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

Tue Apr 26 18:27:23 CDT 2022

Thanks for the answers. One last question related to designing my code.
What I want to do is to build a finite-volume code discretized on "median
dual" unstructured mesh. So basically it will use a vertex-centered
discretization scheme by looping over "median dual faces", which is not
physically existing in my mesh file.

I can acheive this by allocating some vectors to compute required
geometrical metrics (e.g., face normal vectors, face area, etc. that
required to integrate over median dual control volume) as I did before even
without PETSc. However, I think this definitely cannot be an optimal way,
and I believe there should be much larger benefit that can be obtained, if
I well design my DMPlex's data structure (e.g., PetscSection).
Is there any example with this median dual control volume case? or Any
guideline will be helpful.
I was thinking to borrow some functions designed for finite element.

Thanks,
Mike

2022년 4월 26일 (화) 오후 5:40, Matthew Knepley <knepley at gmail.com>님이 작성:

> On Tue, Apr 26, 2022 at 4:48 PM Mike Michell <mi.mike1021 at gmail.com>
> wrote:
>
>> 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.
>>
>
> Here is the explanation. The default distribution comes from
> DMSetFromOptions(), which I am guessing was not called after
> DMPlexCreateGmshFromFile().
>
>
>> - 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?
>>
>
> VTK is generally for debugging, but it should work. I will take a look.
>
> VTU and HDF5 are the preferred formats.
>
>   Thanks,
>
>      Matt
>
>
>> 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/>
>>>
>>
>
> --
> 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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