[petsc-dev] Natural numbering for unstructured meshes

Blaise A Bourdin bourdin at lsu.edu
Mon Feb 17 18:34:49 CST 2014

On Feb 17, 2014, at 6:21 PM, Jed Brown <jed at jedbrown.org> wrote:

> Matthew Knepley <knepley at gmail.com> writes:
>> On Mon, Feb 17, 2014 at 5:14 PM, Jed Brown <jed at jedbrown.org> wrote:
>>> Andrés Alessandro León Baldelli <a.leon.baldelli at gmail.com> writes:
>>>> Hi all,
>>>> I am working with Blaise Bourdin on implementing a concept of "natural
>>> numbering" for unstructured meshes using DMplex.
>>>> Such natural numbering can be, e.g., that of the mesh prior to parallel
>>> distribution.
>>>> I have a working example in which I compute a field on the distributed
>>> DM and I scatter it back to the serial DM on rank0 but I would like to
>>> create a more general interface. To this regard I ask your advice:
>>>> 1) Is it reasonable to add an SF within the DM typedef for this "natural
>>> to global" scatter?
>>> Surely you don't want the (necessarily non-scalable) serial DM to be a
>>> necessary part of this interface?  What do you want to do with this
>>> natural numbering?  Just write output files?
>> Jed, No, no, no. This is not an SF for a serial DM.
> I was responding to the question above.  Yes, we need a genuine parallel
> reader (naive partition) and a way to write back in that ordering.  But
> my question remains: do you want to do something other than IO with that
> "natural" ordering?

At this point, no. We want to do I/O and respect the ordering of the data on the disk. 
Note that this “natural” ordering may not be all on cpu with rank 0. One could easily imagine reading a mesh partitioned on p processors, then repartition it on n tasks.

> Note that in the natural ordering, you likely have elements for which
> you own zero of the vertices, and vice-versa, so it would be _really_
> bad to compute on it.

Let’s not make any assumption on what the natural ordering is.
Another application that comes to my mind would be to do load balancing for iterative coupling of a pde formulated on a domain and on on its boundary.


Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612, Fax  +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin

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