distributions. Could
>>> you say what kind of situation you are trying to optimize for?
>>>
>>
>> Matt, probably clarifying the parallel point location algorithm is
>> helpful.
>>
>> 1/ Does it broadcast all off rank points to every rank?
>> Or
>> 2/ Does it broadcast sub domain bounding boxes  to every rank, and then
>> scatter points to candidate owning ranks based on the bounding boxes
>> containing off rank points?
>>
>> I recall the method (years ago) did  what’s described in (1)
>>
>
> I thought it was 2.
>
> This is one of the things on the list when we scale up the plasmas physics
> code. My reading
> says that a hierarchy of regular divisions is just as efficient for
> location as a structure for
> irregular divisons, like a k-d tree, and we can keep the bottom part of
> the hierarchy everywhere.
> Is that your feeling?
>

Yes.

 (2) is good for general purpose usage. I believe anything better requires
restrictive assumptions which render the interpolation suitable only for
specific use case (eg assuming  an off rank point lives within a nearest or
next nearest neighbor sub domain)



>   Matt
>
>
>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>>
>>>> Thanks,
>>>> Pierre
>>>>
>>>>   Thanks,
>>>>
>>>>     Matt
>>>>
>>>>
>>>>> Thanks in advance for your help,
>>>>> Pierre
>>>>>
>>>>> $ mpirun -n 1 ./ex19 -msh in.msh -init_dm_view ::ascii_info
>>>>> -adapt_dm_view ::ascii_info -mat_view ::ascii_info -do_L2
>>>>> -petscspace_degree 1
>>>>> DM Object: DMinit 1 MPI processes
>>>>>   type: plex
>>>>> DMinit in 3 dimensions:
>>>>>   0-cells: 1331
>>>>>   1-cells: 7930
>>>>>   2-cells: 12600
>>>>>   3-cells: 6000
>>>>> Labels:
>>>>>   depth: 4 strata with value/size (0 (1331), 1 (7930), 2 (12600), 3
>>>>> (6000))
>>>>>   Face Sets: 6 strata with value/size (4 (200), 1 (200), 5 (200), 2
>>>>> (200), 3 (200), 6 (200))
>>>>>   Cell Sets: 1 strata with value/size (0 (6000))
>>>>> DM Object: DMadapt (adapt_) 1 MPI processes
>>>>>   type: plex
>>>>> DMadapt in 3 dimensions:
>>>>>   0-cells: 2905
>>>>>   1-cells: 18888
>>>>>   2-cells: 31368
>>>>>   3-cells: 15384
>>>>> Labels:
>>>>>   depth: 4 strata with value/size (0 (2905), 1 (18888), 2 (31368), 3
>>>>> (15384))
>>>>>   Face Sets: 6 strata with value/size (1 (200), 4 (200), 6 (200), 2
>>>>> (200), 5 (200), 3 (200))
>>>>>   Cell Sets: 1 strata with value/size (0 (15384))
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> 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/>
>>>
>>
>
> --
> 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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