[petsc-users] Re-ordering in DMPlexCreateFromCellListParallelPetsc

[Nicolas Barral]

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 ?


>     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 ?


> 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 ?
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/>