[petsc-users] Using parmetis from petsc

[Matthew Knepley]

On Wed, Feb 10, 2021 at 10:00 AM Edoardo alinovi <edoardo.alinovi at gmail.com>
wrote:

> Thanks Matthew,
>
> Probably in my case is a good idea to use parmetis directly as i just need
> the cell distribution in pre-procrssing. Thanks for the clarification.
>
> On an affine side, it's a while i am interrogating my self about a thing.
> Let's say i have my cell distribution accross processors from parmetis.
> Since petsc needs to have the unknows from 1 to N0 hosted by rank 0,
> N0+1:N2 hosted by rank 2 and so on, what i am doing is relabelling local
> cells in order to meet this requirement . Is that right? I am wondering if
> such a way of things is leading to a suboptimal matrix bandwith. What do
> you think about this?
>

I do not understand. If parmetis gives you a partition, you would have to
move the data to match the new partition.

  Thanks,

    Matt


> Many thanks,
>
> Edoardo
>
> On Wed, 10 Feb 2021, 13:12 Matthew Knepley, <knepley at gmail.com> wrote:
>
>> On Wed, Feb 10, 2021 at 4:07 AM Edoardo alinovi <
>> edoardo.alinovi at gmail.com> wrote:
>>
>>> Hello PETSc friends,
>>>
>>> I am working on a code to partition a mesh in parallel and I am looking
>>> at parmetis. As far as I know petsc is interfaced with metis and parmetis
>>> and I have seen people using it within dmplex. Now, I am not using dmplex,
>>> but  I have petsc compiled along with my code for the linear system part.
>>> I am wondering if there is a way to load up a mesh file in the parmetis
>>> format and use petsc to get the elements partitioning only in output. Is
>>> that possible?
>>>
>>
>> ParMetis does not really have a mesh format. It partitions distributed
>> graphs. Most people want to partition cells in their mesh, and
>> then ParMetis would want the graph for cell connectivity. This is not
>> usually what people store, so typically there is a conversion process
>> here. If you want to use PETSc for partitioning, and not use DMPlex, the
>> easiest way to do it is to put your cell connectivity in a Mat,
>> storing the adjacency graph for cells. Then use MatPartitioning.
>>
>>  Thanks,
>>
>>      Matt
>>
>>
>>> Thank you for the help,
>>>
>>> Edoardo
>>>
>> --
>> 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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