[petsc-users] DMPlex read partitionned Gmsh

[Matthew Knepley]

On Tue, Feb 23, 2021 at 2:37 AM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> wrote:

> Dear all,
>
> I was wondering if there was a plan in motion to implement yet another
> possibility for DMPlexCreateGmshFromFile: read a group of foo_*.msh
> generated from a partition done directly in Gmsh ?
>

What we have implemented now is a system that reads a mesh in parallel from
disk into a naive partition, then repartitions and redistributes.
We have a paper about this strategy: https://arxiv.org/abs/2004.08729 .
Right now it is only implemented in HDF5. This is mainly because:

1) Parallel block reads are easy in HDF5.

2) We use it for checkpointing as well as load, and it is flexible enough
for this

3) Label information can be stored in a scalable way

It is easy to convert from GMsh to HDF5 (it's a few lines of PETSc). The
GMsh format is not ideal for parallelism, and in fact the GMsh reader
was also using MED, which is an HDF5 format. We originally wrote an MED
reader, but the documentation and support for the library were
not up to snuff, so we went with a custom HDF5 format.

  Is this helpful?

     Matt


> Have a great day,
>
> Thibault B.-B.
>


-- 
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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20210223/9f954c42/attachment.html>