[petsc-dev] Cell overlap in DMPlexDistribute

Michael Lange michael.lange at imperial.ac.uk
Mon Feb 3 05:32:06 CST 2014

Hi Matt,

On 31/01/14 05:11, Matthew Knepley wrote:
> On Tue, Jan 28, 2014 at 8:57 AM, Michael Lange 
> <michael.lange at imperial.ac.uk <mailto:michael.lange at imperial.ac.uk>> 
> wrote:
>     Hi,
>     I noticed that the cell overlap created during DMPlexDistribute
>     does not include cells that only share a vertex but no edge with
>     an owned cell. This causes problems when performing local assembly
>     (MAT_IGNORE_OFF_PROC_ENTRIES) based on information from the plex,
>     because one contribution to the shared vertex is missing.
>     As an example consider the 2x2 square with 8 cells (attached).
>     When partitioned across two ranks with overlap=1 each rank owns 4
>     cells and in the current version knows about 2 halo cells, giving
>     a total of 6 cells. The central vertex, however, touches 3 owned
>     and 3 non-owned cells, one of which doesn't share an edge with any
>     owned cells. So, in order to correctly assemble the central vertex
>     locally, the rank owning it needs to know about 7 cells in total.
>     I have attached a patch that fixes this problem by going over the
>     inverse closure of all vertices associated with a given cell
>     instead of using the provided edge graph. Please tell me what you
>     think and whether there might be an easier way to fix this.
> This is true, but unfortunately not what everyone wants. FVM people 
> want just what is there now. This
> same choice comes up in preallocation. There I have put in the "center 
> dimension" which says what
> kind of point do you use for the center, vertex or face? I guess we 
> need that here as well.
Yes, I think the center dimension is exactly what we need here, because 
my proposed fix is to switch from using star(cone(p)) to 
star(closure(p)). So, do you want to make the center dimension a general 
Plex attribute and move the Set/Get functions to plex.c? If so, what 
would be the default? In that case a DMPlexGetAdjacentPoints(dm, p) 
function might also be helpful if this is used in several places? I'm 
happy to provide a pull request, just tell me how you want this to be 

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