[petsc-users] ML - zero pivot error

Tue Jul 17 05:58:53 CDT 2012

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120717/f5f7dc94/attachment.html>