[petsc-users] Zero diagonal Error Code with all non-zero diagonal entries
Matthew Knepley
knepley at gmail.com
Thu Apr 2 23:06:51 CDT 2020
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/>
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