[petsc-users] Inquiry about the preconditioner setup of KSP.

[Xiaodong Liu]

Thanks a lot, Matthew. Very helpful.

Xiaodong Liu, PhD
X: Computational Physics Division
Los Alamos National Laboratory
P.O. Box 1663,
Los Alamos, NM 87544
505-709-0534


On Wed, Mar 4, 2020 at 2:53 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Tue, Mar 3, 2020 at 11:46 PM Jed Brown <jed at jedbrown.org> wrote:
>
>> Xiaodong Liu <xliu29 at ncsu.edu> writes:
>>
>> > Thanks  a lot.  I am transferring  a dense matrix from Julia to Petsc.
>> > I will check this.
>> > In addition, could you please show me where is
>> >
>> >  Where is the subroutine for the GMRES solver, namely,
>> >   ierr=(*KSP->ops->solve)(ksp);
>>
>> $ git grep KSPSolve_GMRES
>> src/docs/tex/manual/developers.tex:\item Names of implementations of
>> class functions should begin with the function name, an underscore, and the
>> name of the implementation, for example, \lstinline{KSPSolve_GMRES()}.
>> src/ksp/ksp/impls/gmres/gmres.c:PetscErrorCode KSPSolve_GMRES(KSP ksp)
>> src/ksp/ksp/impls/gmres/gmres.c:  ksp->ops->solve
>> = KSPSolve_GMRES;
>>
>>
> Note that these implementation links are also at the bottom of the
> interface manpages:
>
>
> https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/KSP/KSPSolve.html
>
>   Thanks,
>
>      Matt
>
>
>> >
>> > Xiaodong Liu, PhD
>> > X: Computational Physics Division
>> > Los Alamos National Laboratory
>> > P.O. Box 1663,
>> > Los Alamos, NM 87544
>> > 505-709-0534
>> >
>> >
>> > On Tue, Mar 3, 2020 at 8:21 PM Jed Brown <jed at jedbrown.org> wrote:
>> >
>> >> Is it possible that Julia is transferring the matrix to PETSc as a
>> dense
>> >> matrix (storing the nonzeros) instead of preserving sparsity?  If you
>> >> store the zeros, then ILU will be allowed to fill those entries,
>> thereby
>> >> becoming LU.
>> >>
>> >> Xiaodong Liu <xliu29 at ncsu.edu> writes:
>> >>
>> >> > I am trying to use Julia to call Petsc.
>> >> > 1) First, I run the built-in example ex2.c
>> >> >
>> >>
>> https://www.mcs.anl.gov/petsc/petsc-current/src/ksp/pc/examples/tutorials/ex2.c.html
>> >> >
>> >> > For this case,  I tried KSPGMRES , initial zero solution and
>> different PC
>> >> > (LU, ILU, ICC, JACOBI). And they work as expected.
>> >> >
>> >> >  75: KSPSetType(ksp,KSPGMRES);
>> >> >  76: KSPSetInitialGuessNonzero(ksp,PETSC_FALSE);
>> >> >  87: KSPGetPC(ksp,&pc);
>> >> >  88: PCSetType(pc,PCICC);
>> >> >
>> >> > 2) Second, I tried to call KSP from Julia using the same matrix and
>> right
>> >> > hand side as ex2.c . A wrapper has been written to call Petsc code
>> from
>> >> > Julia. After I transfer matrix to from Julia to Petsc, I checked the
>> >> matrix
>> >> > and preconditioner matrix in the context of Petsc. These two
>> matrices are
>> >> > right. For no preconditioner,Jacobi precontioner and LU, the
>> residual for
>> >> > Julia version is same as that of original Petsc one for every
>> iteration.
>> >> > However, for ILU preconditioner, the residual for Julia is alwaysthe
>> same
>> >> > as the LU one. This is not expected. For both Julia and original
>> Petsc
>> >> > version, I checked the PC type inside the subroutine PCSetType and
>> the
>> >> > types are correct, namely ilu.I am trying to dig into the source
>> code to
>> >> > check how the preconditioner is interacting with GMRES.
>> >> >
>> >> > Where is the subroutine for the GMRES solver, namely,
>> >> >  ierr=(*KSP->ops->solve)(ksp);
>> >> >
>> >> > Or do you have any suggestions?
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Xiaodong Liu, PhD
>> >> > X: Computational Physics Division
>> >> > Los Alamos National Laboratory
>> >> > P.O. Box 1663,
>> >> > Los Alamos, NM 87544
>> >> > 505-709-0534
>> >>
>>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20200304/2d237285/attachment.html>