> On Sep 20, 2015, at 12:40 PM, Gideon Simpson <[email protected]> wrote: > > Point taken. So this comes back to something that I began asking about in a > previous thread, but took a detour as you guys identified other problems with > my code. The issue is that I have a DMComposite with two blocks. One block > is of size two, and couples certain pieces of the second block, which is, > morally, a vector valued semilinear elliptic equation. Using grid > sequencing, the guesses for the SNES are now quite good, but I’m struggling > with the issue of preconditioning the linear problem. The second block > would, presumably, benefit from multigrid, but jacobi doesn’t do such a good > job on that. At the same time, the first block, as discussed, has these zeros > on the diagonal, and can’t use SOR.
I think we answered this before, this is what PCFIELDSPLIT is for. If the matrix looks like (logically if you reorder rows and columns) (A B ) (C 0 ) you should use something like -ksp_type fgmres -pc_type fieldsplit -pc_fieldsplit_detect_saddle_point -pc_fieldsplit_type schur -fieldsplit_0_ksp_type gmres -fieldsplit_0_pc_type gamg the detect saddle point flag automatically makes the first block fieldsplit_0 the block without the zeros on the diagonal and the second block fieldsplit_1 be the one with zeros on the diagonal. You will likely need to play around a bit with sub options to get great convergence but start by running with -ksp_monitor -fieldsplit_0_ksp_monitor_true_residual and see how it converges. Barry > > -gideon > >> On Sep 19, 2015, at 10:43 PM, Barry Smith <[email protected]> wrote: >> >> >>> On Sep 19, 2015, at 9:14 PM, Gideon Simpson <[email protected]> >>> 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 <[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 >>>>> >>>> >>> >> >
