On Fri, Apr 27, 2012 at 1:49 PM, Wen Jiang <jiangwen84 at gmail.com> wrote:
> 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. > No. Those factorizations an internal data structures to the packages, so we can't write them out. Matt > Regards, > Wen > > > > On Fri, Apr 27, 2012 at 1:06 PM, <petsc-users-request at mcs.anl.gov> wrote: > >> Send petsc-users mailing list submissions to >> petsc-users at mcs.anl.gov >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://lists.mcs.anl.gov/mailman/listinfo/petsc-users >> or, via email, send a message with subject or body 'help' to >> petsc-users-request at mcs.anl.gov >> >> You can reach the person managing the list at >> petsc-users-owner at mcs.anl.gov >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of petsc-users digest..." >> >> >> Today's Topics: >> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/7bd8e1ad/attachment-0001.htm >> > >> >> ------------------------------ >> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/f148b130/attachment-0001.htm >> > >> >> ------------------------------ >> >> 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 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/cca3e1b6/attachment-0001.htm >> > >> >> ------------------------------ >> >> _______________________________________________ >> petsc-users mailing list >> petsc-users at mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/petsc-users >> >> >> End of petsc-users Digest, Vol 40, Issue 102 >> ******************************************** >> > > -- 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 -------------- next part -------------- An HTML attachment was scrubbed... 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