[petsc-dev] Vertex assignment in DMPlexDistribute

[Matthew Knepley]

On Mon, Nov 18, 2013 at 9:47 AM, Matthew Knepley <knepley at gmail.com> wrote:

> 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().
>>
>
Your fix is now merged to next:


https://bitbucket.org/petsc/petsc/branch/knepley/fix-plex-partition-overlap

    Matt


> 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
>



-- 
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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