<div class="gmail_extra">On Fri, Apr 27, 2012 at 1:49 PM, Wen Jiang <span dir="ltr"><<a href="mailto:jiangwen84@gmail.com" target="_blank">jiangwen84@gmail.com</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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? <br>
<br>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.<br>
</blockquote><div><br></div><div>No. Those factorizations an internal data structures to the packages, so we can't write them out.</div><div><br></div><div> Matt</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Regards,<br>Wen<br><br><br><br><div class="gmail_quote">On Fri, Apr 27, 2012 at 1:06 PM, <span dir="ltr"><<a href="mailto:petsc-users-request@mcs.anl.gov" target="_blank">petsc-users-request@mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send petsc-users mailing list submissions to<br>
<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/petsc-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:petsc-users-request@mcs.anl.gov" target="_blank">petsc-users-request@mcs.anl.gov</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:petsc-users-owner@mcs.anl.gov" target="_blank">petsc-users-owner@mcs.anl.gov</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of petsc-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. mumps solve with same nonzero pattern (Wen Jiang)<br>
2. Re: mumps solve with same nonzero pattern (Matthew Knepley)<br>
3. High Re CFD method. (Christian Klettner)<br>
4. Re: writing native PETSc binaries in python<br>
(Ataollah Mesgarnejad)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 27 Apr 2012 09:53:57 -0400<br>
From: Wen Jiang <<a href="mailto:jiangwen84@gmail.com" target="_blank">jiangwen84@gmail.com</a>><br>
Subject: [petsc-users] mumps solve with same nonzero pattern<br>
To: <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
Message-ID:<br>
<CAMJxm+D7kwTZPQ_7xwEKueL2z=<a href="mailto:zKL6a4A1BBTQXxACj_UKJF-Q@mail.gmail.com" target="_blank">zKL6a4A1BBTQXxACj_UKJF-Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi,<br>
<br>
I am using mumps in PETSc to solve a 0.2 million system on 128 cores.<br>
Within Newton-Raphson iteration, the system with same sparse structure but<br>
different values will be solved many times. And I specify the<br>
preconditioning matrix having same nonzero pattern. The first time solving<br>
costs around 900 seconds and later solving only takes around 200 seconds.<br>
So I am wondering why the time differs that much. By setting the same<br>
nonzero pattern of pc, which of the mumps control parameters does PETSc<br>
change? Thanks.<br>
<br>
Regards,<br>
Wen<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/7bd8e1ad/attachment-0001.htm" target="_blank">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/7bd8e1ad/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Fri, 27 Apr 2012 10:11:27 -0400<br>
From: Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>><br>
Subject: Re: [petsc-users] mumps solve with same nonzero pattern<br>
To: PETSc users list <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br>
Message-ID:<br>
<CAMYG4GnbKCA7DOXAP=_+<a href="mailto:YHkDWaDF94TFjqr2eaZ3dQnD7Vy_Dg@mail.gmail.com" target="_blank">YHkDWaDF94TFjqr2eaZ3dQnD7Vy_Dg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On Fri, Apr 27, 2012 at 9:53 AM, Wen Jiang <<a href="mailto:jiangwen84@gmail.com" target="_blank">jiangwen84@gmail.com</a>> wrote:<br>
<br>
> Hi,<br>
><br>
> I am using mumps in PETSc to solve a 0.2 million system on 128 cores.<br>
> Within Newton-Raphson iteration, the system with same sparse structure but<br>
> different values will be solved many times. And I specify the<br>
> preconditioning matrix having same nonzero pattern. The first time solving<br>
> costs around 900 seconds and later solving only takes around 200 seconds.<br>
> So I am wondering why the time differs that much. By setting the same<br>
> nonzero pattern of pc, which of the mumps control parameters does PETSc<br>
> change? Thanks.<br>
><br>
<br>
The difference is that you do not have to perform the symbolic<br>
factorization again if the nonzero pattern does not change,<br>
just the numeric factorization. The symbolic factorization is the costly<br>
step.<br>
<br>
Matt<br>
<br>
<br>
> Regards,<br>
> Wen<br>
><br>
<br>
<br>
<br>
--<br>
What most experimenters take for granted before they begin their<br>
experiments is infinitely more interesting than any results to which their<br>
experiments lead.<br>
-- Norbert Wiener<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/f148b130/attachment-0001.htm" target="_blank">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/f148b130/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 27 Apr 2012 11:26:33 +0100<br>
From: "Christian Klettner" <<a href="mailto:ucemckl@ucl.ac.uk" target="_blank">ucemckl@ucl.ac.uk</a>><br>
Subject: [petsc-users] High Re CFD method.<br>
To: <a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
Message-ID:<br>
<<a href="mailto:ba0801c9e3bd11beb658cbec10d24a7f.squirrel@www.squirrelmail.ucl.ac.uk" target="_blank">ba0801c9e3bd11beb658cbec10d24a7f.squirrel@www.squirrelmail.ucl.ac.uk</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
Dear Petsc users,<br>
<br>
I know this is off topic but the people reading these questions are well<br>
placed to answer the question, being actual CFD developers. Over the last<br>
five years our group has developed a CFD code (using PETSc for parallel<br>
and vectors) based on the characteristic based split scheme to solve the<br>
incompressible Navier-Stokes equation (2D-3D) in a finite element<br>
framework using unstructured meshes. It is first order accurate in time<br>
and space. This has proved effective for high resolution, low Reynolds<br>
number complex geometry flows (e.g. groups of bodies).<br>
<br>
We are hoping to move onto higher Reynolds number flows, with the<br>
intention of using a large eddy simulation model for the turbulence. The<br>
goal is to model the flow in a hospital room with typical Reynolds numbers<br>
of 10^5. At present we are not convinced that the CBS scheme is the best<br>
scheme for these types of flows and are looking for other peoples opinions<br>
on alternative methods. Does anyone have any advice in this direction?<br>
<br>
Best regards,<br>
Christian<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Fri, 27 Apr 2012 10:28:41 -0500<br>
From: Ataollah Mesgarnejad <<a href="mailto:amesga1@tigers.lsu.edu" target="_blank">amesga1@tigers.lsu.edu</a>><br>
Subject: Re: [petsc-users] writing native PETSc binaries in python<br>
To: PETSc users list <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>><br>
Cc: <a href="mailto:petsc-dev@mcs.anl.gov" target="_blank">petsc-dev@mcs.anl.gov</a><br>
Message-ID:<br>
<<a href="mailto:CAC%2BVmGdP1V3DFrfLWextGVU23NRHtKwUoqcD4Ai__mwTdd1ZGw@mail.gmail.com" target="_blank">CAC+VmGdP1V3DFrfLWextGVU23NRHtKwUoqcD4Ai__mwTdd1ZGw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thanks for the replies:<br>
<br>
Just a bug report with petsc4py:<br>
<br>
petsc4py which downloads with --download-petsc4py=1 is the older v1.1.1<br>
which doesn't compile with petsc-dev?<br>
<br>
Thanks,<br>
Ata<br>
<br>
On Fri, Apr 27, 2012 at 8:25 AM, Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>> wrote:<br>
<br>
> On Fri, Apr 27, 2012 at 9:19 AM, Ataollah Mesgarnejad <<br>
> <a href="mailto:amesga1@tigers.lsu.edu" target="_blank">amesga1@tigers.lsu.edu</a>> wrote:<br>
><br>
>> Dear all,<br>
>><br>
>> I was wondering if there is way to write numpy arrays as native PETSc<br>
>> binaries in python so I can open them inside my program with VecView?<br>
>><br>
><br>
> I think what you want is to create a Vec using that array in petsc4py.<br>
><br>
> Matt<br>
><br>
><br>
>> Thanks,<br>
>> Ata<br>
>><br>
><br>
><br>
><br>
> --<br>
> What most experimenters take for granted before they begin their<br>
> experiments is infinitely more interesting than any results to which their<br>
> experiments lead.<br>
> -- Norbert Wiener<br>
><br>
<br>
<br>
<br>
--<br>
A. Mesgarnejad<br>
PhD Student, Research Assistant<br>
Mechanical Engineering Department<br>
Louisiana State University<br>
2203 Patrick F. Taylor Hall<br>
Baton Rouge, La 70803<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/cca3e1b6/attachment-0001.htm" target="_blank">http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120427/cca3e1b6/attachment-0001.htm</a>><br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
petsc-users mailing list<br>
<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a><br>
<a href="https://lists.mcs.anl.gov/mailman/listinfo/petsc-users" target="_blank">https://lists.mcs.anl.gov/mailman/listinfo/petsc-users</a><br>
<br>
<br>
End of petsc-users Digest, Vol 40, Issue 102<br>
********************************************<br>
</blockquote></div><br>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br>
</div>