[petsc-dev] DMPlex overlap redistribution

[Adrian Croucher]

hi Matt,

Thanks for that. I think that is a useful change, even though it doesn't 
actually fix my problem (i.e. my code still gets an error). I think now 
that although the error message I'm getting is similar to the one that 
used to result from just a simple repeated stratification, the 
underlying cause is different.

Looking more closely at the error message, it is saying that the depth 2 
stratum overlaps the depth 1 stratum, e.g.:

[0]PETSC ERROR: New depth 2 range [0,141) overlaps with depth 1 range 
[0,141)

That suggested to me that some of the strata in the re-distributed 
DMPlex are not contiguous. I checked that by looking at the cone and 
support sizes of the DMPlex points inside 
DMPlexStratify_Topological_Private(). On one of the processes they 
looked like this:

p: 0, cone: 7, support: 0
p: 1, cone: 7, support: 0
p: 2, cone: 7, support: 0
p: 3, cone: 6, support: 0
p: 4, cone: 6, support: 0
p: 5, cone: 6, support: 0
p: 6, cone: 2, support: 0
p: 7, cone: 1, support: 0
p: 8, cone: 0, support: 1
p: 9, cone: 0, support: 1
p: 10, cone: 1, support: 2
p: 11, cone: 1, support: 2
p: 12, cone: 1, support: 1
p: 13, cone: 1, support: 1
p: 14, cone: 2, support: 0
p: 15, cone: 2, support: 0
p: 16, cone: 1, support: 0
p: 17, cone: 1, support: 0
p: 18, cone: 0, support: 1
...

So here the cells (support 0) are not contiguous (and neither are the 
other strata) - some of the dual-porosity cells (14 - 17) are getting 
separated from the other cells (0 - 7). So I think that is messing up 
the identification of stratum bounds, because it's right, they do overlap.

Before redistribution, the strata are contiguous and non-overlapping. So 
I think the redistribution is causing the trouble.

When I first add the dual-porosity points to the DM I add them on the 
end of each stratum, after interior points and partition ghost points. 
That used to work, but perhaps something has changed so it doesn't any 
more? Are there any assumptions made about the order of storing interior 
points, partition ghost points and interior ghost points?

Another possibility might be that it's getting confused by the 
dual-porosity faces, edges, and nodes I'm adding which have unusual 
cone/support sizes (e.g. faces with a cone of one edge, which in turn 
have a cone of one node). Again this used to work ok but perhaps 
something has changed so that it doesn't?

- Adrian

On 9/03/24 7:15 am, Matthew Knepley wrote:
> Okay, here are my first steps
>
> 1. I fixed the problem with repeated stratification
>
> knepley/fix-da-periodicity *$:/PETSc3/petsc/petsc-dev$ git diff
> diff --git a/src/dm/impls/plex/plex.c b/src/dm/impls/plex/plex.c
> index 0ffc372ea08..9d27d308538 100644
> --- a/src/dm/impls/plex/plex.c
> +++ b/src/dm/impls/plex/plex.c
> @@ -4439,6 +4439,7 @@ PetscErrorCode DMPlexStratify(DM dm)
>    PetscCall(PetscLogEventBegin(DMPLEX_Stratify, dm, 0, 0, 0));
>
>    // Create depth label
> +  PetscCall(DMRemoveLabel(dm, "depth", NULL));
>    PetscCall(DMCreateLabel(dm, "depth"));
>
>    PetscCall(DMPlexGetDepthLabel(dm, &label));
>
> I put it in an MR: 
> https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7347__;!!G_uCfscf7eWS!dVlGf4V_Zaea88ALYpHklcdDMiJGdkorm-03BoaulIvilbP2X0WO_5rF-Jy6qDOlDCrQpc3EWXV_i5U0pq4jpDMxtYknk40$  
> <https://urldefense.us/v3/__https://gitlab.com/petsc/petsc/-/merge_requests/7347__;!!G_uCfscf7eWS!dVlGf4V_Zaea88ALYpHklcdDMiJGdkorm-03BoaulIvilbP2X0WO_5rF-Jy6qDOlDCrQpc3EWXV_i5U0pq4jpDMxtYknk40$ >
>
> 2. I wrote a small program to load the mesh, and then restratify it. 
> It is attached.
>
> 3. I ran stratification on this mesh, but I did not get an error:
>
-- 
Dr Adrian Croucher
Senior Research Fellow
Department of Engineering Science
Waipapa Taumata Rau / University of Auckland, New Zealand
email:a.croucher at auckland.ac.nz
tel: +64 (0)9 923 4611
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