dolfin team mailing list archive

["Johan Hoffman" <jhoffman@xxxxxxxxxxx>]

> 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

Sounds good.

/Johan


>
>> 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/
>
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>


-- 
Johan Hoffman, PhD
Assistant Professor
School of Computer Science and Communication
Royal Institute of Technology KTH
SE-100 44 Stockholm
Sweden

Email: jhoffman@xxxxxxxxxxx
URL: www.nada.kth.se/~jhoffman