[petsc-users] [DMCreate from a Gmsh with mixed mesh crash for DMPlex]

Matthew Knepley knepley at gmail.com
Mon Jul 18 07:34:02 CDT 2022 

On Thu, Jul 14, 2022 at 6:33 PM Mike Michell <mi.mike1021 at gmail.com> wrote:

> VTK format itself supports pyramids for sure. But I do not think PETSc
> output part through VTK format does not. Is there any possibility to debug
> this issue?
>

VTK output now works with pyramids in

  https://gitlab.com/petsc/petsc/-/merge_requests/5422

Could you send me a much smaller GMsh that has pyramids and tets or hexes
in it? I would like to put in a test
before we merge this.

  Thanks,

      Matt


> Thanks,
>
>
>> On Wed, Jul 13, 2022 at 4:18 PM Mike Michell <mi.mike1021 at gmail.com>
>> wrote:
>>
>>> Before your pull request merged to main, I copied your change to my
>>> local /src/dm/impls/plex/plexgmsh.c to test pyramids.
>>>
>>> Loading DMPlex with the mesh including pyramids works okay, but printing
>>> out the solution field to .vtk or .vtu format causes a problem with
>>> "Unknown Cell Type Error" from post-processing tools (such as tecplot or
>>> paraview).
>>>
>>> I had a look at /src/dm/impls/plex/plexvtk.c  the function,
>>> DMPlexVTKGetCellType_Internal() seems not explicitly including a cellType
>>> marker for prism and pyramids. Probably, "VTK_WEDGE" is prism with
>>> triangular base, but still, there seems no pyramids marker.
>>>
>>
>> Yes, I am not sure it supports pyramids. Will have to look.
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Thanks,
>>>
>>>
>>>> On Wed, Jul 13, 2022 at 11:18 AM Mike Michell <mi.mike1021 at gmail.com>
>>>> wrote:
>>>>
>>>>> Attached is a mixed mesh file that I am testing. I cannot see any
>>>>> special marker for pyramid cells. Version of gmsh is 4.9.0.
>>>>>
>>>>
>>>> You are correct. Pyramids were disabled. I have activated them here:
>>>>
>>>>   https://gitlab.com/petsc/petsc/-/merge_requests/5422
>>>>
>>>> You mesh runs fine after this for me. I am not sure things like
>>>> geometry will work for pyramids. However, if you find something
>>>> broken, just let me know.
>>>>
>>>>    Thanks,
>>>>
>>>>       Matt
>>>>
>>>>
>>>>> Thanks,
>>>>>
>>>>>>
>>>>>> On Wed, Jul 13, 2022 at 10:41 AM Mike Michell <mi.mike1021 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Thank you for the quick response. Below is the full error message I
>>>>>>> get.
>>>>>>>
>>>>>>>
>>>>>>> [0]PETSC ERROR: --------------------- Error Message
>>>>>>> --------------------------------------------------------------
>>>>>>> [0]PETSC ERROR: Argument out of range
>>>>>>> [0]PETSC ERROR: No face description for cell type unknown
>>>>>>>
>>>>>>
>>>>>> Here is the problem. The pyramid (or some other cell) was classified
>>>>>> as "unknown". First, make sure the Gmsh file is version 4.1.
>>>>>> If that fails, send the Gmsh file and I will try to figure out why
>>>>>> the cell is not coming up as a pyramid.
>>>>>>
>>>>>>   Thanks,
>>>>>>
>>>>>>      Matt
>>>>>>
>>>>>>
>>>>>>> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>>>>>> shooting.
>>>>>>> [0]PETSC ERROR: Petsc Release Version 3.17.0, unknown
>>>>>>> [0]PETSC ERROR: /home/Mike/Workspace/test on a named Mike Wed Jul 13
>>>>>>> 10:38:31 2022
>>>>>>> [0]PETSC ERROR: Configure options
>>>>>>> --prefix=/home/Mike/Library/petsc_partition/install-intel
>>>>>>> PETSC_ARCH=linux-gnu-intel --with-cc=mpiicc --with-cxx=mpiicpc
>>>>>>> --with-fc=mpiifort --download-fblaslapack --download-metis
>>>>>>> --download-parmetis --download-eigen --download-pragmatic --download-hdf5
>>>>>>> --download-triangle --with-debugging=1 COPTFLAGS="-O3 -mtune=native"
>>>>>>> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
>>>>>>> [0]PETSC ERROR: #1 DMPlexGetRawFaces_Internal() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:312
>>>>>>> [0]PETSC ERROR: #2 DMPlexInterpolateFaces_Internal() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:350
>>>>>>> [0]PETSC ERROR: #3 DMPlexInterpolate() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:1327
>>>>>>> [0]PETSC ERROR: #4 DMPlexCreateGmsh() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1634
>>>>>>> [0]PETSC ERROR: #5 DMPlexCreateGmshFromFile() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1418
>>>>>>> [0]PETSC ERROR: #6 DMPlexCreateFromFile() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:4721
>>>>>>> [0]PETSC ERROR: #7 DMPlexCreateFromOptions_Internal() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3212
>>>>>>> [0]PETSC ERROR: #8 DMSetFromOptions_Plex() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3433
>>>>>>> [0]PETSC ERROR: #9 DMSetFromOptions() at
>>>>>>> /home/Mike/Library/petsc_partition/src/dm/interface/dm.c:887
>>>>>>> [0]PETSC ERROR: #10 User provided function() at User file:0
>>>>>>> Abort(63) on node 0 (rank 0 in comm 16): application called
>>>>>>> MPI_Abort(MPI_COMM_SELF, 63) - process 0
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Mike
>>>>>>>
>>>>>>>
>>>>>>>> On Wed, Jul 13, 2022 at 10:30 AM Mike Michell <
>>>>>>>> mi.mike1021 at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi, DMCreate() is used to load/distribute grid built from gmsh,
>>>>>>>>> and the function crashes when a mixed mesh of tetra and pyramids in 3D. It
>>>>>>>>> looks PETSc can handle the cell types of
>>>>>>>>> Tetra/Hexa/Prism/Pyramids/Polygon/Polyhedra in 3D. Thus I am unsure why it
>>>>>>>>> crashes when pyramids included in gmsh file.
>>>>>>>>>
>>>>>>>>> Below functions are used to mesh distribution.
>>>>>>>>> call DMCreate(PETSC_COMM_WORLD, dm_g, ierr);CHKERRA(ierr)
>>>>>>>>> call DMSetType(dm_g, DMPLEX, ierr);CHKERRA(ierr)
>>>>>>>>> call DMSetFromOptions(dm_g, ierr);CHKERRA(ierr)
>>>>>>>>>
>>>>>>>>> Below error messages got from run.
>>>>>>>>>
>>>>>>>>
>>>>>>>> I need the complete error message. This is only the stack. I cannot
>>>>>>>> see the error message, or the version of PETSc you are using.
>>>>>>>>
>>>>>>>> This should work, so I do not immediately know what is wrong.
>>>>>>>>
>>>>>>>>   Thanks,
>>>>>>>>
>>>>>>>>      Matt
>>>>>>>>
>>>>>>>>
>>>>>>>>> [0]PETSC ERROR: #1 DMPlexGetRawFaces_Internal() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:312
>>>>>>>>> [0]PETSC ERROR: #2 DMPlexInterpolateFaces_Internal() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:350
>>>>>>>>> [0]PETSC ERROR: #3 DMPlexInterpolate() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexinterpolate.c:1327
>>>>>>>>> [0]PETSC ERROR: #4 DMPlexCreateGmsh() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1634
>>>>>>>>> [0]PETSC ERROR: #5 DMPlexCreateGmshFromFile() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexgmsh.c:1418
>>>>>>>>> [0]PETSC ERROR: #6 DMPlexCreateFromFile() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:4721
>>>>>>>>> [0]PETSC ERROR: #7 DMPlexCreateFromOptions_Internal() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3212
>>>>>>>>> [0]PETSC ERROR: #8 DMSetFromOptions_Plex() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/impls/plex/plexcreate.c:3433
>>>>>>>>> [0]PETSC ERROR: #9 DMSetFromOptions() at
>>>>>>>>> /home/Mike/Library/petsc_partition/src/dm/interface/dm.c:887
>>>>>>>>> [0]PETSC ERROR: #10 User provided function() at User file:0
>>>>>>>>> Abort(63) on node 0 (rank 0 in comm 16): application called
>>>>>>>>> MPI_Abort(MPI_COMM_SELF, 63) - process 0
>>>>>>>>>
>>>>>>>>> Can I get any comments on that?
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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/>
>>
>

-- 
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/20220718/6d9bd5ab/attachment.html>

More information about the petsc-users mailing list