[petsc-dev] DMPlex, Finite Volume, overlap and ghost cells...

[Matthew Knepley]

On Wed, Mar 11, 2015 at 4:11 PM, John O'Sullivan <
jp.osullivan at auckland.ac.nz> wrote:

>  Hi Matt,
>
>
>
> Good morning from NZ! Thanks for the speedy response! That helps a lot.
>
>
>
> I think the problem is the way I’m labelling the grid before setting up
> the ghost cells. I think…
>
>
>
> When you say:
>
> “When DMPlexConstructGhostCells() is called, it will put ghost cells on
> the other side of the true boundary”
>
>
>
> Does that mean that overlap cells are labelled as ghost cells? Aren’t they
> on the other side of the true boundary? Or by true boundary do you mean the
> outer edge of the overlap cells?
>

No, the true boundary is the boundary of the serial mesh.


> I’m testing the code using two different 3 cell exo files. One is the
> simpleblock-100.exo from the shared directory and the other is an exo made
> using a python script and paraview. The simpleblock-100.exo has labels
> already assigned whereas the has none.
>
>
>
> Should we be expecting the exo’s to be labelled appropriately outside of
> Petsc or should we check them and label them within the code? The two grids
> are being labelled very differently at the moment and I’m not sure which is
> right of (mostly likely) if both are wrong…
>

If no labels exist, I try and create sensible labels. Its fine to create
your own after loading, it just complicates the
mesh process a little.

  Thanks,

     Matt


> Thanks again
>
> John
>
>
>
>
>
> --
>
>  Dr John O'Sullivan
>
> Lecturer
>
> Department of Engineering Science
>
> University of Auckland, New Zealand
>
> email: jp.osullivan at auckland.ac.nz
> <https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev>
>
> tel: +64 (0)9 923 85353
>
>
>
>
>
>
>
>
>
> *From:* Matthew Knepley [mailto:knepley at gmail.com]
> *Sent:* Thursday, 12 March 2015 3:06 a.m.
> *To:* John O'Sullivan
> *Cc:* petsc-dev at mcs.anl.gov
> *Subject:* Re: [petsc-dev] DMPlex, Finite Volume, overlap and ghost
> cells...
>
>
>
> On Wed, Mar 11, 2015 at 3:34 AM, John O'Sullivan <
> jp.osullivan at auckland.ac.nz> wrote:
>
> Hi all,
>
> I've managed to get myself very confused about how to use DMPlex correctly
> for a distributed Finite Volume grid...
>
> My understanding was that along partition boundaries the ghost cells are
> used store cell information from neighbouring partitions so that the fluxes
> can be calculated.
>
> Though debugging through ex11 it seems like overlap is set equal to 1?
>
> I'm solving a simple pressure-diffusion equation on a 1D column (from an
> exo grid) which works fine on a single processor but not in parallel. I'm
> certainly not setting things up right or labeling correctly...
>
> Could someone please explain the most appropriate way to set up and label
> the DM, whether the overlap should be 0 or 1 and whether ghost cells should
> be placed on internal partition boundaries.
>
>
>
> Yes, for FV the partition overlap should be 1, as it is in ex11. This
> means that when the partition happens, we will
>
> put a layer of cells on the other side of partition boundaries,
>
>
>
> When DMPlexConstructGhostCells() is called, it will put ghost cells on the
> other side of the true boundary. Both
>
> kinds of cells will be separated from interior cells by the
> DMPlexGetHybridBounds(&cMax), where cMax is the
>
> first ghost cell.
>
>
>
> Now you still need a way to get rid of faces between ghost cells (which
> only occur in cells across a partition boundary).
>
> To do this, you use the "ghost" label we make during partitioning:
>
>
>
>     ierr = DMPlexGetLabel(dm, "ghost", &ghostLabel);CHKERRQ(ierr);
>
>     ierr = DMLabelGetValue(ghostLabel, face, &ghost);CHKERRQ(ierr);
>
>     if (ghost >= 0) continue;
>
>
>
> What exactly is going wrong?
>
>
>
>    Matt
>
>
>
>  Thanks!
> John
>
>
>
> --
> Dr John O'Sullivan
>
> Lecturer
>
> Department of Engineering Science
>
> University of Auckland, New Zealand
>
> email: jp.osullivan at auckland.ac.nz <https://lists.mcs.anl.gov/mailman/listinfo/petsc-dev>
>
> tel: +64 (0)9 923 85353
>
>
>
>
>
> --
>
> 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
>



-- 
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
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