[petsc-users] DMPlex and CGNS

[Jed Brown]

Copying my private reply that appeared off-list. If you have one base with different element types, that's in scope for what I plan to develop soon.

Congrats, you crashed cgnsview.

$ cgnsview dl/HybridGrid.cgns
Error in startup script: file was not found
    while executing
"CGNSfile $ProgData(file)"
    (procedure "file_stats" line 4)
    invoked from within
"file_stats"
    (procedure "file_load" line 53)
    invoked from within
"file_load $fname"
    invoked from within
"if {$argc} {
  set fname [lindex $argv [expr $argc - 1]]
  if {[file isfile $fname] && [file readable $fname]} {
    file_load $fname
  }
}"
    (file "/usr/share/cgnstools/cgnsview.tcl" line 3013)

This file looks okay in cgnscheck and paraview, but I don't have a need for multi-block and I'm stretched really thin so probably won't make it work any time soon. But if
you make a single block with HexElements alongside PyramidElements and TetElements, I should be able to read it. If you don't mind prepping such a file (this size or
smaller), it would help me test.


"Engblom, William A." <engbl7de at erau.edu> writes:

> Jesus,
>
> The CGNS files we get from Pointwise have only one base, so that should not be an issue.  However, sections are needed to contain each cell type, the BCs, and zonal boundaries. So, there are always several sections.  The grid that Spencer made for you must have multiple sections.  We have to be able to deal with grids like Spencer's example or else it's not useful.
>
> B.
>
>
>
>
>
>
> ________________________________
> From: Ferrand, Jesus A. <FERRANJ2 at my.erau.edu>
> Sent: Monday, January 16, 2023 5:41 PM
> To: petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> Subject: DMPlex and CGNS
>
> 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