[petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

[Matthew Knepley]

On Mon, Mar 22, 2021 at 6:22 AM Nicolas Barral <
nicolas.barral at math.u-bordeaux.fr> wrote:

> On 21/03/2021 21:29, Matthew Knepley wrote:
> > On Sat, Mar 20, 2021 at 10:07 AM Nicolas Barral
> > <nicolas.barral at math.u-bordeaux.fr
> > <mailto:nicolas.barral at math.u-bordeaux.fr>> wrote:
> >
> >     Hi all,
> >
> >     I'm building a plex from elements arrays using
> >     DMPlexCreateFromCellListParallelPetsc. Once the plex is built, I
> >     need to
> >     set up boundary labels. I have an array of faces containing a series
> of
> >     3 vertex local indices. To rebuild boundary labels, I need to loop
> over
> >     the array and get the join of 3 consecutive points to find the
> >     corresponding face point in the DAG.
> >
> >
> > This is very common. We should have a built-in thing that does this.
> >
> Ordering apart, it's not very complicated once you figure out "join" is
> the right operation to use. We need more doc on graph layout and
> operations in DMPlex, I think I'm going to make pictures when I'm done
> with that code because I waste too much time every time. Is there a
> starting point you like ?
>

I think the discussion in

@article{LangeMitchellKnepleyGorman2015,
  title     = {Efficient mesh management in {Firedrake} using
{PETSc-DMPlex}},
  author    = {Michael Lange and Lawrence Mitchell and Matthew G. Knepley
and Gerard J. Gorman},
  journal   = {SIAM Journal on Scientific Computing},
  volume    = {38},
  number    = {5},
  pages     = {S143--S155},
  eprint    = {http://arxiv.org/abs/1506.07749},
  doi       = {10.1137/15M1026092},
  year      = {2016}
}

is pretty good.


> >     Problem, vertices get reordered by
> >     DMPlexCreateFromCellListParallelPetsc
> >     so that locally owned vertices are before remote ones, so local
> indices
> >     are changed and the indices in the face array are not good anymore.
> >
> >
> > This is not exactly what happens. I will talk through the algorithm so
> > that maybe we can find a good
> > interface. I can probably write the code quickly:
> >
> > 1) We take in cells[numCells, numCorners], which is a list of all the
> > vertices in each cell
> >
> >       The vertex numbers do not have to be a contiguous set. You can
> > have any integers you want.
> >
> > 2) We create a sorted list of the unique vertex numbers on each process.
> > The new local vertex numbers
> >       are the locations in this list.
> >
>
> Ok It took me re-writing this email a couple times but I think I
> understand. I was too focused on local/global indices. But if I get this
> right, you still make an assumption: that the numVertices*dim
> coordinates passed in vertexCoords are the coordinates of the
> numvertices first vertices in the sorted list. Is that true ?
>

No. It can be arbitrary. That is why we make the vertexSF, so we can map
those coordinates back to the right processes.


> > Here is my proposed interface. We preserve this list of unique vertices,
> > just as we preserve the vertexSF.
> > Then after DMPlexCreateFromCellListParallelPetsc(), can
> > DMPlexInterpolate(), you could call
> >
> >    DMPlexBuildFaceLabelsFromCellList(dm, numFaces, faces, labelName,
> > labelValues)
> >
> > Would that work for you? I think I could do that in a couple of hours.
> >
>
> So that function would be very helpful. But is it as simple as you're
> thinking ? The sorted list gives local index -> unique identifier, but

what we need is the other way round, isn't it ?
>

You get the other way using search.

  Thanks,

     Matt


> Once I understand better, I can have a first draft in my plexadapt code
> and we pull it out later.
>
> Thanks
>
> --
> Nicolas
>
>
> >    Thanks,
> >
> >       Matt
> >
> >     Is there a way to track this renumbering ? For owned vertices, I can
> >     find the local index from the global one (so do old local index ->
> >     global index -> new local index). For the remote ones, I'm not sure.
> I
> >     can hash global indices, but is there a more idiomatic way ?
> >
> >     Thanks,
> >
> >     --
> >     Nicolas
> >
> >
> >
> > --
> > 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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