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

Matthew Knepley knepley at gmail.com
Tue Apr 26 03:56:09 CDT 2022

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


to your code. WHen I do this, you example runs for me.



> 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/>
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