[petsc-users] DMPlex distribution with FVM adjacency

[Matthew Knepley]

On Thu, May 25, 2017 at 9:27 AM, Lawrence Mitchell <
lawrence.mitchell at imperial.ac.uk> wrote:

> Dear petsc-users,
>
> I am trying to distribute a triangle mesh with a cell halo defined by
> FVM adjacency (i.e. if I have a facet in the initial (0-overlap)
> distribution, I want the cell on the other side of it).
>
> Reading the documentation, I think I do:
>
> DMPlexSetAdjacencyUseCone(PETSC_TRUE)
> DMPlexSetAdjacencyUseClosure(PETSC_FALSE)
>
> and then
> DMPlexDistribute(..., ovelap=1)
>
> If I do this for a simple mesh and then try and do anything on it, I
> run into all sorts of problems because I have a plex where I have some
> facets, but not even one cell in the support of the facet.  Is this to
> be expected?
>

Hmm. I don't think so. You should have at least one cell in the support of
every facet.
TS ex11 works exactly this way.

When using that adjacency, the overlap cells you get will not have anything
but the
facet connecting them to that partition. Although, if you have adjacent
cells in that overlap layer,
you can get ghost faces between those.

With the code below, do you get an interpolated mesh when you create it
there. That call in C
has another argument


http://www.mcs.anl.gov/petsc/petsc-master/docs/manualpages/DMPLEX/DMPlexCreateFromCellList.html

If its just cells and vertices, you could get some bizarre things like you
see.

    Matt


> For example the following petsc4py code breaks when run on 3 processes:
>
> $ mpiexec -n 3 python bork.py
> [1] DMPlexGetOrdering() line 133 in
> /data/lmitche1/src/deps/petsc/src/dm/impls/plex/plexreorder.c
> [1] DMPlexCreateOrderingClosure_Static() line 41 in
> /data/lmitche1/src/deps/petsc/src/dm/impls/plex/plexreorder.c
> [1] Petsc has generated inconsistent data
> [1] Number of depth 2 faces 34 does not match permuted nubmer 29
> : error code 77
> [2] DMPlexGetOrdering() line 133 in
> /data/lmitche1/src/deps/petsc/src/dm/impls/plex/plexreorder.c
> [2] DMPlexCreateOrderingClosure_Static() line 41 in
> /data/lmitche1/src/deps/petsc/src/dm/impls/plex/plexreorder.c
> [2] Petsc has generated inconsistent data
> [2] Number of depth 2 faces 33 does not match permuted nubmer 28
> : error code 77
> [0] DMPlexGetOrdering() line 133 in
> /data/lmitche1/src/deps/petsc/src/dm/impls/plex/plexreorder.c
> [0] DMPlexCreateOrderingClosure_Static() line 41 in
> /data/lmitche1/src/deps/petsc/src/dm/impls/plex/plexreorder.c
> [0] Petsc has generated inconsistent data
> [0] Number of depth 2 faces 33 does not match permuted nubmer 31
>
> $ cat > bork.py<<\EOF
> from petsc4py import PETSc
> import numpy as np
> Lx = Ly = 1
> nx = ny = 4
>
> xcoords = np.linspace(0.0, Lx, nx + 1, dtype=PETSc.RealType)
> ycoords = np.linspace(0.0, Ly, ny + 1, dtype=PETSc.RealType)
> coords = np.asarray(np.meshgrid(xcoords, ycoords)).swapaxes(0,
> 2).reshape(-1, 2)
>
> # cell vertices
> i, j = np.meshgrid(np.arange(nx, dtype=PETSc.IntType), np.arange(ny,
> dtype=PETSc.IntType))
> cells = [i*(ny+1) + j, i*(ny+1) + j+1, (i+1)*(ny+1) + j+1,
> (i+1)*(ny+1) + j]
> cells = np.asarray(cells, dtype=PETSc.IntType).swapaxes(0,
> 2).reshape(-1, 4)
> idx = [0, 1, 3, 1, 2, 3]
> cells = cells[:, idx].reshape(-1, 3)
>
> comm = PETSc.COMM_WORLD
> if comm.rank == 0:
>     dm = PETSc.DMPlex().createFromCellList(2, cells, coords, comm=comm)
> else:
>     dm = PETSc.DMPlex().createFromCellList(2, np.zeros((0, 4),
> dtype=PETSc.IntType),
>                                            np.zeros((0, 2),
> dtype=PETSc.RealType),
>                                            comm=comm)
>
> dm.setAdjacencyUseClosure(False)
> dm.setAdjacencyUseCone(True)
>
> dm.distribute(overlap=1)
>
> dm.getOrdering(PETSc.Mat.OrderingType.RCM)
>
> dm.view()
> EOF
>
> Am I doing something wrong?  Is this not expected to work?
>
> Cheers,
>
> Lawrence
>
>


-- 
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

http://www.caam.rice.edu/~mk51/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20170525/b7d31fa5/attachment.html>