[petsc-users] Vertex only unstructured mesh with DMPlex and DMSWARM

[Hill, Reuben]

I'm a new Firedrake developer working on getting my head around PETSc. As far as I'm aware, all our PETSc calls are done via petsc4py.

I'm after general help and advise on two fronts:


1:

I’m trying to represent a point cloud as a vertex-only mesh in an attempt to play nicely with the firedrake stack. If I try to do this using firedrake I manage to cause a PETSc seg fault error at the point of calling

PETSc.DMPlex().createFromCellList(dim, cells, coords, comm=comm)

with dim=0, cells=[[0]], coords=[[1., 2.]] and comm=COMM_WORLD.

Output:

[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
application called MPI_Abort(MPI_COMM_WORLD, 50152059) - process 0

I’m now looking into getting firedrake to make a DMSWARM which seems to have been designed for doing something closer to this and allows nice things such as being able to make the particles (for me - the vertices of the mesh) move and jump between MPI ranks a-la particle in cell. I note DMSwarm docks don't suggest there is an equivalent of the plex.distribute() method in petsc4py (which I believe calls DMPlexDistribute) that a DMPlex has. In firedrake we create empty DMPlexes on each rank except 0, then call plex.distribute() to take care of parallel partitioning. How, therefore, should I meant to go about distributing particles across MPI ranks?


2:

I'm aware these questions may be very naive. Any advice for learning about relevant bits of PETSc for would be very much appreciated. I'm in chapter 2 of the excellent manual (https://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf) and I'm also attempting to understand the DMSwarm example. I presume in oder to understand DMSWARM I really ought to understand DMs more generally (i.e. read the whole manual)?


Many thanks
Reuben Hill


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