[petsc-users] DMPlex with dof in cells AND at nodes

[Matthew Knepley]

On Mon, Jan 11, 2021 at 6:41 AM Thibault Bridel-Bertomeu <
thibault.bridelbertomeu at gmail.com> wrote:

> Dear all,
>
> I haven't been on this mailing list since december, so first of all, happy
> new year to everyone !
>
> I am facing another challenge with the DMPlex structure : although I am
> doing cell-centered finite volume (using PetscFV), I also need to do some
> manipulations and store information that are vertex-based.
> The problem I have is when I run the code in parallel : when I visualize
> the nodal data using a vtk viewer, it shows NaN at all the vertices in
> close proximity to the MPI partition line.
> Here is how I proceed to work on the vertex-based data :
>
> First comes the creation of the DM that I'll be using for the
> cell-centered FVM
>
> call DMPlexCreateFromFile(comm, name, PETSC_TRUE, dm, ierr)
> call DMSetBasicAdjacency(dm, PETSC_TRUE, PETSC_TRUE, ierr)
> call DMPlexDistribute(dm, 1, PETSC_NULL_SF, dmDist, ierr)
> ...
> dm = dmDist
> ...
> call DMConstructGhostCells(dm, ..., ..., dmGhost, ierr)
> ...
> dm = dmGhost
> ...
>
> I set both boolean to PETSC_TRUE in the SetBasicAdjacency so even in MPI
> the neighbouring relationships are conserved for all strata. Is that true ?
> Like, does doing this actually enable to get all the transitive closure of
> a given vertex, even if part of it is in another MPI block ?
>

What you say should be true, but it is not. When I designed everything, I
was very much stuck in the traditional mesh way of looking at things, and
made some limiting decisions. You can still get what you want (almost), but
you need to distribute the mesh with an overlap of 1. If you do, then you
can get the transitive support of vertices.

The problem is basically that many places in the code assume that the
overlap always contains the closure of any point in it. It is difficult to
be able to switch this assumption to the star (transitive support)so I have
not done that yet.


> Then I need a vertex-based DM, so I figure it's pretty much what's done in
> CreateMassMatrix in TS ex11.c.
>
> call DMClone(dm, dmNodal, ierr)
> call DMGetCoordinateSection(dm, coordSection, ierr); CHKERRA(ierr)
> call DMGetCoordinatesLocal(dm, coordinates, ierr); CHKERRA(ierr)
> call DMSetCoordinateSection(dmNodal, PETSC_DETERMINE, coordSection, ierr);
> call PetscSectionCreate(PETSC_COMM_WORLD, sectionNodal, ierr);
> CHKERRA(ierr)
> call DMPlexGetDepthStratum(dm, 0, vstart, vend, ierr); CHKERRA(ierr)
> call PetscSectionSetChart(sectionNodal, vstart, vend, ierr); CHKERRA(ierr)
> do inode = vstart, vend-1
>  ! 3 dof per node, ndim = 3
> call PetscSectionSetDof(sectionNodal, inode, ndim, ierr); CHKERRA(ierr)
> end do
> call PetscSectionSetUp(sectionNodal, ierr); CHKERRA(ierr)
> call DMSetLocalSection(dmNodal, sectionNodal, ierr); CHKERRA(ierr)
> call PetscSectionDestroy(sectionNodal, ierr); CHKERRA(ierr)
>
> From what I understood, this new dmNodal basically has all the
> characteristics of the ori dm, except it's primary layer is vertex-based
> with 3 DOF per vertex.
>

Take out the coordinate stuff above. This is now handled internally in a
better way. Other than that, it looks good.


> Then I get a local vector and work on it :
>
> call DMGetLocalVector(dmNodal, nodalvec, ierr)
> call VecGetArrayF90(nodalvec, nodalvecarray, ierr)
> call DMPlexGetDepthStratum(dm, 0, vstart, vend, ierr)
> call DMPlexGetDepthStratum(dm, 2, fstart, fend, ierr)
> ! For each node ...
> do inode = vstart, vend-1
> A = 0 ! matrix, ndim x ndim
> b = 0 ! vector, ndim
> call DMPlexGetTransitiveClosure(dmNodal, inode, PETSC_FALSE,
> vertexclosure, ierr);
> ! For each face attached to that node
> do iface = 1, size(vertexclosure)
> if ((vertexclosure(iface) < fstart) .or. (vertexclosure(iface) >= fend))
> cycle
> A = A + ...
> b = b + ...
> end do
> nodalvecarray(1+(inode-vstart)*ndim:3+(inode-vstart)*ndim) = matmul(A, b)
> ...
> end do
>

There are some subtleties here I think. You are looping over all vertices,
but you only own some of them.
What do you do when putting these values in the global vector? I think
there are at least three choices:

1) Everyone has everything, so you compute all the vertex stuff
redundantly, and then use INSERT_VALUES for the scatter

2) Only vertices are redundant, so the transitive supports of vertices are
partial but non-overlapping, and you use ADD_VALUES for the scatter

3) Only cells are redundant, so you do the complete vertex computation only
for local vertices


> Then I want to visualize it :
>
> call VecRestoreArrayF90(nodalvec, nodalvecarray, ierr)
> call DMCreateGlobalVector(dmNodal, globalnodalvec, ierr)
> call DMLocalToGlobal(dmNodal, nodalvec, INSERT_VALUES, globalnodalvec,
> ierr)
> call PetscViewerCreate(PETSC_COMM_WORLD, vtkViewer, ierr); CHKERRA(ierr)
> call PetscViewerSetType(vtkViewer, PETSCVIEWERVTK, ierr); CHKERRA(ierr)
> call PetscViewerFileSetName(vtkViewer, "toto.vtk", ierr); CHKERRA(ierr)
> call VecView(globalnodalvec, vtkViewer, ierr); CHKERRA(ierr)
> call PetscViewerDestroy(vtkViewer, ierr); CHKERRA(ierr)
>
> In the toto.vtk file, I get vertex-based values as expected, and the whole
> shebang works in sequential. Now when I run it in parallel, I get
> vertex-based values inside the MPI blocks, but in the neighbourhood of the
> join between the MPI blocks, all the vertex-based values are NaN (see
> attachment).
>

If you have redundant cells, meaning you distributed with overlap = 1, did
you remember to full up the values for those ghost cells using
DMGlobalToLocal() or something like that? If not, they will start as NaNs.

  Thanks,

     Matt


> All in all, I think I do not understand fully the consequences of the
> DMPlexDistribute with useCone=true & useClosure=true ... but I cannot
> figure out where the NaN are coming from : is it because the vertices do
> not actually know all their closure through the MPI join, or is it some
> Global / Local error I made ?
>
> Thank you very much in advance for your support !!
>
> Thibault
>


-- 
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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