date:20240212

Re: [petsc-users] question on PCLSC with matrix blocks of type MATNEST

2024-02-12 Thread Pierre Jolivet



> On 13 Feb 2024, at 12:33 AM, Zhang, Hong  wrote:
> 
> Pierre,
> I just modified the error message of MatProductSymbolic() and added a testing 
> segment in src/mat/tests/ex195.c. I have not pushed my change yet.
> 
> Your fix at 
> https://gitlab.com/petsc/petsc/-/commit/9dcea022de3b0309e5c16b8c554ad9c85dea29cf?merge_request_iid=7283
>  is more general. Has this fix merged to release and main? With latest main 
> and release, I get same previous error message.

I don’t (anymore, but could prior to my fix).
The trigger is MatMatMult() with MAT_INITIAL_MATRIX in PCSetUp_LSC().
Reproducible with:
diff --git a/src/ksp/ksp/tutorials/ex27.c b/src/ksp/ksp/tutorials/ex27.c
index 116b7df8522..9bdf4d7334a 100644
--- a/src/ksp/ksp/tutorials/ex27.c
+++ b/src/ksp/ksp/tutorials/ex27.c
@@ -245,2 +245,5 @@ int main(int argc, char **args)
 PetscCall(MatCreateNest(PETSC_COMM_WORLD, 2, NULL, 2, NULL, array, ));
+Mat D;
+PetscCall(MatMatMult(C, C, MAT_INITIAL_MATRIX, PETSC_DECIDE, ));
+PetscCall(MatDestroy());
 if (!sbaij) PetscCall(MatNestSetVecType(C, VECNEST));
Which now generates:
$ ./ex27 -f ${DATAFILESPATH}/matrices/farzad_B_rhs -truncate -solve_augmented 
Failed to load RHS, so use a vector of all ones.
Failed to load initial guess, so use a vector of all zeros.
[0]PETSC ERROR: - Error Message 
--
[0]PETSC ERROR: No support for this operation for this object type
[0]PETSC ERROR: MatProduct AB not supported for nest and nest
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.

Thanks,
Pierre

> Hong
> 
> From: Pierre Jolivet 
> Sent: Sunday, February 11, 2024 7:43 AM
> To: Zhang, Hong 
> Cc: Hana Honnerová ; petsc-users@mcs.anl.gov 
> 
> Subject: Re: [petsc-users] question on PCLSC with matrix blocks of type 
> MATNEST
>  
> 
> On 8 Feb 2024, at 5:37 PM, Zhang, Hong via petsc-users 
>  wrote:
> 
> Hana,
> "product AB with A nest, B nest" is not supported by PETSc. I do not know why 
> PETSc does not display such an error message. I'll check it.
> 
> Did you?
> A naive fix is to simply add the missing PetscCheck() in MatProduct_Private() 
> right after 
> MatProductSetFromOptions()https://petsc.org/release/src/mat/interface/matrix.c.html#line10026
>  (notice that it is there line 10048 in the other code branch)
> I have this at 
> https://gitlab.com/petsc/petsc/-/commit/9dcea022de3b0309e5c16b8c554ad9c85dea29cf?merge_request_iid=7283
>  (coupled with code refactoring to avoid missing any other operations), but 
> maybe we could do things more elegantly.
> 
> Thanks,
> Pierre
> 
> Hong
> From: petsc-users  on behalf of Hana 
> Honnerová 
> Sent: Thursday, February 8, 2024 4:45 AM
> To: petsc-users@mcs.anl.gov 
> Subject: [petsc-users] question on PCLSC with matrix blocks of type MATNEST
>  
> Hi all,
> I am trying to solve linear systems arising from isogeometric discretization 
> (similar to FEM) of the Navier-Stokes equations in parallel using PETSc. The 
> linear systems are of saddle-point type, so I would like to use the 
> PCFIELDSPLIT preconditioner with the -pc_fieldsplit_detect_saddle_point 
> option, Schur complement factorization and the LSC Schur complement 
> preconditioner. I do not provide any user-defined operators for PCLSC in my 
> codes (at least for now).
> I store the matrix as a MATNEST consisting of 4 blocks (F for 
> velocity-velocity part, Bt for velocity-pressure part, B for 
> pressure-velocity part and NULL for pressure-pressure part). It is also 
> convenient for me to store the blocks F, Bt and B as another MATNEST 
> consisting of blocks corresponding to individual velocity components. 
> 
> However, in this setting, I get the following error message:
> [0]PETSC ERROR: Petsc has generated inconsistent data
> [0]PETSC ERROR: Unspecified symbolic phase for product AB with A nest, B 
> nest. Call MatProductSetFromOptions() first
> [0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.20.4, unknown 
> [0]PETSC ERROR: 
> /home/hhornik/gismo/build-petsc-mpi/RelWithDebInfo/bin/gsINSSolverPETScTest 
> on a arch-debug named ThinkPad-T14 by hhornik Thu Feb  8 11:04:17 2024
> [0]PETSC ERROR: Configure options PETSC_ARCH=arch-debug --with-debugging=1 
> --download-mumps --download-scalapack
> [0]PETSC ERROR: #1 MatProductSymbolic() at 
> /home/hhornik/Software/PETSc/src/mat/interface/matproduct.c:807
> [0]PETSC ERROR: #2 MatProduct_Private() at 
> /home/hhornik/Software/PETSc/src/mat/interface/matrix.c:10027
> [0]PETSC ERROR: #3 MatMatMult() at 
> /home/hhornik/Software/PETSc/src/mat/interface/matrix.c:10103
> [0]PETSC ERROR: #4 PCSetUp_LSC() at 
> /home/hhornik/Software/PETSc/src/ksp/pc/impls/lsc/lsc.c:79
> [0]PETSC ERROR: #5 PCSetUp() at 
> /home/hhornik/Software/PETSc/src/ksp/pc/interface/precon.c:1080
> [0]PETSC ERROR: #6 KSPSetUp() at 
> /home/hhornik/Software/PETSc/src/ksp/ksp/interface/itfunc.c:415
> [0]PETSC

Re: [petsc-users] question on PCLSC with matrix blocks of type MATNEST

2024-02-12 Thread Zhang, Hong via petsc-users

Pierre,
I just modified the error message of MatProductSymbolic() and added a testing 
segment in src/mat/tests/ex195.c. I have not pushed my change yet.

Your fix at 
https://gitlab.com/petsc/petsc/-/commit/9dcea022de3b0309e5c16b8c554ad9c85dea29cf?merge_request_iid=7283
 is more general. Has this fix merged to release and main? With latest main and 
release, I get same previous error message.
Hong


From: Pierre Jolivet 
Sent: Sunday, February 11, 2024 7:43 AM
To: Zhang, Hong 
Cc: Hana Honnerová ; petsc-users@mcs.anl.gov 

Subject: Re: [petsc-users] question on PCLSC with matrix blocks of type MATNEST


On 8 Feb 2024, at 5:37 PM, Zhang, Hong via petsc-users 
 wrote:

Hana,
"product AB with A nest, B nest" is not supported by PETSc. I do not know why 
PETSc does not display such an error message. I'll check it.

Did you?
A naive fix is to simply add the missing PetscCheck() in MatProduct_Private() 
right after MatProductSetFromOptions() 
https://petsc.org/release/src/mat/interface/matrix.c.html#line10026 (notice 
that it is there line 10048 in the other code branch)
I have this at 
https://gitlab.com/petsc/petsc/-/commit/9dcea022de3b0309e5c16b8c554ad9c85dea29cf?merge_request_iid=7283
 (coupled with code refactoring to avoid missing any other operations), but 
maybe we could do things more elegantly.

Thanks,
Pierre

Hong

From: petsc-users  on behalf of Hana Honnerová 

Sent: Thursday, February 8, 2024 4:45 AM
To: petsc-users@mcs.anl.gov 
Subject: [petsc-users] question on PCLSC with matrix blocks of type MATNEST

Hi all,
I am trying to solve linear systems arising from isogeometric discretization 
(similar to FEM) of the Navier-Stokes equations in parallel using PETSc. The 
linear systems are of saddle-point type, so I would like to use the 
PCFIELDSPLIT preconditioner with the -pc_fieldsplit_detect_saddle_point option, 
Schur complement factorization and the LSC Schur complement preconditioner. I 
do not provide any user-defined operators for PCLSC in my codes (at least for 
now).
I store the matrix as a MATNEST consisting of 4 blocks (F for velocity-velocity 
part, Bt for velocity-pressure part, B for pressure-velocity part and NULL for 
pressure-pressure part). It is also convenient for me to store the blocks F, Bt 
and B as another MATNEST consisting of blocks corresponding to individual 
velocity components.

However, in this setting, I get the following error message:
[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Unspecified symbolic phase for product AB with A nest, B nest. 
Call MatProductSetFromOptions() first
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.20.4, unknown
[0]PETSC ERROR: 
/home/hhornik/gismo/build-petsc-mpi/RelWithDebInfo/bin/gsINSSolverPETScTest on 
a arch-debug named ThinkPad-T14 by hhornik Thu Feb  8 11:04:17 2024
[0]PETSC ERROR: Configure options PETSC_ARCH=arch-debug --with-debugging=1 
--download-mumps --download-scalapack
[0]PETSC ERROR: #1 MatProductSymbolic() at 
/home/hhornik/Software/PETSc/src/mat/interface/matproduct.c:807
[0]PETSC ERROR: #2 MatProduct_Private() at 
/home/hhornik/Software/PETSc/src/mat/interface/matrix.c:10027
[0]PETSC ERROR: #3 MatMatMult() at 
/home/hhornik/Software/PETSc/src/mat/interface/matrix.c:10103
[0]PETSC ERROR: #4 PCSetUp_LSC() at 
/home/hhornik/Software/PETSc/src/ksp/pc/impls/lsc/lsc.c:79
[0]PETSC ERROR: #5 PCSetUp() at 
/home/hhornik/Software/PETSc/src/ksp/pc/interface/precon.c:1080
[0]PETSC ERROR: #6 KSPSetUp() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/interface/itfunc.c:415
[0]PETSC ERROR: #7 KSPSolve_Private() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/interface/itfunc.c:832
[0]PETSC ERROR: #8 KSPSolve() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/interface/itfunc.c:1079
[0]PETSC ERROR: #9 PCApply_FieldSplit_Schur() at 
/home/hhornik/Software/PETSc/src/ksp/pc/impls/fieldsplit/fieldsplit.c:1165
[0]PETSC ERROR: #10 PCApply() at 
/home/hhornik/Software/PETSc/src/ksp/pc/interface/precon.c:498
[0]PETSC ERROR: #11 KSP_PCApply() at 
/home/hhornik/Software/PETSc/include/petsc/private/kspimpl.h:383
[0]PETSC ERROR: #12 KSPFGMRESCycle() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c:123
[0]PETSC ERROR: #13 KSPSolve_FGMRES() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/impls/gmres/fgmres/fgmres.c:235
[0]PETSC ERROR: #14 KSPSolve_Private() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/interface/itfunc.c:906
[0]PETSC ERROR: #15 KSPSolve() at 
/home/hhornik/Software/PETSc/src/ksp/ksp/interface/itfunc.c:1079
[0]PETSC ERROR: #16 applySolver() at 
/home/hhornik/gismo/optional/gsIncompressibleFlow/src/gsINSSolver.hpp:531

I could not find any solution for this so far. My question is: Is it possible 
to use the LSC preconditioner in such case, where the matrix blocks are of type 
MATNEST? And if so, how?
Thank you,
Hana Honnerova

Re: [petsc-users] Near nullspace lost in fieldsplit

2024-02-12 Thread Barry Smith


   7279 does change the code for MatZeroRowsColumns_MPIAIJ(). But perhaps that 
does not resolve the problem you are seeing? If that is the case we will need a 
reproducible example so we can determine exactly what else is happening in your 
code to cause the difficulties. 

Here is the diff for  MatZeroRowsColumns_MPIAIJ()

@@ -1026,7 +1023,7 @@ static PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A, 
PetscInt N, const PetscIn
   PetscCall(PetscFree(lrows));
 
   /* only change matrix nonzero state if pattern was allowed to be changed */
-  if (!((Mat_SeqAIJ *)(l->A->data))->keepnonzeropattern) {
+  if (!((Mat_SeqAIJ *)(l->A->data))->nonew) {
 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate;
 PetscCall(MPIU_Allreduce(, >nonzerostate, 1, MPIU_INT64, MPI_SUM, 
PetscObjectComm((PetscObject)A)));
   }




> On Feb 12, 2024, at 7:02 AM, Jeremy Theler (External) 
>  wrote:
> 
> Hi Barry
> 
> >   The bug fix for 2 is availabel in 
> > https://gitlab.com/petsc/petsc/-/merge_requests/7279
> 
> Note that our code goes through   MatZeroRowsColumns_MPIAIJ() not through 
> MatZeroRows_MPIAIJ() so this fix does not change anything for the case I 
> mentioned.
> 
> --
> jeremy

Re: [petsc-users] Near nullspace lost in fieldsplit

2024-02-12 Thread Matthew Knepley

On Mon, Feb 12, 2024 at 7:10 AM Jeremy Theler (External) <
jeremy.theler-...@ansys.com> wrote:

> Hi Barry
>
> >   The bug fix for 2 is availabel in
> https://gitlab.com/petsc/petsc/-/merge_requests/7279
>
> Note that our code goes through   MatZeroRowsColumns_MPIAIJ() not through
> MatZeroRows_MPIAIJ() so this fix does not change anything for the case I
> mentioned.
>

The other fixes are in https://gitlab.com/petsc/petsc/-/merge_requests/7279

  Thanks,

 Matt


> --
> jeremy
>


-- 
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/

Re: [petsc-users] Near nullspace lost in fieldsplit

2024-02-12 Thread Jeremy Theler (External)

Hi Barry

>   The bug fix for 2 is availabel in 
> https://gitlab.com/petsc/petsc/-/merge_requests/7279

Note that our code goes through   MatZeroRowsColumns_MPIAIJ() not through 
MatZeroRows_MPIAIJ() so this fix does not change anything for the case I 
mentioned.

--
jeremy

Re: [petsc-users] question on PCLSC with matrix blocks of type MATNEST

Re: [petsc-users] question on PCLSC with matrix blocks of type MATNEST

Re: [petsc-users] Near nullspace lost in fieldsplit

Re: [petsc-users] Near nullspace lost in fieldsplit

Re: [petsc-users] Near nullspace lost in fieldsplit

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