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 <[email protected]> wrote: > *External Email* > On Thu, Apr 2, 2020 at 11:33 PM Alexander B Prescott < > [email protected]> 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 [email protected] >> 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 >> [email protected] >> 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 [email protected] PhD Candidate, The University of Arizona Department of Geosciences 1040 E. 4th Street Tucson, AZ, 85721
