What is the best solver a poisson type eqn.
Christian Klettner
christian.klettner at ucl.ac.uk
Thu Jun 18 10:48:32 CDT 2009
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()).
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
>
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