[petsc-users] ML - zero pivot error
Benjamin Sanderse
B.Sanderse at cwi.nl
Tue Jul 17 07:07:50 CDT 2012
The two processor case does not reach far enough that ksp_view gives me output. The one processor case gives me the output below.
I also added -mg_levels_pc_factor_shift_type nonzero, but still with the same error.
Benjamin
KSP Object: 1 MPI processes
type: cg
maximum iterations=500
tolerances: relative=1e-10, absolute=1e-10, divergence=10000
left preconditioning
has attached null space
using nonzero initial guess
using PRECONDITIONED norm type for convergence test
PC Object: 1 MPI processes
type: ml
MG: type is MULTIPLICATIVE, levels=4 cycles=v
Cycles per PCApply=1
Using Galerkin computed coarse grid matrices
Coarse grid solver -- level -------------------------------
KSP Object: (mg_coarse_) 1 MPI processes
type: preonly
maximum iterations=1, initial guess is zero
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using NONE norm type for convergence test
PC Object: (mg_coarse_) 1 MPI processes
type: lu
LU: out-of-place factorization
tolerance for zero pivot 2.22045e-14
using diagonal shift to prevent zero pivot
matrix ordering: nd
factor fill ratio given 5, needed 1
Factored matrix follows:
Matrix Object: 1 MPI processes
type: seqaij
rows=1, cols=1
package used to perform factorization: petsc
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
not using I-node routines
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=1, cols=1
total: nonzeros=1, allocated nonzeros=1
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Down solver (pre-smoother) on level 1 -------------------------------
KSP Object: (mg_levels_1_) 1 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_1_) 1 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=6, cols=6
total: nonzeros=36, allocated nonzeros=36
total number of mallocs used during MatSetValues calls =0
using I-node routines: found 2 nodes, limit used is 5
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 2 -------------------------------
KSP Object: (mg_levels_2_) 1 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_2_) 1 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=130, cols=130
total: nonzeros=2704, allocated nonzeros=2704
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Up solver (post-smoother) same as down solver (pre-smoother)
Down solver (pre-smoother) on level 3 -------------------------------
KSP Object: (mg_levels_3_) 1 MPI processes
type: richardson
Richardson: damping factor=1
maximum iterations=2
tolerances: relative=1e-05, absolute=1e-50, divergence=10000
left preconditioning
using nonzero initial guess
using NONE norm type for convergence test
PC Object: (mg_levels_3_) 1 MPI processes
type: sor
SOR: type = local_symmetric, iterations = 1, local iterations = 1, omega = 1
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=1000, cols=1000
total: nonzeros=6400, allocated nonzeros=6400
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Up solver (post-smoother) same as down solver (pre-smoother)
linear system matrix = precond matrix:
Matrix Object: 1 MPI processes
type: seqaij
rows=1000, cols=1000
total: nonzeros=6400, allocated nonzeros=6400
total number of mallocs used during MatSetValues calls =0
not using I-node routines
Op 17 jul 2012, om 12:58 heeft Matthew Knepley het volgende geschreven:
> On Tue, Jul 17, 2012 at 3:23 AM, Benjamin Sanderse <B.Sanderse at cwi.nl> wrote:
> Hello all,
>
> I am trying to use ML to solve a Poisson equation with Neumann BC (singular matrix) and found the thread below to avoid a zero pivot error. I used the option that Barry suggests, -mg_coarse_pc_factor_shift_type nonzero, which works, but only when I run on a single processor. For two or more processors I still get a zero pivot error. Are there more options to be set for the parallel case?
>
> Should still work. Can you check that the prefix for the coarse solver is correct with -ksp_view?
>
> Matt
>
> Benjamin
>
>
> [1]PETSC ERROR: --------------------- Error Message ------------------------------------
> [1]PETSC ERROR: Detected zero pivot in LU factorization:
> see http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot!
> [1]PETSC ERROR: Zero pivot row 1 value 5.7431e-18 tolerance 2.22045e-14!
> [1]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 1, Fri Jun 15 09:30:49 CDT 2012
> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> [1]PETSC ERROR: [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Detected zero pivot in LU factorization:
> see http://www.mcs.anl.gov/petsc/documentation/faq.html#ZeroPivot!
> [0]PETSC ERROR: Zero pivot row 1 value 5.7431e-18 tolerance 2.22045e-14!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 1, Fri Jun 15 09:30:49 CDT 2012
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: bin/navier-stokes on a linux-gnu named gb-r3n32.irc.sara.nl by sanderse Tue Jul 17 10:04:05 2012
> [0]PETSC ERROR: Libraries linked from /home/sanderse/Software/petsc-3.3-p1/linux-gnu-c-debug/lib
> [0]PETSC ERROR: Configure run at Mon Jul 16 21:06:33 2012
> [0]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx --with-shared-libraries --with-hypre --download-hypre --with-blas-lapack-dir=/sara
> /sw/intel/Compiler/11.0/069 --with-hdf5 --download-hdf5 --with-debugging=0 --download-ml
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: MatPivotCheck_none() line 583 in /home/sanderse/Software/petsc-3.3-p1/include/petsc-private/matimpl.h
> [0]PETSC ERROR: MatPivotCheck() line 602 in /home/sanderse/Software/petsc-3.3-p1/include/petsc-private/matimpl.h
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [1]PETSC ERROR: See docs/index.html for manual pages.
> [1]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: bin/navier-stokes on a linux-gnu named gb-r3n32.irc.sara.nl by sanderse Tue Jul 17 10:04:05 2012
> [1]PETSC ERROR: Libraries linked from /home/sanderse/Software/petsc-3.3-p1/linux-gnu-c-debug/lib
> [1]PETSC ERROR: Configure run at Mon Jul 16 21:06:33 2012
> [1]PETSC ERROR: Configure options --with-cc=mpicc --with-fc=mpif90 --with-cxx=mpicxx --with-shared-libraries --with-hypre --download-hypre --with-blas-lapack-dir=/sara
> /sw/intel/Compiler/11.0/069 --with-hdf5 --download-hdf5 --with-debugging=0 --download-ml
> [1]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: MatPivotCheck_none() line 583 in /home/sanderse/Software/petsc-3.3-p1/include/petsc-private/matimpl.h
> MatLUFactorNumeric_SeqAIJ_Inode() line 1469 in /home/sanderse/Software/petsc-3.3-p1/src/mat/impls/aij/seq/inode.c
> [0]PETSC ERROR: MatLUFactorNumeric() line 2790 in /home/sanderse/Software/petsc-3.3-p1/src/mat/interface/matrix.c
> [0]PETSC ERROR: PCSetUp_LU() line 160 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/factor/lu/lu.c
> [0]PETSC ERROR: PCSetUp() line 832 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 278 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: PCSetUp_Redundant() line 176 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/redundant/redundant.c
> [0]PETSC ERROR: PCSetUp() line 832 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 278 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: PCSetUp_MG() line 729 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/mg/mg.c
> [0]PETSC ERROR: [1]PETSC ERROR: MatPivotCheck() line 602 in /home/sanderse/Software/petsc-3.3-p1/include/petsc-private/matimpl.h
> [1]PETSC ERROR: MatLUFactorNumeric_SeqAIJ_Inode() line 1469 in /home/sanderse/Software/petsc-3.3-p1/src/mat/impls/aij/seq/inode.c
> [1]PETSC ERROR: MatLUFactorNumeric() line 2790 in /home/sanderse/Software/petsc-3.3-p1/src/mat/interface/matrix.c
> [1]PETSC ERROR: PCSetUp_LU() line 160 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/factor/lu/lu.c
> [1]PETSC ERROR: PCSetUp_ML() line 820 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/ml/ml.c
> [0]PETSC ERROR: PCSetUp() line 832 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: KSPSetUp() line 278 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/ksp/interface/itfunc.c
> PCSetUp() line 832 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/interface/precon.c
> [1]PETSC ERROR: KSPSetUp() line 278 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/ksp/interface/itfunc.c
> [1]PETSC ERROR: PCSetUp_Redundant() line 176 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/redundant/redundant.c
> [1]PETSC ERROR: PCSetUp() line 832 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/interface/precon.c
> [1]PETSC ERROR: KSPSetUp() line 278 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/ksp/interface/itfunc.c
> [1]PETSC ERROR: PCSetUp_MG() line 729 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/mg/mg.c
> [1]PETSC ERROR: PCSetUp_ML() line 820 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/impls/ml/ml.c
> [1]PETSC ERROR: PCSetUp() line 832 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/pc/interface/precon.c
> [1]PETSC ERROR: KSPSetUp() line 278 in /home/sanderse/Software/petsc-3.3-p1/src/ksp/ksp/interface/itfunc.c
>
>
> Op 3 jun 2011, om 14:26 heeft Barry Smith het volgende geschreven:
>
> >
> > It is the direct solver on the the coarse grid that is finding the zero pivot (since the coarse grid problem like all the levels has a null space).
> >
> > You can use the option -mg_coarse_pc_factor_shift_type nonzero (in petsc-3.1 or petsc-dev) Also keep the KSPSetNullSpace() function you are using.
> >
> >
> > Barry
> >
> > On Jun 3, 2011, at 3:54 AM, Stijn A. M. Vantieghem wrote:
> >
> >> Dear all,
> >>
> >> I am using PETSc (Fortran interface) to solve a Poisson equation with Neumann boundary conditions. Up till now, I managed to do this with Hypre's BoomerAMG. Now, I am investigating whether I can improve the performance of my code by using ML. However, at execution I receive a zero pivot error; I tried to remove the (constant) null space with KSPSetNullSpace, but this didn't solve my problem. Do you have an idea of what I'm doing wrong? Thanks.
> >>
> >> The relevant portions of my code are as follows:
> >>
> >> !****************************************************
> >> call KSPCreate(PETSC_COMM_WORLD,ksp,ierr)
> >> call KSPSetOperators(ksp,M,M,DIFFERENT_NONZERO_PATTERN,ierr)
> >>
> >> call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL,sp,ierr)
> >> call KSPSetNullSpace(ksp,sp,ierr)
> >>
> >> call KSPGetPC(ksp,pc,ierr)
> >> call PCSetType(pc,PCML,ierr)
> >>
> >> call KSPSetFromOptions(ksp,ierr)
> >> ...
> >> call KSPSetInitialGuessNonzero(ksp,PETSC_TRUE,ierr)
> >> call KSPSolve(ksp,petsc_rhs,petsc_pressure,ierr)
> >> !****************************************************
> >>
> >> and the error message is:
> >>
> >> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> >> [0]PETSC ERROR: Detected zero pivot in LU factorization
> >> see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#ZeroPivot!
> >> [0]PETSC ERROR: Zero pivot row 0 value 3.57045e-20 tolerance 1e-12!
> >> [0]PETSC ERROR: ------------------------------------------------------------------------
> >> ...
> >> [0]PETSC ERROR: ------------------------------------------------------------------------
> >> [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 574 in src/mat/impls/aij/seq/aijfact.c
> >> [0]PETSC ERROR: MatLUFactorNumeric() line 2587 in src/mat/interface/matrix.c
> >> [0]PETSC ERROR: PCSetUp_LU() line 158 in src/ksp/pc/impls/factor/lu/lu.c
> >> [0]PETSC ERROR: PCSetUp() line 795 in src/ksp/pc/interface/precon.c
> >> [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c
> >> [0]PETSC ERROR: PCSetUp_MG() line 602 in src/ksp/pc/impls/mg/mg.c
> >> [0]PETSC ERROR: PCSetUp_ML() line 668 in src/ksp/pc/impls/ml/ml.c
> >> [0]PETSC ERROR: PCSetUp() line 795 in src/ksp/pc/interface/precon.c
> >> [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c
> >> [0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c
> >>
> >> Regards
> >> Stijn
> >>
> >> Stijn A.M. Vantieghem
> >> Earth and Planetary Magnetism
> >> Institute for Geophysics
> >> ETH Zürich
> >> Sonneggstrasse 5 - CH 8092 Zürich
> >> tel: +41 44 632 39 90
> >> e-mail: stijn.vantieghem at erdw.ethz.ch
> >>
> >>
> >>
> >>
> >
>
>
>
>
>
> --
> 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
--
Ir. B. Sanderse
Centrum Wiskunde en Informatica
Science Park 123
1098 XG Amsterdam
t: +31 20 592 4161
e: sanderse at cwi.nl
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