[petsc-users] Inquiry regarding DMAdaptLabel function

[Matthew Knepley]

On Mon, Feb 27, 2023 at 10:26 AM Pierre Jolivet <pierre at joliv.et> wrote:

> On 27 Feb 2023, at 4:16 PM, Matthew Knepley <knepley at gmail.com> wrote:
>
> On Mon, Feb 27, 2023 at 10:13 AM Pierre Jolivet <pierre at joliv.et> wrote:
>
>> On 27 Feb 2023, at 3:59 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Mon, Feb 27, 2023 at 9:53 AM Zongze Yang <yangzongze at gmail.com> wrote:
>>
>>> Hi, Matt,
>>>
>>> I tested coarsening a mesh by using ParMMg without firedrake, and found
>>> some issues:
>>>  see the code and results here:
>>> https://gitlab.com/petsc/petsc/-/issues/1331
>>>
>>> Could you have a look and give some comments or suggestions?
>>>
>>
>> I replied on the issue. More generally, the adaptive refinement software
>> has not seen wide use
>>
>>
>> :)
>> Matt probably meant “the _DMPlex interface_ to adaptive refinement
>> software has not seen wide use”, Mmg has been rather widely used for 10+
>> years (here is a 13-year old presentation
>> https://www.ljll.math.upmc.fr/hecht/ftp/ff++days/2010/exposes/Morice-MeshMetric.pdf
>> ).
>>
>
> The interface is certainly new, but even ParMMG is only from Nov 2016,
> which is very new if you are an old person :)
>
>
> Indeed. In fact, I do believe we should add a DMPlex mechanism to
> centralize (redistribute on a single process) a DMPlex and to call Mmg
> instead of ParMmg.
> It would certainly not be scalable for large meshes but:
> 1) there is no need for ParMmg on small-/medium-scale meshes
> 2) Mmg is more robust than ParMmg at this point in time
> 3) Mmg has more feature than ParMmg at this point in time, e.g., implicit
> remeshing using a level-set
> 4) there is more industry money funnelled into Mmg than into ParMmg
> I think the mechanism I mentioned initially was in the TODO list of the
> Firedrake people (or yours?), maybe it’s already done, but in any case it’s
> not hooked in the Mmg adaptor code, though it should (erroring out in the
> case where the communicator is of size greater than one would then not
> happen anymore).
>

Yes, we used to do the same thing with partitioners. We can use
DMPlexGather().

I thought MMG only did 2D and ParMMG only did 3D, but this must be wrong
now. Can MMG do both?

  Thanks,

     Matt


> Thanks,
> Pierre
>
>   Thanks,
>
>     Matt
>
>
>> Thanks,
>> Pierre
>>
>> , and I expect
>> more of these kinds of bugs until more people use it.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Best wishes,
>>> Zongze
>>>
>>>
>>> On Mon, 27 Feb 2023 at 20:19, Matthew Knepley <knepley at gmail.com> wrote:
>>>
>>>> On Sat, Feb 18, 2023 at 6:41 AM Zongze Yang <yangzongze at gmail.com>
>>>> wrote:
>>>>
>>>>> Another question on mesh coarsening is about `DMCoarsen` which will
>>>>> fail when running in parallel.
>>>>>
>>>>> I generate a mesh in Firedrake, and then create function space and
>>>>> functions, after that, I get the dmplex and coarsen it.
>>>>> When running in serials, I get the mesh coarsened correctly. But it
>>>>> failed with errors in ParMMG when running parallel.
>>>>>
>>>>> However, If I did not create function space and functions on the
>>>>> original mesh, everything works fine too.
>>>>>
>>>>> The code and the error logs are attached.
>>>>>
>>>>
>>>> I believe the problem is that Firedrake and PETSc currently have
>>>> incompatible coordinate spaces. We are working
>>>> to fix this, and I expect it to work by this summer.
>>>>
>>>>   Thanks,
>>>>
>>>>      Matt
>>>>
>>>>
>>>>> Thank you for your time and attention。
>>>>>
>>>>> Best wishes,
>>>>> Zongze
>>>>>
>>>>>
>>>>> On Sat, 18 Feb 2023 at 15:24, Zongze Yang <yangzongze at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear PETSc Group,
>>>>>>
>>>>>> I am writing to inquire about the function DMAdaptLabel in PETSc.
>>>>>> I am trying to use it coarse a mesh, but the resulting mesh is
>>>>>> refined.
>>>>>>
>>>>>> In the following code, all of the `adpat` label values were set to 2
>>>>>> (DM_ADAPT_COARSEN).
>>>>>> There must be something wrong. Could you give some suggestions?
>>>>>>
>>>>>> ```python
>>>>>> from firedrake import *
>>>>>> from firedrake.petsc import PETSc
>>>>>>
>>>>>> def mark_all_cells(mesh):
>>>>>>     plex = mesh.topology_dm
>>>>>>     with PETSc.Log.Event("ADD_ADAPT_LABEL"):
>>>>>>         plex.createLabel('adapt')
>>>>>>         cs, ce = plex.getHeightStratum(0)
>>>>>>         for i in range(cs, ce):
>>>>>>             plex.setLabelValue('adapt', i, 2)
>>>>>>
>>>>>>     return plex
>>>>>>
>>>>>> mesh = RectangleMesh(10, 10, 1, 1)
>>>>>>
>>>>>> x = SpatialCoordinate(mesh)
>>>>>> V = FunctionSpace(mesh, 'CG', 1)
>>>>>> f = Function(V).interpolate(10 + 10*sin(x[0]))
>>>>>> triplot(mesh)
>>>>>>
>>>>>> plex = mark_all_cells(mesh)
>>>>>> new_plex = plex.adaptLabel('adapt')
>>>>>> mesh = Mesh(new_plex)
>>>>>> triplot(mesh)
>>>>>> ```
>>>>>>
>>>>>> Thank you very much for your time.
>>>>>>
>>>>>> Best wishes,
>>>>>> Zongze
>>>>>>
>>>>>
>>>>
>>>> --
>>>> 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/>
>>
>>
>>
>
> --
> 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/>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20230227/1523e7a1/attachment-0001.html>