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

Thu Apr 2 22:32:29 CDT 2020

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
.....

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
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