[petsc-users] ML - zero pivot error

Tue Jul 17 03:23:12 CDT 2012

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?

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
>> 
>> 
>> 
>> 
> 