dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Dec 27, 2005 at 11:01:13PM +0100, Garth N. Wells wrote:
> On Tue, 2005-12-27 at 15:39 -0600, Anders Logg wrote:
> > Looks good, should go into the parameter system.
> > 
> > Does anyone have an opinion if this should be a global parameter (add
> > to src/kernel/parameter/dolfin/DefaultParameters.h) or we should just
> > add it locally in the constructor of KrylovSolver? Maybe the parameter
> > could have meaning elsewhere, like LU and Preconditioner.?
> > 
> 
> Would be better to make this local to the solver.

ok. Maybe that can be the default way to handle parameters. Always put
them in the solver and if we discover a common parameter it might in
some cases make sense to make it global.

/Anders

> Garth
> 
> 
> > In any case, we should make KrylovSolver a subclass of Parametrized
> > and remove all the setFoo() functions from KrylovSolver.
> > 
> > /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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-- 
Anders Logg
Research Assistant Professor
Toyota Technological Institute at Chicago
http://www.tti-c.org/logg/