[petsc-users] DMPlex overlap

[Nicolas Barral]

@+

-- 
Nicolas

On 31/03/2021 17:51, Matthew Knepley wrote:
> On Sat, Mar 27, 2021 at 9:27 AM Nicolas Barral 
> <nicolas.barral at math.u-bordeaux.fr 
> <mailto:nicolas.barral at math.u-bordeaux.fr>> wrote:
> 
>     Hi all,
> 
>     First, I'm not sure I understand what the overlap parameter in
>     DMPlexDistributeOverlap does. I tried the following: generate a small
>     mesh on 1 rank with DMPlexCreateBoxMesh, then distribute it with
>     DMPlexDistribute. At this point I have two nice partitions, with shared
>     vertices and no overlapping cells. Then I call DMPlexDistributeOverlap
>     with the overlap parameter set to 0 or 1, and get the same resulting
>     plex in both cases. Why is that ?
> 
> 
> The overlap parameter says how many cell adjacencies to go out. You 
> should not get the same
> mesh out. We have lots of examples that use this. If you send your small 
> example, I can probably
> tell you what is happening.
> 

Ok so I do have a small example on that and the DMClone thing I set up 
to understand! I attach it to the email.

For the overlap, you can change the overlap constant at the top of the 
file. With OVERLAP=0 or 1, the distributed overlapping mesh (shown using 
-over_dm_view, it's DMover) are the same, and different from the mesh 
before distributing the overlap (shown using -distrib_dm_view). For 
larger overlap values they're different.

The process is:
1/ create a DM dm on 1 rank
2/ clone dm into dm2
3/ distribute dm
4/ clone dm into dm3
5/ distribute dm overlap

I print all the DMs after each step. dm has a distributed overlap, dm2 
is not distributed, dm3 is distributed but without overlap. Since 
distribute and distributeOverlap create new DMs, I don't seem have a 
problem with the shallow copies.


>     Second, I'm wondering what would be a good way to handle two overlaps
>     and associated local vectors. In my adaptation code, the remeshing
>     library requires a non-overlapping mesh, while the refinement criterion
>     computation is based on hessian computations, which require a layer of
>     overlap. What I can do is clone the dm before distributing the overlap,
>     then manage two independent plex objects with their own local sections
>     etc. and copy/trim local vectors manually. Is there a more automatic
>     way
>     to do this ?
> 
> 
> DMClone() is a shallow copy, so that will not work. You would maintain 
> two different Plexes, overlapping
> and non-overlapping, with their own sections and vecs. Are you sure you 
> need to keep around the non-overlapping one?
> Maybe if I understood what operations you want to work, I could say 
> something more definitive.
> 
I need to be able to pass the non-overlapping mesh to the remesher. I 
can either maintain 2 plexes, or trim the overlapping plex when I create 
the arrays I give to the remesher. I'm not sure which is the best/worst ?

Thanks

-- 
Nicolas


>    Thanks,
> 
>       Matt
> 
>     Thanks
> 
>     -- 
>     Nicolas
> 
> 
> 
> -- 
> 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
> 
> https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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