[petsc-users] mumps solve with same nonzero pattern

Fri Apr 27 12:49:21 CDT 2012

Thanks for your reply. I also tested the exactly same problem with SUPERLU.
The mumps and superlu dist both are using sequential symbolic
factorization. However, superlu dist takes only 20 seconds but mumps takes
almost 700 seconds. I am wondering whether such a big difference is
possible. Do those two direct solver use quite different algorithm?

And also since I might have the same nonzero structure system to be solved
many times at different places. I am wondering whether I could save the
symbolic factorization output somewhere and then read them as the input for
future solving. Thanks.

Regards,
Wen

On Fri, Apr 27, 2012 at 1:06 PM, <petsc-users-request at mcs.anl.gov> wrote:

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> Today's Topics:
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>   1.  mumps solve with same nonzero pattern (Wen Jiang)
>   2. Re:  mumps solve with same nonzero pattern (Matthew Knepley)
>   3.  High Re CFD method. (Christian Klettner)
>   4. Re:  writing native PETSc binaries in python
>      (Ataollah Mesgarnejad)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 27 Apr 2012 09:53:57 -0400
> From: Wen Jiang <jiangwen84 at gmail.com>
> Subject: [petsc-users] mumps solve with same nonzero pattern
> To: petsc-users at mcs.anl.gov
> Message-ID:
>        <CAMJxm+D7kwTZPQ_7xwEKueL2z=zKL6a4A1BBTQXxACj_UKJF-Q at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I am using mumps in PETSc to solve a 0.2 million system on 128 cores.
> Within Newton-Raphson iteration, the system with same sparse structure but
> different values will be solved many times. And I specify the
> preconditioning matrix having same nonzero pattern. The first time solving
> costs around 900 seconds and later solving only takes around 200 seconds.
> So I am wondering why the time differs that much. By setting the same
> nonzero pattern of pc, which of the mumps control parameters does PETSc
> change? Thanks.
>
> Regards,
> Wen
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> ------------------------------
>
> Message: 2
> Date: Fri, 27 Apr 2012 10:11:27 -0400
> From: Matthew Knepley <knepley at gmail.com>
> Subject: Re: [petsc-users] mumps solve with same nonzero pattern
> To: PETSc users list <petsc-users at mcs.anl.gov>
> Message-ID:
>        <CAMYG4GnbKCA7DOXAP=_+YHkDWaDF94TFjqr2eaZ3dQnD7Vy_Dg at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> On Fri, Apr 27, 2012 at 9:53 AM, Wen Jiang <jiangwen84 at gmail.com> wrote:
>
> > Hi,
> >
> > I am using mumps in PETSc to solve a 0.2 million system on 128 cores.
> > Within Newton-Raphson iteration, the system with same sparse structure
> but
> > different values will be solved many times. And I specify the
> > preconditioning matrix having same nonzero pattern. The first time
> solving
> > costs around 900 seconds and later solving only takes around 200 seconds.
> > So I am wondering why the time differs that much. By setting the same
> > nonzero pattern of pc, which of the mumps control parameters does PETSc
> > change? Thanks.
> >
>
> The difference is that you do not have to perform the symbolic
> factorization again if the nonzero pattern does not change,
> just the numeric factorization. The symbolic factorization is the costly
> step.
>
>   Matt
>
>
> > Regards,
> > Wen
> >
>
>
>
> --
> 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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> ------------------------------
>
> Message: 3
> Date: Fri, 27 Apr 2012 11:26:33 +0100
> From: "Christian Klettner" <ucemckl at ucl.ac.uk>
> Subject: [petsc-users] High Re CFD method.
> To: petsc-users at mcs.anl.gov
> Message-ID:
>        <
> ba0801c9e3bd11beb658cbec10d24a7f.squirrel at www.squirrelmail.ucl.ac.uk>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear Petsc users,
>
> I know this is off topic but the people reading these questions are well
> placed to answer the question, being actual CFD developers. Over the last
> five years our group has developed a CFD code (using PETSc for parallel
> and vectors) based on the characteristic based split scheme to solve the
> incompressible Navier-Stokes equation (2D-3D) in a finite element
> framework using unstructured meshes. It is first order accurate in time
> and space. This has proved effective for high resolution, low Reynolds
> number complex geometry flows (e.g. groups of bodies).
>
> We are hoping to move onto higher Reynolds number flows, with the
> intention of using a large eddy simulation model for the turbulence. The
> goal is to model the flow in a hospital room with typical Reynolds numbers
> of 10^5. At present we are not convinced that the CBS scheme is the best
> scheme for these types of flows and are looking for other peoples opinions
> on alternative methods. Does anyone have any advice in this direction?
>
> Best regards,
> Christian
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 27 Apr 2012 10:28:41 -0500
> From: Ataollah Mesgarnejad <amesga1 at tigers.lsu.edu>
> Subject: Re: [petsc-users] writing native PETSc binaries in python
> To: PETSc users list <petsc-users at mcs.anl.gov>
> Cc: petsc-dev at mcs.anl.gov
> Message-ID:
>        <CAC+VmGdP1V3DFrfLWextGVU23NRHtKwUoqcD4Ai__mwTdd1ZGw at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks for the replies:
>
> Just a bug report with petsc4py:
>
> petsc4py which downloads with --download-petsc4py=1 is the older v1.1.1
> which doesn't compile with petsc-dev?
>
> Thanks,
> Ata
>
> On Fri, Apr 27, 2012 at 8:25 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
>
> > On Fri, Apr 27, 2012 at 9:19 AM, Ataollah Mesgarnejad <
> > amesga1 at tigers.lsu.edu> wrote:
> >
> >> Dear all,
> >>
> >> I was wondering if there is way to write numpy arrays as native PETSc
> >>  binaries in python so I can open them inside my program with VecView?
> >>
> >
> > I think what you want is to create a Vec using that array in petsc4py.
> >
> >    Matt
> >
> >
> >> Thanks,
> >> Ata
> >>
> >
> >
> >
> > --
> > 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
> >
>
>
>
> --
> A. Mesgarnejad
> PhD Student, Research Assistant
> Mechanical Engineering Department
> Louisiana State University
> 2203 Patrick F. Taylor Hall
> Baton Rouge, La 70803
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