[petsc-users] DMPlex and CGNS

[Matthew Knepley]

On Mon, Jan 16, 2023 at 6:15 PM Jed Brown <jed at jedbrown.org> wrote:

> How soon do you need this? I understand the grumbling about CGNS, but it's
> easy to build, uses HDF5 parallel IO in a friendly way, supports high order
> elements, and is generally pretty expressive. I wrote a parallel writer
> (with some limitations that I'll remove) and plan to replace the current
> reader with a parallel reader because I have need to read big CGNS meshes.
> Alas, my semester is starting so it's hard to make promises, but this is a
> high priority for my research group and if you share your mesh file, I hope
> to be able to make the parallel reader work in the next couple weeks.
>

The biggest hurdle for me is understanding the CGNS format. If you can tell
me what is going on, I can help write the Plex code that
interprets it.

  Thanks,

    Matt


> "Ferrand, Jesus A." <FERRANJ2 at my.erau.edu> writes:
>
> > Dear PETSc team:
> >
> > I would like to use DMPlex to partition a mesh stored as a CGNS file. I
> configured my installation with --download_cgns = 1, got me a .cgns file
> and called DMPlexCreateCGNSFromFile() on it. Doing so got me this error:
> >
> > [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> > [0]PETSC ERROR: Error in external library
> > [0]PETSC ERROR: CGNS file must have a single section, not 4
> > [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> > [0]PETSC ERROR: Petsc Release Version 3.18.3, unknown
> > [0]PETSC ERROR: ./program.exe on a arch-linux-c-debug named F86 by jesus
> Mon Jan 16 17:25:11 2023
> > [0]PETSC ERROR: Configure options --download-mpich=yes
> --download-hdf5=yes --download-cgns=yes --download-metis=yes
> --download-parmetis=yes --download-ptscotch=yes --download-chaco=yes
> --with-32bits-pci-domain=1
> > [0]PETSC ERROR: #1 DMPlexCreateCGNS_Internal() at
> /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/cgns/plexcgns2.c:104
> > [0]PETSC ERROR: #2 DMPlexCreateCGNS() at
> /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexcgns.c:60
> > [0]PETSC ERROR: #3 DMPlexCreateCGNSFromFile_Internal() at
> /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/cgns/plexcgns2.c:27
> > [0]PETSC ERROR: #4 DMPlexCreateCGNSFromFile() at
> /home/jesus/Desktop/JAF_NML/3rd_Party/PETSc/petsc/src/dm/impls/plex/plexcgns.c:29
> >
> > I looked around mail archives for clused and found this one (
> https://lists.mcs.anl.gov/pipermail/petsc-users/2018-June/035544.html).
> There, Matt provides a link to the source code for
> DMPlexCreateCGNSFromFile() and another (seemingly broken) link to CGNS
> files that can be opened with the former.  After reading the source code I
> now understand that it is hardcoded for CGNS files that feature a single
> "base" and a single "section", whatever those are.
> >
> > After navigating the CGNS documentation, I can sympathize with the
> comments in the source code.
> >
> > Anyhow, I wanted to ask if I could be furnished with one such CGNS file
> that is compatible with DMPlexCreateCGNSFromFile() to see if I can modify
> my CGNS files to conform to it. If not, I will look into building the DAG
> myself using DMPlex APIs.
> >
> >
> > Sincerely:
> >
> > J.A. Ferrand
> >
> > Embry-Riddle Aeronautical University - Daytona Beach FL
> >
> > M.Sc. Aerospace Engineering
> >
> > B.Sc. Aerospace Engineering
> >
> > B.Sc. Computational Mathematics
> >
> >
> > Phone: (386)-843-1829
> >
> > Email(s): ferranj2 at my.erau.edu
> >
> >     jesus.ferrand at gmail.com
>


-- 
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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