Yes, I know exactly where the zero diagonal entries are. Is there a way to compensate for that?
-gideon > On Sep 19, 2015, at 10:09 PM, Barry Smith <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: >>> >>> On Sat, Sep 19, 2015 at 6:10 PM, Gideon Simpson <[email protected]> >>> 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 <[email protected]> wrote: >>>> >>>> >>>>> On Sep 18, 2015, at 10:42 PM, Gideon Simpson <[email protected]> >>>>> 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 >> >
