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.crouc...@auckland.ac.nz
tel: +64 (0)9 923 4611
