What is the best solver a poisson type eqn.

Matthew Knepley knepley at gmail.com
Tue Jun 16 07:52:04 CDT 2009 

On Tue, Jun 16, 2009 at 7:40 AM, Christian Klettner <
christian.klettner at ucl.ac.uk> wrote:

> Hi Matt,
> I have tried to use MUMPS and came across the following problems. My
> application solves Ax=b about 10000-100000 times with A remaining
> constant.
> When I tried to use it through KSP I was not finding good performance.
> Could this be because it was refactoring etc. at each time step?
> With this in mind I have tried to implement the following:


1) I have no idea what you would mean by good performance. Always, always,
always
send the -log_summary.

2) A matrix is never refactored during the KSP iteration


> A is a parallel matrix created with MatCreateMPIAIJ().
> rows is a list of the global row numbers on the process.cols is a list of
> the global columns that are on the process.
> I run the program with ./mpiexec -n 4 ./ex4 -pc_factor_mat_solver_package
> mumps
>
> (1)     MatFactorInfo *info;
> (2)     ierr=MatFactorInfoInitialize(info);CHKERRQ(ierr);


You have passed a meaningless pointer here.

(1)     MatFactorInfo info;
(2)     ierr=MatFactorInfoInitialize(&info);CHKERRQ(ierr);

   Matt


> (3)
> ierr=MatGetFactor(A,MAT_SOLVER_MUMPS,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
> (4)     ierr=MatLUFactorSymbolic(F, A, rows, cols,info);CHKERRQ(ierr);
> (5)     MatLUFactorNumeric(F, A,info);CHKERRQ(ierr);
>
>
>        for(){  ///TEMPORAL LOOP
>
>                /*CODING*/
>
>                ierr=MatSolve(A,vecr,vecu);CHKERRQ(ierr);
>        }
>
> I get the following error messages:
>
> Line (2) above gives the following error message:
>
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [2]PETSC ERROR: [0]PETSC ERROR: Null argument, when expecting valid
> pointer!
> [0]PETSC ERROR: Trying to zero at a null pointer!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 4, Fri Mar  6 14:46:08
> CST 2009
> [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: ./ex4 on a linux-gnu named christian-desktop by christian
> Tue Jun 16 13:33:33 2009
> [0]PETSC ERROR: Libraries linked from
> /home/christian/Desktop/petsc-3.0.0-p4/linux-gnu-c-debug/lib
> [0]PETSC ERROR: Configure run at Mon Jun 15 17:05:31 2009
> [0]PETSC ERROR: Configure options --with-cc="gcc -fPIC" --download-mpich=1
> --download-f-blas-lapack --download-scalapack --download-blacs
> --download-mumps --download-parmetis --download-hypre --download-triangle
> --with-shared=0
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: PetscMemzero() line 189 in src/sys/utils/memc.c
> [0]PETSC ERROR: MatFactorInfoInitialize() line 7123 in
> src/mat/interface/matrix.c
> [0]PETSC ERROR: main() line 1484 in src/dm/ao/examples/tutorials/ex4.c
> application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0[cli_0]:
> aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 85) - process 0
> --------------------- Error Message ------------------------------------
> [2]PETSC ERROR: Null argument, when expecting valid pointer!
> [2]PETSC ERROR: Trying to zero at a null pointer!
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: Petsc Release Version 3.0.0, Patch 4, Fri Mar  6 14:46:08
> CST 2009
> [2]PETSC ERROR: See docs/changes/index.html for recent updates.
> [2]PETSC ERROR: See docs/faq.html[0]0:Return code = 85
> [0]1:Return code = 0, signaled with Interrupt
> [0]2:Return code = 0, signaled with Interrupt
> [0]3:Return code = 0, signaled with Interrupt
>
> /////////////////////////////////////////////////////////////////
>
> Line (3) gives the following error messages:
>
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Invalid argument!
> [0]PETSC ERROR: Wrong type of object: Parameter # 2!
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [2]PETSC ERROR: Invalid argument!
> [2]PETSC ERROR: Wrong type of object: Parameter # 2!
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: Petsc Release Version 3.0.0, Patch 4, Fri Mar  6 14:46:08
> CST 2009
> [2]PETSC ERROR: See docs/changes/index.html for recent updates.
> [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [2]PETSC ERROR: See docs/index.html for manual pages.
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: ./ex4 on a linux-gnu named christian-desktop by christian
> Tue Jun 16 13:37:36 2009
> [2]PETSC ERROR: Libraries linked from
> /home/christian/Desktop/petsc-3.0.0-p4/linux-gnu-c-debug/lib
> [2]PETSC ERROR: Configure run at Mon Jun 15 17:05:31 2009
> [2]PETSC ERROR: Configure options --with-cc="gcc -fPIC" --download-mpich=1
> --download-f-blas-lapack --download-scalapack --download-blacs
> --downlPetsc Release Version 3.0.0, Patch 4, Fri Mar  6 14:46:08 CST 2009
> [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: ./ex4 on a linux-gnu named christian-desktop by christian
> Tue Jun 16 13:37:36 2009
> [0]PETSC ERROR: Libraries linked from
> /home/christian/Desktop/petsc-3.0.0-p4/linux-gnu-c-debug/lib
> [0]PETSC ERROR: Configure run at Mon Jun 15 17:05:31 2009
> [0]PETSC ERROR: Configure options --with-cc="gcc -fPIC" --download-mpich=1
> --download-f-blas-lapack --download-scalapack --download-blacs
> --download-mumps --download-parmetis --download-hypre --download-triangle
> --with-shared=0
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: MatLUFactorSymbolic() line 2311 in
> src/mat/interface/matrix.c
> [0]PETSC ERROR: main() line 148oad-mumps --download-parmetis
> --download-hypre --download-triangle --with-shared=0
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: MatLUFactorSymbolic() line 2311 in
> src/mat/interface/matrix.c
> [2]PETSC ERROR: main() line 1488 in src/dm/ao/examples/tutorials/ex4.c
> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 2[cli_2]:
> aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 2
> 8 in src/dm/ao/examples/tutorials/ex4.c
> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0[cli_0]:
> aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 62) - process 0
> [0]0:Return code = 62
> [0]1:Return code = 0, signaled with Interrupt
> [0]2:Return code = 62
> [0]3:Return code = 0, signaled with Interrupt
>
> Is the matrix (ie parameter 2) in teh wrong state because it's not a MUMPS
> matrix?
>
> Any help would be greatly appreciated,
> Best regards,
> Christian Klettner
>
>
>
> > The problem is small enough that you might be able to use MUMPS.
> >
> >   Matt
> >
> > On Fri, Jun 12, 2009 at 9:31 AM, Lisandro Dalcin <dalcinl at gmail.com>
> > wrote:
> >
> >> On Fri, Jun 12, 2009 at 11:13 AM, Christian
> >> Klettner<christian.klettner at ucl.ac.uk> wrote:
> >> > Sorry that I sent this twice. No subject in the first one.
> >> >
> >> > Dear PETSc Team,
> >> > I am writing a CFD finite element code in C. From the discretization
> >> of
> >> > the governing equations I have to solve a Poisson type equation which
> >> is
> >> > really killing my performance. Which solver/preconditioner from PETSc
> >> or
> >> > any external packages would you recommend? The size of my problem is
> >> from
> >> > ~30000-100000 DOF per core. What kind of performance would I be able
> >> to
> >> > expect with this solver/preconditioner?
> >>
> >> I would suggest KSPCG. As preconditioner I would use ML or
> >> HYPRE/BoomerAMG (both are external packages)
> >>
> >> > I am using a 2*quad core 2.3 GHz Opteron. I have decomposed the domain
> >> > with Parmetis. The mesh is unstructured.
> >> > Also, I am writing a code which studies free surface phenomena so the
> >> mesh
> >> > is continually changing. Does this matter when choosing a
> >> > solver/preconditioner? My left hand side matrix (A in Ax=b) does not
> >> > change in time.
> >>
> >> ML has a faster setup that BoomerAMG, but the convergence is a bit
> >> slower. If your A matrix do not change, then likely BoomerAMG will be
> >> better for you. In any case, you can try both: just build PETSc with
> >> both packages, then you can change the preconditioner by just passing
> >> a command line option.
> >>
> >> >
> >> > Best regards and thank you in advance,
> >> > Christian Klettner
> >> >
> >>
> >> Disclaimer: the convergence of multigrid preconditioners depends a lot
> >> on your actual problem. What I've suggested is just my limited
> >> experience in a few problems I've run solving electric potentials.
> >>
> >>
> >> --
> >> Lisandro Dalcín
> >> ---------------
> >> Centro Internacional de Métodos Computacionales en Ingeniería (CIMEC)
> >> Instituto de Desarrollo Tecnológico para la Industria Química (INTEC)
> >> Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
> >> PTLC - Güemes 3450, (3000) Santa Fe, Argentina
> >> Tel/Fax: +54-(0)342-451.1594
> >>
> >
> >
> >
> > --
> > 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
> >
>
>
>


-- 
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
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