[petsc-dev] DMPLEX with VecGhost

[Barry Smith]

  Jed, Matt, Junchao, Lawrence,

   I need some expert advice with this https://gitlab.com/petsc/petsc/-/merge_requests/4542 <https://gitlab.com/petsc/petsc/-/merge_requests/4542>. I was able to translate the cython to PETSc C for moving the ghost points to the end in the local section.

 But I don't know 

   * the best way to generate the ghosts list needed by VecCreateGhost()?   or should I not use VecCreateGhost() 

   * but somehow instead use the existing DMGetSectionSF() to be able to PetscSF between the owned part and the ghosted part of a hybrid vector (that is, don't use VecCreateGhost() but create an equivalent somehow using the sf that already exists?)

   Thanks

  Barry




> On Oct 28, 2021, at 6:37 PM, Jed Brown <jed at jedbrown.org> wrote:
> 
> Yeah, I think that's about true. Should the interface for this be to set a flag before creating fields (and perhaps that flag can become true by default at some point)?
> 
> Barry Smith <bsmith at petsc.dev> writes:
> 
>>  Seems like it should be possible to simply "rewrite" the cython code into PETSc C.
>> 
>>  Barry
>> 
>> 
>>> On Oct 28, 2021, at 12:36 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>> 
>>> I agree it is.
>>> 
>>>  Matt
>>> 
>>> On Thu, Oct 28, 2021 at 11:53 AM Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>>> 
>>>  Thanks, sounds like something DMPLEX should be automatically optionally doing directly.
>>> 
>>>> On Oct 28, 2021, at 10:58 AM, Lawrence Mitchell <wence at gmx.li <mailto:wence at gmx.li>> wrote:
>>>> 
>>>> Hi Barry et al.,
>>>> 
>>>>> On 28 Oct 2021, at 15:37, Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>>>>> 
>>>>> 
>>>>> 
>>>>>> On Oct 28, 2021, at 10:31 AM, Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>> wrote:
>>>>>> 
>>>>>> On Thu, Oct 28, 2021 at 9:37 AM Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>> wrote:
>>>>>> 
>>>>>> Matt,
>>>>>> 
>>>>>>   How difficult would it be to rework DMPLEX to allow the use of VecGhost? We have performance problems with GPUs with simple DMNETWORK models because the code spends more time uselessly copying the local part of the vector to another vector in global to local and local to global;  more than 1/2 the time of the total simulation.
>>>>>> 
>>>>>> Firedrake already does this because they "vec ghost" their vectors by default. Here is what you need:
>>>>>> 
>>>>>> When you create the PetscSection, by default it orders the unknowns according to the default point numbering. This
>>>>>> is what causes the ghost unknowns to be mixed in with the local unknowns. However, PetscSection allows you to set
>>>>>> a point permutation
>>>>>> 
>>>>>>   https://petsc.org/main/docs/manualpages/PetscSection/PetscSectionSetPermutation.html <https://petsc.org/main/docs/manualpages/PetscSection/PetscSectionSetPermutation.html>
>>>>>> 
>>>>>> This determines the order of dogs by iterating through points in this permutation, and you can put all shared points at the end.
>>>>> 
>>>>> How do I know what are shared points to put at the end? Couldn't DMPLEX do this automatically with an option? Where is the Firedrake code that does this with DMPLEX so I can see it?
>>>> 
>>>> The DM's "point sf" indicates shared points. To label them, do something like:
>>>> 
>>>> DMCreateLabel(dm, "ghost_points");
>>>> DMGetPointSF(dm, &pointsf);
>>>> PetscSFGetGraph(pointsf, NULL, &nleaves, &ilocal, NULL);
>>>> for (PetscInt p = 0; p < nleaves; p++) {
>>>>  DMSetLabelValue(dm, "ghost_points", p, 1);
>>>> }
>>>> 
>>>> Then you do something like (this is more pseudo-codey):
>>>> 
>>>> PetscInt *permutation;
>>>> DMPlexGetChart(dm, &pStart, &pEnd);
>>>> PetscMalloc1(pEnd - pStart, &permutation);
>>>> PetscInt offsets[2] = {0, pEnd - pStart - nleaves};
>>>> DMGetLabel(dm, &ghosts);
>>>> DMLabelCreateIndex(ghosts, pStart, pEnd);
>>>> for (PetscInt p = pStart, p < pEnd; p++) {
>>>>  DMLabelHasPoint(ghosts, p, &has);
>>>>  if (has) {
>>>>     // this point is ghost point
>>>>     permutation[offsets[1]++] = p;
>>>>  } else {
>>>>     permutation[offsets[0]++] = p;
>>>>  }
>>>> }
>>>> DMLabelDestroyIndex(ghosts, pStart, pEnd);
>>>> ISCreateGeneral(..., permutation, &isperm);
>>>> 
>>>> // Now whenever your do PetscSectionCreate, do
>>>> PetscSectionSetPermutation(..., isperm);
>>>> 
>>>> And now ghost point dofs will appear after local ones.
>>>> 
>>>> Note that this is probably more complicated for multi-field setups, depending whether you are point major or field major.
>>>> 
>>>> You can see what we actually do (if you like reading Cython) here: https://github.com/firedrakeproject/firedrake/blob/master/firedrake/cython/dmcommon.pyx#L1734 <https://github.com/firedrakeproject/firedrake/blob/master/firedrake/cython/dmcommon.pyx#L1734>
>>>> 
>>>> It's more complicated because here we are doing some additional things:
>>>> 
>>>> 1. We compute an RCM-order traversal for cells with DMPlexGetOrdering;
>>>> 2. Rather than ordering all plex points in the permutation, we walk the cells in the RCM order and then greedily number points in the transitive closure (so that in a section cell and vertex dofs from the same cell will be "close" to each other in the final Vec).
>>>> 
>>>> Thanks,
>>>> 
>>>> Lawrence
>>> 
>>> 
>>> 
>>> -- 
>>> 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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