[petsc-users] dmplex extruded layers

Bhargav Subramanya bhargav.subramanya at kaust.edu.sa
Mon Nov 22 11:09:11 CST 2021

Dear All,

I have a prismatic mesh generated by extruding a base icosahedron
spherical surface mesh. The mesh is distributed on 2 processes after
extrusion. The dof for my problem are defined only on the simplices of the
spherical layers.

1. For a given spherical layer, I want to get points, which are basically
simplices, lying on that layer only. DMPlexGetHeightStratum returns the
points on all the spherical Layers. I can probably use DMPlexFindVertices
(based on the radius of the spherical layer) and
DMPlexGetSimplexOrBoxCells. Could you suggest if there is a better way to
retrieve the points (which are simplices) on a given spherical layer in the
extruded mesh?

2. I am able to visualize the entire mesh using dm_view. Is there a way to
get the mesh file for the local dm from a specific process?

3. One of my previous emails might have got lost as I mistakenly attached a
large mesh file and sent it. So I am repeating the question here.
DMPlexExtrude gives the following error after distributing the base 2D
spherical mesh. Both refinement or/and extrusion after dm distribution does
not work for me. In fact, I tried with src/dm/impls/plex/tutorials/ex10.c
also. Although the mesh is distributed after the extrusion in ex10.c (which
is working fine for me), I tried to distribute before extrusion, and I get
the following error. Could you please suggest where I might be making a

[0]PETSC ERROR: --------------------- Error Message
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: This DMPlex is distributed but its PointSF has no graph set
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.16.1, unknown
[0]PETSC ERROR: ./cavity_flow.out on a arch-darwin-c-debug named kl-21859
by subrambm Mon Nov 22 19:47:14 2021
[0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
--with-fc=gfortran --download-mpich --download-fblaslapack
--download-superlu_dist --download-hypre --download-fiat
--download-generator --download-triangle --download-tetgen --download-chaco
--download-make -download-boost --download-cmake --download-ml
--download-mumps-commit=v5.4.1-p1 --download-scalapack --download-ptscotch
--download-hdf5 --force
[0]PETSC ERROR: #1 DMPlexCheckPointSF() at
[0]PETSC ERROR: #2 DMPlexOrientInterface_Internal() at
[0]PETSC ERROR: #3 DMPlexInterpolate() at
[0]PETSC ERROR: #4 DMPlexExtrude() at
[0]PETSC ERROR: #5 CreateMesh() at ex10.c:161
[0]PETSC ERROR: #6 main() at ex10.c:180
[0]PETSC ERROR: PETSc Option Table entries:
[0]PETSC ERROR: -dm_plex_extrude_layers 3
[0]PETSC ERROR: -dm_view vtk:mesh.vtk
[0]PETSC ERROR: -init_dm_plex_dim 2
[0]PETSC ERROR: -petscpartitioner_type simple
[0]PETSC ERROR: -srf_dm_distribute
[0]PETSC ERROR: -srf_dm_refine 0
[0]PETSC ERROR: ----------------End of Error Message -------send entire
error message to petsc-maint at mcs.anl.gov----------



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