What is the best solver a poisson type eqn.

Matthew Knepley knepley at gmail.com
Thu Jun 18 10:59:15 CDT 2009 

On Thu, Jun 18, 2009 at 10:48 AM, Christian Klettner <
christian.klettner at ucl.ac.uk> wrote:

> Hi Matt,
> Thank you for the reply. I have now gotten MUMPS to work with the
> following implementation:
>
> MatFactorInfoInitialize(&info);
> MatGetFactor(A,MAT_SOLVER_MUMPS,MAT_FACTOR_LU,&B);
> MatLUFactorSymbolic(B,A, rows_ck_is, cols_ck_is,&info);
> MatLUFactorNumeric(B,A,&info);
>
> for(){         ///temporal loop
> /*coding*/
> ierr=MatSolve(A,vecr,vecu);CHKERRQ(ierr);
> }
>
> I explicitly use MUMPS to factor the matrix. However, from my
> implementation I do not see what package is being used to solve Ax=b.
> Could I be using PETSc to solve the system?? Is there any way of knowing
> if MUMPS is actually being used to solve the system?
> I am not passing in any arguments to use MUMPS explicitly from the command
> line, have
> not put in any MUMPS header files and I do not use any other MUMPS
> functions (e.g. MatCreate_AIJMUMPS()).


Yes, it is determined from the type. However, I think this is completely the
wrong way
to program. Why hardcode yourself into a corner? It is hard to change
packages, to
wrap this in a Krylov solver, compare with other PCs. This is crazy. I
recommend

  KSPCreate(comm, &ksp);
  KSPSetOperators(ksp, A, A, ...);
  KSPSetFromOptions(ksp);
  KSPSolve(ksp, b, x);

Now with options you can control everything

  -ksp_type preonly -pc_type lu -mat *-pc_factor_mat_solver_package mumps*

will reproduce what you have, but you can test it against

 -ksp_type gmres -pc_type asm -sub_pc_type ilu

To see what is happening you can always use

  -ksp_view

   Matt


> Thank you for any advice,
> Best regards,
> Christian Klettner
>
>
> > 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
> >
>
>
>


-- 
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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