dolfin team mailing list archive

[Alexander Jarosch <alexanj@xxxxx>]

Hi,

I experience zero pivot problems when I solve Stokes problems with high 
viscosities, order of 1e13 and such viscous fluids like ice and earth 
mantle material. I helped myself with this Petsc parameter in the 
KrylovSolver.cpp

PCFactorSetShiftPd(pc, PETSC_TRUE);

works nice.

Alex

Garth N. Wells wrote:

> I've never observed the KrylovSolver (or preconditioner)to have 
> problems with zero pivots. Things work OK for the Taylor-Hood element 
> at least. The PETSC LU solver does have problems (and did have with 
> Taylor-Hood element), and something was added a while ago to LU to 
> deal with this.
>
> Garth
>
> Anders Logg wrote:
>
> > I have added this to KrylovSolver as a temporary fix. All parameters 
> > should
> > be moved to the new parameter system (including tolerances, iterations
> > etc).
> >
> > /Anders
> >
> > On Fri, Dec 23, 2005 at 10:46:05AM +0100, hetzel.devel@xxxxxx wrote:
> >
> > > Hi,
> > > I made a quick implementation for my dolfin 0.5.10. I got no time to 
> > > check the 0.5.11 so I'm just telling you what I did, perhaps you can 
> > > simply add it to the current version or to next release. If you 
> > > think that it's not so urgent and you can wait till mid of january I 
> > > can submit a patch then.
> > >
> > > In src/la/dolfin/GMRES.h I added the lines (after setPreconditioner)
> > > ---------------
> > >    /// Set ZeroPivot Boundary
> > >    void setZeroPivot(real zeropivot);
> > > ---------------
> > >
> > > In src/la/GMRES.cpp I added:
> > > ---------------
> > >    
> > > //----------------------------------------------------------------------------- 
> > >
> > >    void GMRES::setZeroPivot(real zeropivot)
> > >    {
> > >      // Choose preconditioner
> > >      PC pc;
> > >      KSPGetPC(ksp, &pc);
> > >         PCFactorSetZeroPivot(pc, zeropivot);
> > >      dolfin_info("Changing ZeroPivot for GMRES solver from to %e.", 
> > > zeropivot);
> > >    }
> > > ---------------
> > >
> > > That's all.
> > > Now within my program I can simple set the ZeroPivot option like 
> > > follows:
> > > ---------------
> > >    // Set solver
> > >    GMRES solver;
> > >    solver.setZeroPivot(1e-14);
> > > ---------------
> > >
> > > I think it should work the same for LU.
> > >
> > > /Haiko
> > >
> > >  
> > > Discussion of DOLFIN development <dolfin-dev@xxxxxxxxxx> schrieb am 
> > > 22.12.05 20:21:37:
> > >
> > > > ok, perhaps we should make KrylovSolver inherit from Parametrized and
> > > > add an option "zero pivot tolerance"?
> > > >
> > > > /Anders
> > > >
> > > >
> > > > On Thu, Dec 22, 2005 at 06:46:09PM +0100, Garth N. Wells wrote:
> > > >
> > > > > It's possible to change the tolerance for zero pivots in PETSc. 
> > > > > Have a
> > > > > look at 
> > > > > http://www-unix.mcs.anl.gov/petsc/petsc-as/snapshots/petsc-current/docs/manualpages/PC/PCFactorSetZeroPivot.html#PCFactorSetZeroPivot 
> > > > >
> > > > >
> > > > > I made a change to the LU class a while ago so that it could deal 
> > > > > with
> > > > > matrices that have zeroes on the diagonal, such as Stokes flow with
> > > > > Taylor-Hood elements.
> > > > >
> > > > > Garth
> > > > >
> > > > > On Thu, 2005-12-22 at 11:38 -0600, Anders Logg wrote:
> > > > >
> > > > > > Then I have no idea. You can specify the tolerance for the GMRES
> > > > > > solver in DOLFIN, but not the tolerance for checking for zero pivots
> > > > > > in the ILU preconditioner. This is probably in the PETSc manual
> > > > > > somewhere. If you find out how to make the adjustment in PETSc, then
> > > > > > we can add a corresponding parameter in DOLFIN.
> > > > > >
> > > > > > /Anders
> > > > > >
> > > > > >
> > > > > > On Thu, Dec 22, 2005 at 06:24:33PM +0100, H. Etzel wrote:
> > > > > >
> > > > > > > Like the message is telling.
> > > > > > > The matrix is bad conditioned, but it values are not zero if the 
> > > > > > > tolerance
> > > > > > > is not 1e-12 but 1e-20.
> > > > > > > So the question is how to change the tolerance.
> > > > > > >
> > > > > > > /Haiko
> > > > > > >
> > > > > > > -----Ursprüngliche Nachricht-----
> > > > > > > Von: dolfin-dev-bounces@xxxxxxxxxx 
> > > > > > > [mailto:dolfin-dev-bounces@xxxxxxxxxx] Im
> > > > > > > Auftrag von Anders Logg
> > > > > > > Gesendet: Donnerstag, 22. Dezember 2005 16:20
> > > > > > > An: Discussion of DOLFIN development
> > > > > > > Betreff: Re: [DOLFIN-dev] zero pivot
> > > > > > >
> > > > > > >
> > > > > > > Looks like you are trying to solve a singular system. Most likely,
> > > > > > > something is wrong with the matrix which PETSc rightly detects.
> > > > > > >
> > > > > > > To be sure, try exporting the matrix to MATLAB/Octave and see if 
> > > > > > > you
> > > > > > > can invert it there or compute the condition number:
> > > > > > >
> > > > > > > File file("matrix.m");
> > > > > > > file << A;
> > > > > > >
> > > > > > > Then just type
> > > > > > >
> > > > > > >     matrix
> > > > > > >
> > > > > > > in MATLAB/Octave and check if it looks ok.
> > > > > > >
> > > > > > > /Anders
> > > > > > >
> > > > > > >
> > > > > > > On Thu, Dec 22, 2005 at 04:02:19PM +0100, hetzel.devel@xxxxxx 
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hello everyone,
> > > > > > > > I get a problem with my solver.
> > > > > > > > I'm using the LU or alternative the GMRES solver, but by 
> > > > > > > > solving my
> > > > > > >
> > > > > > > System, I always get the following message from Petsc:
> > > > > > >
> > > > > > > > [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 516 in
> > > > > > >
> > > > > > > src/mat/impls/aij/seq/aijfact.c
> > > > > > >
> > > > > > > > [0]PETSC ERROR: Detected zero pivot in LU factorization
> > > > > > > > see
> > > > > > >
> > > > > > > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Zer 
> > > > > > >
> > > > > > > oPivot!
> > > > > > >
> > > > > > > > [0]PETSC ERROR: Zero pivot row 2950 value 4.17812e-13 tolerance 
> > > > > > > > 1e-12 * rs
> > > > > > >
> > > > > > > 0.450719!
> > > > > > >
> > > > > > > > [0]PETSC ERROR: MatLUFactorNumeric() line 1994 in
> > > > > > >
> > > > > > > src/mat/interface/matrix.c
> > > > > > >
> > > > > > > > [0]PETSC ERROR: PCSetUp_ILU() line 798 in
> > > > > > >
> > > > > > > src/ksp/pc/impls/factor/ilu/ilu.c
> > > > > > >
> > > > > > > > [0]PETSC ERROR: PCSetUp() line 798 in 
> > > > > > > > src/ksp/pc/interface/precon.c
> > > > > > > > [0]PETSC ERROR: KSPSetUp() line 234 in 
> > > > > > > > src/ksp/ksp/interface/itfunc.c
> > > > > > > > [0]PETSC ERROR: KSPSolve() line 332 in 
> > > > > > > > src/ksp/ksp/interface/itfunc.c
> > > > > > > >
> > > > > > > > Is there an option for the solver to set the tolerance?
> > > > > > > >
> > > > > > > > /Haiko
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--
Alexander H. Jarosch

Jarðvísindastofnun Háskólans
Institute of Earth Sciences, University of Iceland
Náttúrufræðahús, Askja
Building of Natural Sciences, Askja
Sturlugata 7
IS - 101 Reykjavík
Iceland

Tel.: +354 525 4906
http://raunvis.hi.is/~jarosch/