What is the best solver a poisson type eqn.
Barry Smith
bsmith at mcs.anl.gov
Thu Jun 18 10:56:41 CDT 2009
On Jun 18, 2009, at 10:48 AM, Christian Klettner 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?
It is using MUMPS. Each external factorization package uses its own
data structures and solvers.
The PETSc triangular solvers only work for the PETSc data structures
and cannot work with the
MUMPS factorization.
Barry
> 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()).
^^^^^^^^^^^^^^^^^^^^^
This stuff no longer exists since PETSc 3.0.0
> 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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