[petsc-users] Coloring of a finite volume unstructured mesh

[Matthew Knepley]

On Tue, Nov 7, 2017 at 10:18 AM, SIERRA-AUSIN Javier <
Javier.SIERRA-AUSIN at isae-supaero.fr> wrote:

> Hi,
>
> I would like to  ask you concerning the computation of the Jacobian matrix
> via finite difference and coloring of the connectivity graph.
> I wonder whether it is possible or not to color the Jacobian matrix of a
> given solver that evaluates the RHS with its associated connectivity in the
> global indeces of my solver (not PETSc).
> As well, if it is possible to do this from an already partioned domain in
> parallel.
> All of this is better explained in this post :
> https://scicomp.stackexchange.com/questions/28209/linking-
> petsc-with-an-already-parallel-in-house-finite-volume-solver
>

The simplest thing you can do is to use the finite-difference Jacobian
action (MatMFFD). This is setup automatically by SNES
if you give a FormFunction pointer, but no FormJacobian routine. Just tell
the PETSc Vecs to use your ParMetis layout (by
setting the local sizes), and it should run fine in SNES.

However, usually you need some kind of preconditioning. Thus you either
have to form the Jacobian or some approximation. If
you cannot form an approximation, then you can use coloring. Once option is
to create a DMPlex with your mesh information.
This can be done in parallel after you have already partitioned with
ParMetis (as long as you know the "overlap" of vertices, or
adjacency of cells). Then the coloring can be done automatically using that
DM information. Otherwise, you will have to supply
a coloring to the SNES.

  Thanks,

     Matt


> Thanks in advance,
>
> Javier.
>




-- 
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.caam.rice.edu/~mk51/>
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