[petsc-users] Finite difference approximation of Jacobian

[Tang, Qi]

Matt and Dave,

Thanks, this is consistent with what we found. If Patrick or someone can add some basic coloring option with DMStag, that would be very useful for our project.

Qi



On Dec 13, 2021, at 11:52 AM, Dave May <dave.mayhem23 at gmail.com<mailto:dave.mayhem23 at gmail.com>> wrote:



On Mon, 13 Dec 2021 at 19:29, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:
On Mon, Dec 13, 2021 at 1:16 PM Dave May <dave.mayhem23 at gmail.com<mailto:dave.mayhem23 at gmail.com>> wrote:


On Sat 11. Dec 2021 at 22:28, Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:
On Sat, Dec 11, 2021 at 1:58 PM Tang, Qi <tangqi at msu.edu<mailto:tangqi at msu.edu>> wrote:
Hi,
Does anyone have comment on finite difference coloring with DMStag? We are using DMStag and TS to evolve some nonlinear equations implicitly. It would be helpful to have the coloring Jacobian option with that.

Since DMStag produces the Jacobian connectivity,

This is incorrect.
The DMCreateMatrix implementation for DMSTAG only sets the number of nonzeros (very inaccurately). It does not insert any zero values and thus the nonzero structure is actually not defined.
That is why coloring doesn’t work.

Ah, thanks Dave.

Okay, we should fix that.It is perfectly possible to compute the nonzero pattern from the DMStag information.

Agreed. The API for DMSTAG is complete enough to enable one to
loop over the cells, and for all quantities defined on the cell (centre, face, vertex),
insert values into the appropriate slot in the matrix.
Combined with MATPREALLOCATOR, I believe a compact and readable
code should be possible to write for the preallocation (cf DMDA).

I think the only caveat with the approach of using all quantities defined on the cell is
It may slightly over allocate depending on how the user wishes to impose the boundary condition,
or slightly over allocate for says Stokes where there is no pressure-pressure coupling term.

Thanks,
Dave


Paging Patrick :)

  Thanks,

    Matt

Thanks,
Dave


you can use -snes_fd_color_use_mat. It has many options. Here is an example of us using that:

  https://gitlab.com/petsc/petsc/-/blob/main/src/snes/tutorials/ex19.c#L898<https://urldefense.com/v3/__https://gitlab.com/petsc/petsc/-/blob/main/src/snes/tutorials/ex19.c*L898__;Iw!!HXCxUKc!h_StfE5Flul2AzB6sJ3ooEa2GBhV-GZ4s8KWEB2soynkpcpilsVmmHUbsYezUA$>

  Thanks,

     Matt

Thanks,
Qi


On Oct 15, 2021, at 3:07 PM, Jorti, Zakariae via petsc-users <petsc-users at mcs.anl.gov<mailto:petsc-users at mcs.anl.gov>> wrote:

Hello,

Does the Jacobian approximation using coloring and finite differencing of the function evaluation work in DMStag?
Thank you.
Best regards,

Zakariae



--
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/<https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!HXCxUKc!h_StfE5Flul2AzB6sJ3ooEa2GBhV-GZ4s8KWEB2soynkpcpilsVmmHUXuu3a8g$>


--
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/<https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!HXCxUKc!h_StfE5Flul2AzB6sJ3ooEa2GBhV-GZ4s8KWEB2soynkpcpilsVmmHUXuu3a8g$>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20211213/6f7be721/attachment-0001.html>