On Sun, 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. > Chebyshev/Jacobi is the obvious next try. Matt > -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 > > > > > > > -- 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
