[petsc-users] [EXT]Re: Zero diagonal Error Code with all non-zero diagonal entries

Fri Apr 3 11:20:14 CDT 2020

Hi Matt,

Thanks for your help. I've done as you suggested and it still doesn't work
-- I get the same error message as before if I add the -snes_fd flag to the
command line. I also added -info and included that output below. Also, a
similar error is returned with other PC types, e.g LU.

[0] PetscInitialize(): PETSc successfully started: number of processors = 1
[0] PetscGetHostName(): Rejecting domainname, likely is NIS login2.(none)
[0] PetscInitialize(): Running on machine: login2
[0] PetscCommDuplicate(): Duplicating a communicator 1140850688 -2080374784
max tags = 268435455
[0] PetscCommDuplicate(): Using internal PETSc communicator 1140850688
-2080374784
[0] DMGetDMSNES(): Creating new DMSNES
[0] PetscGetHostName(): Rejecting domainname, likely is NIS login2.(none)
[0] SNESSetFromOptions(): Setting default finite difference Jacobian matrix
[0] DMCreateMatrix_Shell(): Naively creating matrix using global vector
distribution without preallocation
[0] MatSetUp(): Warning not preallocating matrix storage
[0] DMGetDMKSP(): Creating new DMKSP
  0 SNES Function norm 1.000000000000e+01
[0] MatAssemblyEnd_SeqAIJ(): Matrix size: 25 X 25; storage space: 70
unneeded,55 used
[0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues() is 0
[0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 3
[0] MatCheckCompressedRow(): Found the ratio (num_zerorows
0)/(num_localrows 25) < 0.6. Do not use CompressedRow routines.
[0] MatSeqAIJCheckInode(): Found 25 nodes out of 25 rows. Not using Inode
routines
[0] SNESComputeJacobian(): Rebuilding preconditioner
[0] PCSetUp(): Setting up PC for first time
[0] PCSetUp_MG(): Using outer operators to define finest grid operator
  because PCMGGetSmoother(pc,nlevels-1,&ksp);KSPSetOperators(ksp,...); was
not called.
[0] PCSetUp(): Setting up PC for first time
[0] PCSetUp(): Leaving PC with identical preconditioner since operator is
unchanged
[0] PCSetUp(): Leaving PC with identical preconditioner since operator is
unchanged
[0] PCSetUp(): Leaving PC with identical preconditioner since operator is
unchanged
[0]PETSC ERROR: --------------------- Error Message
--------------------------------------------------------------
[0]PETSC ERROR: Arguments are incompatible
[0]PETSC ERROR: Zero diagonal on row 0
[0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for
trouble shooting.
....

Best,
Alexander

On Thu, Apr 2, 2020 at 9:07 PM Matthew Knepley <knepley at gmail.com> wrote:

> *External Email*
> On Thu, Apr 2, 2020 at 11:33 PM Alexander B Prescott <
> alexprescott at email.arizona.edu> wrote:
>
>> Hello,
>>
>> I am teaching myself how to use Petsc for nonlinear equations and I've
>> run into a problem that I can't quite figure out. I am trying to use the
>> matrix coloring routines for the finite difference Jacobian approximation,
>> and I've followed the steps in the manual to do this.
>> When I run the program with a MG preconditioner, I get back the error:
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> ----------------------------
>> [0]PETSC ERROR: Arguments are incompatible
>> [0]PETSC ERROR: Zero diagonal on row 0
>> .....
>>
>>
> The easiest thing to try is just comment out all your matrix stuff
> including SNESSetJacobian(). PETSc will do the coloring automatically.
> If this works, you know its your coloring. If not, then its something with
> the MG setup.
>
>   Thanks,
>
>     Matt
>
>
>> What's interesting is that after I've added non-zero entries to the
>> matrix with MatrixSetValues() and assembled the matrix
>> with MatAssemblyBegin() + MatAssemblyEnd(), I can verify that every
>> diagonal entry is non-zero with a call to MatGetValues. I've included a
>> relevant code snippet below and I'm happy to send more. Any guidance is
>> greatly appreciated.
>>
>> Command line:
>>
>> mpirun -n 1 ./program -snes_view -snes_converged_reason -snes_monitor
>> -ksp_monitor -ksp_converged_reason -pc_type mg
>>
>> Code snippet:
>>
>> ierr = FormJacobianColoring(snes,J);CHKERRQ(ierr); // this function set's
>> matrix values and assembles the matrix
>>
>> // removed the code, but this is where I've used MatGetValues() to ensure
>> that the diagonal of J (as well as other entries) has been set to 1.0
>>
>> ierr = MatColoringCreate(J,&coloring);CHKERRQ(ierr);
>> ierr = MatColoringSetType(coloring,MATCOLORINGSL);CHKERRQ(ierr);
>> ierr = MatColoringSetFromOptions(coloring);CHKERRQ(ierr);
>> ierr = MatColoringApply(coloring,&iscoloring);CHKERRQ(ierr);
>> ierr = MatColoringDestroy(&coloring);CHKERRQ(ierr);
>> /*
>> Create the data structure that SNESComputeJacobianDefaultColor() uses to
>> compute the actual Jacobians via finite differences.
>> */
>> ierr = MatFDColoringCreate(J,iscoloring,&fdcoloring);CHKERRQ(ierr);
>> ierr = MatFDColoringSetFunction(fdcoloring,(PetscErrorCode
>> (*)(void))FormFunction,NULL);CHKERRQ(ierr);
>> ierr = MatFDColoringSetFromOptions(fdcoloring);CHKERRQ(ierr);
>> ierr = MatFDColoringSetUp(J,iscoloring,fdcoloring);CHKERRQ(ierr);
>> ierr =
>> SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,fdcoloring);CHKERRQ(ierr);
>>
>> ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
>>
>> ierr = VecSet(x,0.001);CHKERRQ(ierr);
>> ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr);
>>
>>
>>
>> And here's the full error code:
>>
>> [0]PETSC ERROR: --------------------- Error Message
>> --------------------------------------------------------------
>> [0]PETSC ERROR: Arguments are incompatible
>> [0]PETSC ERROR: Zero diagonal on row 0
>> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> for trouble shooting.
>> [0]PETSC ERROR: Petsc Release Version 3.10.3, Dec, 18, 2018
>> [0]PETSC ERROR: ./petsc_flowroute on a  named i0n22 by alexprescott Thu
>> Apr  2 20:14:01 2020
>> [0]PETSC ERROR: Configure options --prefix=/cm/shared/uaapps/petsc/3.10.3
>> --download-fblaslapack --download-metis --download-parmetis
>> --download-hypre PETSC_ARCH=linux-gnu --with-debugging=no COPTFLAGS=-O3
>> CXXOPTFLAGS=-O3
>> [0]PETSC ERROR: #1 MatInvertDiagonal_SeqAIJ() line 1662 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/mat/impls/aij/seq/aij.c
>> [0]PETSC ERROR: #2 MatSOR_SeqAIJ() line 1693 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/mat/impls/aij/seq/aij.c
>> [0]PETSC ERROR: #3 MatSOR() line 3932 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/mat/interface/matrix.c
>> [0]PETSC ERROR: #4 PCApply_SOR() line 31 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/pc/impls/sor/sor.c
>> [0]PETSC ERROR: #5 PCApply() line 462 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/pc/interface/precon.c
>> [0]PETSC ERROR: #6 KSP_PCApply() line 281 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/include/petsc/private/kspimpl.h
>> [0]PETSC ERROR: #7 KSPInitialResidual() line 67 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/interface/itres.c
>> [0]PETSC ERROR: #8 KSPSolve_GMRES() line 233 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/impls/gmres/gmres.c
>> [0]PETSC ERROR: #9 KSPSolve() line 780 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/interface/itfunc.c
>> [0]PETSC ERROR: #10 KSPSolve_Chebyshev() line 367 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/impls/cheby/cheby.c
>> [0]PETSC ERROR: #11 KSPSolve() line 780 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/interface/itfunc.c
>> [0]PETSC ERROR: #12 PCMGMCycle_Private() line 20 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/pc/impls/mg/mg.c
>> [0]PETSC ERROR: #13 PCApply_MG() line 377 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/pc/impls/mg/mg.c
>> [0]PETSC ERROR: #14 PCApply() line 462 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/pc/interface/precon.c
>> [0]PETSC ERROR: #15 KSP_PCApply() line 281 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/include/petsc/private/kspimpl.h
>> [0]PETSC ERROR: #16 KSPInitialResidual() line 67 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/interface/itres.c
>> [0]PETSC ERROR: #17 KSPSolve_GMRES() line 233 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/impls/gmres/gmres.c
>> [0]PETSC ERROR: #18 KSPSolve() line 780 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/ksp/ksp/interface/itfunc.c
>> [0]PETSC ERROR: #19 SNESSolve_NEWTONLS() line 224 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/snes/impls/ls/ls.c
>> [0]PETSC ERROR: #20 SNESSolve() line 4397 in
>> /cm/local/uabuild/petsc/petsc-3.10.3/src/snes/interface/snes.c
>> [0]PETSC ERROR: #21 main() line 705 in
>> /home/u16/alexprescott/petsc_example/flowroute/petsc_flowroute.c
>> [0]PETSC ERROR: PETSc Option Table entries:
>> [0]PETSC ERROR: -ksp_converged_reason
>> [0]PETSC ERROR: -ksp_monitor
>> [0]PETSC ERROR: -pc_type mg
>> [0]PETSC ERROR: -snes_converged_reason
>> [0]PETSC ERROR: -snes_monitor
>> [0]PETSC ERROR: -snes_view
>> [0]PETSC ERROR: ----------------End of Error Message -------send entire
>> error message to petsc-maint at mcs.anl.gov----------
>> application called MPI_Abort(MPI_COMM_WORLD, 75) - process 0
>>
>>
>> Printed matrix for a 25 x 25 example
>>
>> 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 1 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 1 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0 0 0 0
>> 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 0
>> 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 1 1 0 0 0
>> 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0 0
>> 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1 0
>> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 1 1 1
>>
>>
>>
>> Best,
>> Alexander
>>
>>
>>
>> --
>> Alexander Prescott
>> alexprescott at email.arizona.edu
>> PhD Candidate, The University of Arizona
>> Department of Geosciences
>> 1040 E. 4th Street
>> Tucson, AZ, 85721
>>
>
>
> --
> 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/
> <http://www.cse.buffalo.edu/~knepley/>
>

-- 
Alexander Prescott
alexprescott at email.arizona.edu
PhD Candidate, The University of Arizona
Department of Geosciences
1040 E. 4th Street
Tucson, AZ, 85721
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