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

Fri Apr 3 12:39:18 CDT 2020

On Fri, Apr 3, 2020 at 12:20 PM Alexander B Prescott <
alexprescott at email.arizona.edu> wrote:

> 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.
>

Great. I now suspect your residual is flawed. I have several suggestions:

  a) It looks like you might have an indexing bug, since your residual does
not depend on dof 0. PETSc uses 0-based indexing.

  b) I think the best initial check is to put in the exact solution and
check that the residual is 0. I do this in SNES ex5 using MMS.

  c) -snes_fd forms the Jacobian without coloring. Giving no options uses
coloring.

  Thanks,

     Matt

> [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
>

-- 
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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