[petsc-users] MatColoring

[Dave May]

On Tue 10. May 2022 at 18:51, Tang, Qi <tangqi at msu.edu> wrote:

> We are using SNES + TS + dmstag. The current bottleneck is the number of
> residual evaluation (more than 300 per Jacobian building using the default
> coloring from dmstag).
>

I suspect that this high count stems from the fact that non zero pattern
defined by MatCreate for dmstag is not specialized for your particular
stencil. Ie it just considers the stencil width, shape and assumes all
cell, face, vertex dofs are connected. Is that correct?

Would a simple solution to drop the 300 residual evals be just to define
your own Amat with a non-zero pattern which is specific to your actually
stencil?

The code to define such a non zero pattern is probably not too hard to
write using MatPreallocator.

Just a thought.

Thanks,
Dave


We talked to Patrick and we are not sure how to improve further.
>
> So it looks like we should play with mat_coloring_type and see if others
> give us better performance.
>
> If there is anything else we can play with, please also let us know. We
> also lag Jacobian and only build once every three Newton iterations, which
> works well. Thanks,
>
> Qi
>
>
>
> On May 10, 2022, at 10:35 AM, Barry Smith <bsmith at petsc.dev> wrote:
>
>
>   This depends to some degree on how you are accessing applying the
> Jacobian construction process.
>
>    If you are using SNES or TS then the SNES object handles most of the
> work of organizing the PETSc objects needed to compute the Jacobian and you
> can control the choices via the options database.
>
>    With SNES/TS using a DM you can skip calling SNESSetJacobian() and
> simply use the option -snes_fd_color to have SNES compute the Jacobian for
> you. By default, the coloring is obtained from the DM (which is generally
> the best available coloring), you can have it use a coloring computed
> directly from the matrix structure with the
> options -snes_fd_color_use_mat -mat_coloring_type  jp power sl lf ld or
> greedy (see MatColoringType, MatColoringSetFromOptions)
> Use  -mat_fd_coloring_view to get information on the computation of the
> Jacobian from the coloring. Use  -mat_coloring_view to get information on
> the coloring used. (see MatFDColoringSetFromOptions)
>
>   If you are using SNES/TS but not using a DM you need to compute the
> nonzero structure of the matrix yourself into J and call
> SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);
> you need to create the matfdcoloring object with MatFDColoringCreate()
> using an iscoloring you obtained with MatColoringCreate() etc.  The same
> command line arguments as above allow you to control the coloring algorithm
> used and to view them etc.
>
>   Barry
>
>
>
>
>
>
>
>
> On May 10, 2022, at 11:40 AM, Jorti, Zakariae via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
> Hi,
>
> I am solving a non-linear problem and using a finite difference
> approximation with coloring to compute the Jacobian matrix.
>
> There are several coloring algorithms available in PETSc as indicated here:
> https://petsc.org/release/docs/manualpages/Mat/MatColoring.html
> <https://urldefense.com/v3/__https://petsc.org/release/docs/manualpages/Mat/MatColoring.html__;!!HXCxUKc!1czn7o25s7aYCp0mPqVxWzr-S-Fc0qBskSUMuqiRAf5CiUQoJAYOwuyAak2yJhKKkULePn_T7-fyd0U$>
>
> And I was wondering how to switch from one to another in the Jacobian
> setup routine and also how to check which coloring algorithm I am currently
> using.
>
> Thank you.
>
> Zakariae Jorti
>
>
>
>
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