[petsc-users] PCFIELDSPLIT with MATSBAIJ

[Carl-Johan Thore]

 "Naïve question, but is your problem really symmetric?
For example, if you do FEM, how do you impose Dirichlet boundary
conditions?"

The structure of the matrix is K =  [A B; B^T C] with A and C symmetric, so
the problem should be symmetric. Numerically, the maximum relative
difference between K and K^T is
on the order of, let's say, 1e-18 which I guess is a good as can be
expected? I'm using FEM with (homogeneous) Dirichlet boundary conditions
imposed by zeroing rows and columns
for the fixed DOFs and adding ones to the corresponding diagonal elements,
i.e. same as what MatZeroRowsColumns does.  MatZeroRowsColumns doesn't work
for sbaij but we already have an implementation in which rows and columns
are cancelled in the element matrices before assembly which is well-tested
for the aij-case. We've also verified numerically that aij and sbaij yields
the same upper triangular part, and that the RHS is the same in both cases.

"If you can reproduce this on a smaller example and are at liberty to share
the Mat, IS, and RHS Vec, feel free to send them at petsc-maint at mcs.anl.gov,
I can have a look."

Yes, this is reproducible on smaller problems. In case I send you Mat, IS,
and RHS, which format is preferable?

Kind regards,
Carl-Johan


On Wed, Sep 6, 2023 at 8:21 AM Pierre Jolivet <pierre.jolivet at lip6.fr>
wrote:

> Naïve question, but is your problem really symmetric?
> For example, if you do FEM, how do you impose Dirichlet boundary
> conditions?
> If you can reproduce this on a smaller example and are at liberty to share
> the Mat, IS, and RHS Vec, feel free to send them at
> petsc-maint at mcs.anl.gov, I can have a look.
>
> Thanks,
> Pierre
>
> On 6 Sep 2023, at 8:14 AM, Carl-Johan Thore <carljohanthore at gmail.com>
> wrote:
>
> 
> Thanks for this!
> I now get convergence with sbaij and fieldsplit. However, as can be seen
> in the attached file, it requires around three times as many outer
> iterations as with aij to reach the same point (to within rtol). Switching
> from -pc_fieldsplit_schur_fact_type LOWER to FULL (which is the "correct"
> choice?) helps quite a bit, but still sbaij takes many more iterations. So
> it seems that your sbaij-implementation works but that I'm doing something
> wrong when setting up the fieldsplit pc, or that some of the subsolvers
> doesn't work properly with sbaij. I've tried bjacobi as you had in your
> logs, but not hypre yet. But anyway, one doesn't expect the matrix format
> to have this much impact on convergence? Any other suggestions?
> /Carl-Johan
>
> On Mon, Sep 4, 2023 at 9:31 PM Pierre Jolivet <Pierre.Jolivet at lip6.fr>
> wrote:
>
>> The branch should now be good to go (
>> https://gitlab.com/petsc/petsc/-/merge_requests/6841).
>> Sorry, I made a mistake before, hence the error on PetscObjectQuery().
>> I’m not sure the code will be covered by the pipeline, but I have tested
>> this on a Raviart—Thomas discretization with PCFIELDSPLIT.
>> You’ll see in the attached logs that:
>> 1) the numerics match
>> 2) in the SBAIJ case, PCFIELDSPLIT extract the (non-symmetric) A_{01}
>> block from the global (symmetric) A and we get the A_{10} block cheaply by
>> just using MatCreateHermitianTranspose(), instead of calling another time
>> MatCreateSubMatrix()
>> Please let me know if you have some time to test the branch and whether
>> it fails or succeeds on your test cases.
>>
>> Also, I do not agree with what Hong said.
>> Sometimes, the assembly of a coefficient can be more expensive than the
>> communication of the said coefficient.
>> So they are instances where SBAIJ would be more efficient than AIJ even
>> if it would require more communication, it is not a black and white picture.
>>
>> Thanks,
>> Pierre
>>
>>
>> On 28 Aug 2023, at 12:12 PM, Pierre Jolivet <Pierre.Jolivet at lip6.fr>
>> wrote:
>>
>>
>> On 28 Aug 2023, at 6:50 PM, Carl-Johan Thore <carljohanthore at gmail.com>
>> wrote:
>>
>> I've tried the new files, and with them, PCFIELDSPLIT now gets set up
>> without crashes (but the setup is significantly slower than for MATAIJ)
>>
>>
>> I’ll be back from Japan at the end of this week, my schedule is too
>> packed to get anything done in the meantime.
>> But I’ll let you know when things are working properly (last I checked, I
>> think it was working, but I may have forgotten about a corner case or two).
>> But yes, though one would except things to be faster and less memory
>> intensive with SBAIJ, it’s unfortunately not always the case.
>>
>> Thanks,
>> Pierre
>>
>> Unfortunately I still get errors later in the process:
>>
>> [0]PETSC ERROR: Null argument, when expecting valid pointer
>> [0]PETSC ERROR: Null Pointer: Parameter # 1
>> [0]PETSC ERROR: Petsc Development GIT revision: v3.19.4-1023-ga6d78fcba1d
>>  GIT Date: 2023-08-22 20:32:33 -0400
>> [0]PETSC ERROR: Configure options -f --with-fortran-bindings=0
>> --with-cuda --with-cusp --download-scalapack --download-hdf5
>> --download-zlib --download-mumps --download-parmetis --download-metis
>> --download-ptscotch --download-hypre --download-spai
>> [0]PETSC ERROR: #1 PetscObjectQuery() at
>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/sys/objects/inherit.c:742
>> [0]PETSC ERROR: #2 MatCreateSubMatrix_MPISBAIJ() at
>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/impls/sbaij/mpi/mpisbaij.c:1414
>> [0]PETSC ERROR: #3 MatCreateSubMatrix() at
>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/mat/interface/matrix.c:8476
>> [0]PETSC ERROR: #4 PCSetUp_FieldSplit() at
>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/impls/fieldsplit/fieldsplit.c:826
>> [0]PETSC ERROR: #5 PCSetUp() at
>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/pc/interface/precon.c:1069
>> [0]PETSC ERROR: #6 KSPSetUp() at
>> /mnt/c/mathware/petsc/petsc-v3-19-4/src/ksp/ksp/interface/itfunc.c:415
>>
>> The code I'm running here works without any problems for MATAIJ. To run
>> it with MATSBAIJ I've simply used the command-line option
>> -dm_mat_type sbaij
>>
>>
>> Kind regards,
>> Carl-Johan
>>
>>
>> On Sat, Aug 26, 2023 at 5:21 PM Pierre Jolivet via petsc-users <
>> petsc-users at mcs.anl.gov> wrote:
>>
>>>
>>>
>>> On 27 Aug 2023, at 12:14 AM, Carl-Johan Thore <carl-johan.thore at liu.se>
>>> wrote:
>>>
>>> “Well, your A00 and A11 will possibly be SBAIJ also, so you’ll end up
>>> with the same issue.”
>>> I’m not sure I follow. Does PCFIELDSPLIT extract further submatrices
>>> from these blocks, or is there
>>> somewhere else in the code that things will go wrong?
>>>
>>>
>>> Ah, no, you are right, in that case it should work.
>>>
>>> For the MATNEST I was thinking to get some savings from the
>>> block-symmetry at least
>>> even if symmetry in A00 and A11 cannot be exploited; using SBAIJ for
>>> them would just be a
>>> (pretty big) bonus.
>>>
>>> “I’ll rebase on top of main and try to get it integrated if it could be
>>> useful to you (but I’m traveling
>>> right now so everything gets done more slowly, sorry).”
>>> Sound great, Thanks again!
>>>
>>>
>>> The MR is there https://gitlab.com/petsc/petsc/-/merge_requests/6841.
>>> I need to add a new code path in MatCreateRedundantMatrix() to make sure
>>> the resulting Mat is indeed SBAIJ, but that is orthogonal to the
>>> PCFIELDSPLIT issue.
>>> The branch should be usable in its current state.
>>>
>>> Thanks,
>>> Pierre
>>>
>>>
>>> *From:* Pierre Jolivet <pierre.jolivet at lip6.fr>
>>> *Sent:* Saturday, August 26, 2023 4:36 PM
>>> *To:* Carl-Johan Thore <carl-johan.thore at liu.se>
>>> *Cc:* Carl-Johan Thore <carljohanthore at gmail.com>;
>>> petsc-users at mcs.anl.gov
>>> *Subject:* Re: [petsc-users] PCFIELDSPLIT with MATSBAIJ
>>>
>>>
>>>
>>>
>>> On 26 Aug 2023, at 11:16 PM, Carl-Johan Thore <carl-johan.thore at liu.se>
>>> wrote:
>>>
>>> "(Sadly) MATSBAIJ is extremely broken, in particular, it cannot be used
>>> to retrieve rectangular blocks in MatCreateSubMatrices, thus you cannot get
>>> the A01 and A10 blocks in PCFIELDSPLIT.
>>> I have a branch that fixes this, but I haven’t rebased in a while (and
>>> I’m AFK right now), would you want me to rebase and give it a go, or must
>>> you stick to a release tarball?"
>>>
>>> Ok, would be great if you could look at this! I don't need to stick to
>>> any particular branch.
>>>
>>> Do you think MATNEST could be an alternative here?
>>>
>>>
>>> Well, your A00 and A11 will possibly be SBAIJ also, so you’ll end up
>>> with the same issue.
>>> I’m using both approaches (monolithic SBAIJ or Nest + SBAIJ), it was
>>> crashing but I think it was thoroughly fixed in
>>> https://gitlab.com/petsc/petsc/-/commits/jolivet/feature-matcreatesubmatrices-rectangular-sbaij/
>>> It is ugly code on top of ugly code, so I didn’t try to get it
>>> integrated and just used the branch locally, and then moved to some other
>>> stuff.
>>> I’ll rebase on top of main and try to get it integrated if it could be
>>> useful to you (but I’m traveling right now so everything gets done more
>>> slowly, sorry).
>>>
>>> Thanks,
>>> Pierre
>>>
>>>
>>> My matrix is
>>> [A00 A01;
>>> A01^t A11]
>>> so perhaps with MATNEST I can make use of the block-symmetry at least,
>>> and then use MATSBAIJ for
>>> A00 and A11 if it's possible to combine matrix types which the manual
>>> seems to imply.
>>>
>>> Kind regards
>>> Carl-Johan
>>>
>>>
>>>
>>> On 26 Aug 2023, at 10:09 PM, Carl-Johan Thore <carljohanthore at gmail.com>
>>> wrote:
>>> 
>>> Hi,
>>>
>>> I'm trying to use PCFIELDSPLIT with MATSBAIJ in PETSc 3.19.4.
>>> According to the manual "[t]he fieldsplit preconditioner cannot
>>> currently be used with the MATBAIJ or MATSBAIJ data formats if the
>>> blocksize is larger than 1". Since my blocksize is exactly 1 it would
>>> seem that I can use PCFIELDSPLIT. But this fails with "PETSC ERROR: For
>>> symmetric format, iscol must equal isrow"
>>> from MatCreateSubMatrix_MPISBAIJ. Tracing backwards one ends up in
>>> fieldsplit.c at
>>>
>>> /* extract the A01 and A10 matrices */ ilink = jac->head;
>>> PetscCall(ISComplement(ilink->is_col, rstart, rend, &ccis)); if
>>> (jac->offdiag_use_amat) { PetscCall(MatCreateSubMatrix(pc->mat,
>>> ilink->is, ccis, MAT_INITIAL_MATRIX, &jac->B)); } else {
>>>        PetscCall(MatCreateSubMatrix(pc->pmat, ilink->is, ccis,
>>> MAT_INITIAL_MATRIX, &jac->B)); }
>>>
>>> This, since my A01 and A10 are not square, seems to explain why iscol is
>>> not equal to isrow.
>>> From this I gather that it is in general NOT possible to use
>>> PCFIELDSPLIT with MATSBAIJ even with block size 1?
>>>
>>> Kind regards,
>>> Carl-Johan
>>>
>>>
>>>
>>
>> <experiment_with_sbaij.txt>
>
>
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