[petsc-dev] Vertex assignment in DMPlexDistribute

[Matthew Knepley]

On Mon, Nov 18, 2013 at 3:24 AM, Michael Lange <michael.lange at imperial.ac.uk
> wrote:

>  Hi Matt,
>
> I think there is a misunderstanding here. I am referring to the case where
> DMPlexDistribute() is run with overlap=1 (which is not the case in SNES
> ex12) and vertices in the overlap/halo region are assigned to the wrong
> rank. This can lead to a case where a proc may own a vertex that is not in
> its original (non-overlapping) partition, although the attached cell is not
> owned and will be marked as "ghost" by DMPlexConstructGhostCells().
>
> To illustrate this, I have attached an example consisting of a unit square
> with 3 faces in each dimension and a section with only vertex dofs. If run
> with two ranks, rank 1 will own all its vertices (13 roots), whereas rank 0
> only owns vertices not in the overlap/halo of rank 1 (3 roots). My
> understanding is that, since the original partition splits the square along
> its diagonal, the vertex distribution should be 10 to 6 with the 4 diagonal
> vertices assigned to rank 1 and all other vertices assigned according to
> the original partition. Is this correct, or am I missing something here?
>

I have simplified the example so that I can easily do things in my head.
Now we just have 2 faces per side. Here is the run with overlap = 0:

next *$:/PETSc3/petsc/petsc-dev$
/PETSc3/petsc/petsc-dev/arch-c-exodus-next/bin/mpiexec -host localhost -n 2
/PETSc3/petsc/petsc-dev/arch-c-exodus-next/lib/plex_overlap-obj/plex_overlap
-dm_view -overlap 0
Parallel Mesh in 2 dimensions:
  0-cells: 6 6
  1-cells: 9 9
  2-cells: 4 4
Labels:
  depth: 3 strata of sizes (6, 9, 4)
  exterior_facets: 1 strata of sizes (4)
  marker: 2 strata of sizes (9, 3)
PetscSF Object: 2 MPI processes
  type: basic
    sort=rank-order
  [0] Number of roots=19, leaves=5, remote ranks=1
  [0] 4 <- (1,6)
  [0] 5 <- (1,8)
  [0] 7 <- (1,9)
  [0] 10 <- (1,13)
  [0] 11 <- (1,17)
  [1] Number of roots=19, leaves=0, remote ranks=0

Each partition gets 4 cells and 6 vertices since it is split along the
diagonal. The overlap
region contains the 3 vertices and 2 faces that lie on the diagonal, and
they are all owned by proc 1.
Now if we run with an overlap of 1:

next *$:/PETSc3/petsc/petsc-dev$
/PETSc3/petsc/petsc-dev/arch-c-exodus-next/bin/mpiexec -host localhost -n 2
/PETSc3/petsc/petsc-dev/arch-c-exodus-next/lib/plex_overlap-obj/plex_overlap
-dm_view -overlap 1
Parallel Mesh in 2 dimensions:
  0-cells: 8 8
  1-cells: 13 13
  2-cells: 6 6
Labels:
  depth: 3 strata of sizes (8, 13, 6)
  exterior_facets: 1 strata of sizes (6)
  marker: 2 strata of sizes (13, 5)
PetscSF Object: 2 MPI processes
  type: basic
    sort=rank-order
  [0] Number of roots=27, leaves=19, remote ranks=1
  [0] 0 <- (1,1)
  [0] 2 <- (1,4)
  [0] 6 <- (1,7)
  [0] 7 <- (1,8)
  [0] 8 <- (1,9)
  [0] 9 <- (1,10)
  [0] 10 <- (1,11)
  [0] 11 <- (1,12)
  [0] 12 <- (1,13)
  [0] 14 <- (1,17)
  [0] 15 <- (1,18)
  [0] 16 <- (1,19)
  [0] 17 <- (1,20)
  [0] 18 <- (1,21)
  [0] 19 <- (1,22)
  [0] 20 <- (1,23)
  [0] 21 <- (1,24)
  [0] 25 <- (1,25)
  [0] 26 <- (1,26)
  [1] Number of roots=27, leaves=2, remote ranks=1
  [1] 3 <- (0,1)
  [1] 5 <- (0,5)

Each process gets 2 more cells (those who faces lie on the diagonal), 2
more vertices and 4 more edges. This is correct. The
two overlap cells are ghost for proc 1, but the 4 edges and 2 vertices are
owned. So you are correct, I need to mark all those
overlap points as "unownable" by the original process.

  Thanks for finding this,

      Matt


> Many thanks for all your help
> Michael
>
> On 16/11/13 13:54, Matthew Knepley wrote:
>
>  On Sat, Nov 16, 2013 at 7:22 AM, Michael Lange <
> michael.lange at imperial.ac.uk> wrote:
>
>> Hi,
>>
>> I notice that, when creating the point SF for the parallel partition in
>> DMPlexDistribute, cells are assigned to procs according to the original
>> partition but vertices aren't. Was this done by design or is this a bug?
>>
>
>  If this were true, there would be no communication for the P1 test of
> SNES ex12. Here is running it with
> -interpolate 1 and -dm_view ::ascii_info_detail
>
>  PetscSF Object: 2 MPI processes
>   type: basic
>     sort=rank-order
>   [0] Number of roots=19, leaves=5, remote ranks=1
>   [0] 4 <- (1,6)
>   [0] 5 <- (1,8)
>    [0] 7 <- (1,9)
>   [0] 10 <- (1,13)
>   [0] 11 <- (1,17)
>   [1] Number of roots=19, leaves=0, remote ranks=0
>   [0] Roots referenced by my leaves, by rank
>   [0] 1: 5 edges
>   [0]    4 <- 6
>   [0]    5 <- 8
>   [0]    7 <- 9
>   [0]    10 <- 13
>   [0]    11 <- 17
>   [1] Roots referenced by my leaves, by rank
>
>  So there are 3 vertices and 2 edges in the point SF.
>
>     Matt
>
>
>> In case it is a bug, I have attached a patch that fixes this by using the
>> closure of the original partition instead.
>>
>> Thanks and kind regards
>> Michael
>>
>
>
>
>  --
> 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
>
>
>


-- 
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
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