[petsc-users] DMPlex Parallel Output and DMPlexCreateSection Crashes when DMPlexCreateGmshFromFile used

[Mike Michell]

Below two interesting things are found:
- If DMPlexCreateGmshFromFile() is used, DMPlexDistribute() is not done by
default. I should call DMPlexDistribute() to distribute DMPlex over the
procs.
- If {DMCreate(), DMSetType(), DMSetFromOptions()} in serially used with
"-dm_plex_filename ./new.msh" option in command line, DMPlexDistribute() is
done by default even though DMPlex object is created by reading the same
.msh file.


Thanks for the modification to the example ex1f90.F90, now it works with 2
procs.
But still, if I print my output to "sol.vtk", the file has only a part of
whole mesh. However, the file is okay if I print to "sol.vtu".
>From "sol.vtu" I can see the entire field with rank. Is using .vtu format
preferred by petsc?

2022년 4월 26일 (화) 오후 2:26, Matthew Knepley <knepley at gmail.com>님이 작성:

> On Tue, Apr 26, 2022 at 9:33 AM Mike Michell <mi.mike1021 at gmail.com>
> wrote:
>
>> Thank you for the answers.
>> For the first question, basically, I cannot
>> run "/dm/impls/plex/ex1f90.F90" example with more than 1 proc. I removed
>> DMPlexDistribute() following your comment and what I tried is:
>>
>> - no modification to ex1f90.F90 (as it is)
>> - make "ex1f90"
>> - mpirun -np 2 ./ex1f90
>>
>> It gives me "Bad termination of one of ..." for Rank 1. The code runs
>> okay with "mpirun -np 1 ./ex1f90".
>>
>
> You are correct. It evidently never worked in parallel, since those checks
> will only work in serial.
> I have fixed the code, and added a parallel test. I have attached the new
> file, but it is also in this MR:
>
>   https://gitlab.com/petsc/petsc/-/merge_requests/5173
>
>   Thanks,
>
>      Matt
>
>
>> Thanks,
>> Mike
>>
>> 2022년 4월 26일 (화) 오전 3:56, Matthew Knepley <knepley at gmail.com>님이 작성:
>>
>>> On Mon, Apr 25, 2022 at 9:41 PM Mike Michell <mi.mike1021 at gmail.com>
>>> wrote:
>>>
>>>> Dear PETSc developer team,
>>>>
>>>> I'm trying to learn DMPlex to build a parallel finite volume code in 2D
>>>> & 3D. More specifically, I want to read a grid from .msh file by Gmsh.
>>>> For practice, I modified /dm/impls/plex/ex1f90.F90 case to read &
>>>> distribute my sample 2D grid, which is attached. I have two questions as
>>>> below:
>>>>
>>>> (1) First, if I do not use my grid, but use the default box grid built
>>>> by ex1f90.F90 and if I try "DMPlexDistribute" over mpi processors, the
>>>> output file (sol.vtk) has only some portion of the entire mesh. How can I
>>>> print out the entire thing into a single file? Is there any example for
>>>> parallel output? (Related files attached to "/Question_1/") Paraview gives
>>>> me some error messages about data size mismatching.
>>>>
>>>
>>> For the last release, we made parallel distribution the default. Thus,
>>> you do not need to call DMPlexDIstribute() explicitly here. Taking it out,
>>> I can run your example.
>>>
>>>
>>>> (2) If I create DMPlex object through "DMPlexCreateGmshFromFile",
>>>> "DMPlexCreateSection" part is crashed. I do not understand why my example
>>>> code does not work, because the only change was switching from "DMCreate"
>>>> to "DMPlexCreateGmshFromFile" and providing "new.msh" file. Without the
>>>> PetscSection object, the code works fine. Any comments about this? (Related
>>>> files attached to "/Question_2/")
>>>>
>>>
>>> If I remove DMPlexDistribute() from this code, it is clear that the
>>> problem is with the "marker" label. We do not create this by default from
>>> GMsh since we assume people have defined their own labels. You can pass
>>>
>>>   -dm_plex_gmsh_use_marker
>>>
>>> to your code. WHen I do this, you example runs for me.
>>>
>>>   Thanks,
>>>
>>>     Matt
>>>
>>>
>>>> Thanks,
>>>> Mike
>>>>
>>>
>>>
>>> --
>>> 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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