[petsc-dev] DMPlex + P_1 FE interpolation
Matthew Knepley
knepley at gmail.com
Mon Feb 10 07:16:53 CST 2020
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?
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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