[petsc-users] DMPlex partition problem

[Matthew Knepley]

On Wed, Apr 8, 2020 at 7:25 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Wed, Apr 8, 2020 at 12:48 AM Danyang Su <danyang.su at gmail.com> wrote:
>
>> Dear All,
>>
>>
>>
>> Hope you are safe and healthy.
>>
>>
>>
>> I have a question regarding pretty different partition results of prism
>> mesh. The partition in PETSc generates much more ghost nodes/cells than the
>> partition in Gmsh, even though both use metis as partitioner. Attached
>> please find the prism mesh in both vtk and exo format, the test code
>> modified based on ex1f90 example. Similar problem are observed for larger
>> dataset with more layers.
>>
>
> I will figure this out by next week.
>

I have run your mesh and do not get those weird partitions. I am running in
master. What are you using? Also, here is an easy way
to do this using a PETSc test:

cd $PETSC_DIR
make -f ./gmakefile test globsearch="dm_impls_plex_tests-ex1_cylinder"
EXTRA_OPTIONS="-filename ${HOME}/Downloads/basin2layer.exo -dm_view
hdf5:$PWD/mesh.h5 -dm_partition_view" NP=5
./lib/petsc/bin/petsc_gen_xdmf.py mesh.h5

and then load mesh.xmf into Paraview. Here is what I see (attached). Is it
possible for you to try the master branch?

  Thanks,

    Matt

  Thanks,
>
>      Matt
>
>
>> For example, in Gmsh, I get partition results using two processors and
>> four processors as shown below, which are pretty reasonable.
>>
>>
>>
>>
>>
>> However, in PETSc, the partition looks a bit weird. Looks like it takes
>> layer partition first and then inside layer. If the number of nodes per
>> layer is very large, this kind of partitioning results into much more ghost
>> nodes/cells.
>>
>>
>>
>> Anybody know how to improve the partitioning in PETSc? I have tried
>> parmetis and chaco. There is no big difference between them.
>>
>>
>>
>>
>>
>>
>>
>> Thanks,
>>
>>
>>
>> Danyang
>>
>>
>>
>
>
> --
> 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/>
>


-- 
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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