[petsc-users] gamg and zero pivots

[Barry Smith]

> On Sep 19, 2015, at 9:14 PM, Gideon Simpson <gideon.simpson at gmail.com> wrote:
> 
> Yes, I know exactly where the zero diagonal entries are.  Is there a way to compensate for that?

  Not really. How can you update x_i if A_ii = 0 ?


> 
> -gideon
> 
>> On Sep 19, 2015, at 10:09 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>> 
>> 
>>  Oh, it is a different kind of zero pivot value. There is a zero on the diagonal while it is trying to do SOR.  Should there be zeros on the diagonal of your matrix? 
>> 
>>   You can use -mg_levels_pc_type jacobi  and it will ignore those zero values.
>> 
>>   Barry
>> 
>> 
>>> On Sep 19, 2015, at 7:12 PM, Gideon Simpson <gideon.simpson at gmail.com> wrote:
>>> 
>>> I never get to see the output.  When it runs, I get:
>>> 
>>>  0 SNES Function norm 8.405398322914e-02 
>>> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>>> [0]PETSC ERROR: Zero pivot in LU factorization: http://www.mcs.anl.gov/petsc/documentation/faq.html#zeropivot
>>> [0]PETSC ERROR: Zero pivot 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 3.6.1, unknown 
>>> [0]PETSC ERROR: ./blowup_refine on a arch-darwin-c-debug named gs_air by gideon Sat Sep 19 20:11:44 2015
>>> [0]PETSC ERROR: Configure options --download-mpich=yes --download-suitesparse=yes --download-superlu=yes --download-superlu_dist=yes --download-mumps=yes --download-sprng=yes --with-cxx=clang++ --with-cc=clang --with-fc=gfortran --download-metis=yes --download-parmetis=yes --download-scalapack=yes
>>> [0]PETSC ERROR: #1 MatSOR_SeqAIJ_Inode() line 2795 in /opt/petsc/src/mat/impls/aij/seq/inode.c
>>> [0]PETSC ERROR: #2 MatSOR_MPIAIJ() line 1496 in /opt/petsc/src/mat/impls/aij/mpi/mpiaij.c
>>> [0]PETSC ERROR: #3 MatSOR() line 3697 in /opt/petsc/src/mat/interface/matrix.c
>>> [0]PETSC ERROR: #4 PCApply_SOR() line 37 in /opt/petsc/src/ksp/pc/impls/sor/sor.c
>>> [0]PETSC ERROR: #5 PCApply() line 483 in /opt/petsc/src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: #6 KSP_PCApply() line 242 in /opt/petsc/include/petsc/private/kspimpl.h
>>> [0]PETSC ERROR: #7 KSPInitialResidual() line 63 in /opt/petsc/src/ksp/ksp/interface/itres.c
>>> [0]PETSC ERROR: #8 KSPSolve_GMRES() line 235 in /opt/petsc/src/ksp/ksp/impls/gmres/gmres.c
>>> [0]PETSC ERROR: #9 KSPSolve() line 604 in /opt/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: #10 KSPSolve_Chebyshev() line 381 in /opt/petsc/src/ksp/ksp/impls/cheby/cheby.c
>>> [0]PETSC ERROR: #11 KSPSolve() line 604 in /opt/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: #12 PCMGMCycle_Private() line 19 in /opt/petsc/src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: #13 PCApply_MG() line 340 in /opt/petsc/src/ksp/pc/impls/mg/mg.c
>>> [0]PETSC ERROR: #14 PCApply() line 483 in /opt/petsc/src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: #15 KSP_PCApply() line 242 in /opt/petsc/include/petsc/private/kspimpl.h
>>> [0]PETSC ERROR: #16 KSPInitialResidual() line 63 in /opt/petsc/src/ksp/ksp/interface/itres.c
>>> [0]PETSC ERROR: #17 KSPSolve_GMRES() line 235 in /opt/petsc/src/ksp/ksp/impls/gmres/gmres.c
>>> [0]PETSC ERROR: #18 KSPSolve() line 604 in /opt/petsc/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: #19 SNESSolve_NEWTONLS() line 233 in /opt/petsc/src/snes/impls/ls/ls.c
>>> [0]PETSC ERROR: #20 SNESSolve() line 3906 in /opt/petsc/src/snes/interface/snes.c
>>> [1]PETSC ERROR: #1 VecNorm_MPI() line 63 in /opt/petsc/src/vec/vec/impls/mpi/pvec2.c
>>> [1]PETSC ERROR: #2 VecNorm() line 242 in /opt/petsc/src/vec/vec/interface/rvector.c
>>> [1]PETSC ERROR: #3 VecNormalize() line 337 in /opt/petsc/src/vec/vec/interface/rvector.c
>>> [1]PETSC ERROR: #4 KSPGMRESCycle() line 127 in /opt/petsc/src/ksp/ksp/impls/gmres/gmres.c
>>> [1]PETSC ERROR: #5 KSPSolve_GMRES() line 236 in /opt/petsc/src/ksp/ksp/impls/gmres/gmres.c
>>> [1]PETSC ERROR: #6 KSPSolve() line 604 in /opt/petsc/src/ksp/ksp/interface/itfunc.c
>>> [1]PETSC ERROR: #7 KSPSolve_Chebyshev() line 381 in /opt/petsc/src/ksp/ksp/impls/cheby/cheby.c
>>> [1]PETSC ERROR: #8 KSPSolve() line 604 in /opt/petsc/src/ksp/ksp/interface/itfunc.c
>>> [1]PETSC ERROR: #9 PCMGMCycle_Private() line 19 in /opt/petsc/src/ksp/pc/impls/mg/mg.c
>>> [1]PETSC ERROR: #10 PCApply_MG() line 340 in /opt/petsc/src/ksp/pc/impls/mg/mg.c
>>> [1]PETSC ERROR: #11 PCApply() line 483 in /opt/petsc/src/ksp/pc/interface/precon.c
>>> [1]PETSC ERROR: #12 KSP_PCApply() line 242 in /opt/petsc/include/petsc/private/kspimpl.h
>>> [1]PETSC ERROR: #13 KSPInitialResidual() line 63 in /opt/petsc/src/ksp/ksp/interface/itres.c
>>> [1]PETSC ERROR: #14 KSPSolve_GMRES() line 235 in /opt/petsc/src/ksp/ksp/impls/gmres/gmres.c
>>> [1]PETSC ERROR: #15 KSPSolve() line 604 in /opt/petsc/src/ksp/ksp/interface/itfunc.c
>>> [1]PETSC ERROR: #16 SNESSolve_NEWTONLS() line 233 in /opt/petsc/src/snes/impls/ls/ls.c
>>> [1]PETSC ERROR: #17 SNESSolve() line 3906 in /opt/petsc/src/snes/interface/snes.c
>>> 
>>> and then it just sits there.
>>> 
>>> -gideon
>>> 
>>>> On Sep 19, 2015, at 7:18 PM, Matthew Knepley <knepley at gmail.com> wrote:
>>>> 
>>>> On Sat, Sep 19, 2015 at 6:10 PM, Gideon Simpson <gideon.simpson at gmail.com> wrote:
>>>> It gives zero pivots on:
>>>> 
>>>> Send -ksp_view
>>>> 
>>>>  Matt
>>>> 
>>>> -ksp_type gmres -pc_type gamg -mg_coarse_sub_pc_factor_shift_type NONZERO
>>>> 
>>>> It has no problem with:
>>>> 
>>>> -ksp_type gmres -pc_type bjacobi -sub_pc_factor_shift_type NONZERO
>>>> 
>>>> -gideon
>>>> 
>>>>> On Sep 19, 2015, at 12:37 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>>>>> 
>>>>> 
>>>>>> On Sep 18, 2015, at 10:42 PM, Gideon Simpson <gideon.simpson at gmail.com> wrote:
>>>>>> 
>>>>>> I’m getting a zero pivot in LU factorization error when I use the gamg preconditioner.  I know there is some issue with my matrix, as I get the same error if I use pc_type lu in serial, or if I use pc_type bjacobi in parallel, both of which are corrected by adding -pc_factor_shift_type NONZERO -sub_pc_factor_shift_type NONZERO, respectively.  However, I can’t quite seem to figure out the analogous command to use for the gamg preconditioner.
>>>>> 
>>>>> You need to figure out the prefix to the option that is added by gamg to set it. One way is to run with the gamg options and -help and grep for factor_shift.
>>>>> 
>>>>>  The option is like something like -mg_coarse_pc_factor_shift_type nonzero or -mg_coarse_sub_pc_factor_shift_type
>>>>> 
>>>>> Barry
>>>>> 
>>>>>> 
>>>>>> -gideon
>>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> -- 
>>>> 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
>>> 
>> 
>