[petsc-users] MatColoring

[Patrick Sanan]

Am Mi., 11. Mai 2022 um 21:28 Uhr schrieb Barry Smith <bsmith at petsc.dev>:

>
>   It is unlikely that the true number of colors is much less than 230 so I
> don't think you can save by reducing the number of colors more.
>
>   Are you using IS_COLORING_LOCAL it eliminates much parallel
> communication so you would definitely benefit by using this, depending on
> how your FormFunction is written you may need to refactor your code
> slightly.
>
>   There is also a hidden parameter which is a tradeoff of memory usage vs
> speed. If memory is not an issue for you then you could change this
> parameter. It is computed in MatFDColoringCreate_MPIXAIJ() called bcols You
> can just hardware bcols to iscoloring->n This may help a bit.
>
>    The only way to drastically improve the time after the above is to
> reorganize the PETSc code and your code to evaluate multiple function
> evaluations "at the same time" but this is a major project (it has to be
> done for GPUs).
>
>   MATCOLORINGMIS doesn't exist, it is a typo in the docs.
>
https://gitlab.com/petsc/petsc/-/merge_requests/5249

>
>   Barry
>
>
> On May 11, 2022, at 2:25 PM, Jorti, Zakariae <zjorti at lanl.gov> wrote:
>
> Hello,
>
> I have used the -mat_coloring_view and -mat_fd_coloring_view flags as you
> suggested and it turns out that the coloring used was MATCOLORINGSL.
> I have also tried other methods and obtained the following numbers of
> function evaluations per Jacobian building:
> - MATCOLORINGJP : 593
> - MATCOLORINGID : 327
> - MATCOLORINGSL : 321
> - MATCOLORINGGREEDY : 316
> - MATCOLORINGLF : 230
>
> Is there any parameter/trick we can try to further cut down the number of
> function evaluations? And also how could we use MATCOLORINGMIS as this
> latter does not appear in the MatColoringType options?
> Many thanks.
>
> Zakariae
> ------------------------------
> *From:* Tang, Qi <tangqi at msu.edu>
> *Sent:* Tuesday, May 10, 2022 10:51:07 AM
> *To:* Barry Smith; petsc-users at mcs.anl.gov
> *Cc:* Jorti, Zakariae; Tang, Xianzhu
> *Subject:* [EXTERNAL] Re: [petsc-users] MatColoring
>
> 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). 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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