[gmx-users] 2nd question related to load imbalance

delara aghaie d_aghaie at yahoo.com
Wed Apr 13 11:41:47 CEST 2011

Dear Dr. van der Spoel
many thanks for your explanations.
I want to know how I can overcome the performance loss due to load imbalance?
--- On Wed, 4/13/11, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] 2nd question related to load imbalance
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, April 13, 2011, 2:01 PM

On 2011-04-13 11.26, delara aghaie wrote:
> Hello
> Previously I used gromacs/3.3 for my simulations of DPPc
> monolayer+Tip4P2005. I saw that it uses particle decomposition
> Now I want to use versin 4.0.7 because I need tcoupl=v-rescale
> This version does the domain decomposition which causes load imbalance.
> with this version because of load imbalance and loss of performance the
> simulation needs longer time to run.
> so the question:
> what is the benefit of this domain decomposition. I think it causes the
> runs to be done slower !!!.
> thanks
> D.aghaie
4.0.7 is a lot better than 3.3 for scaling, but the latest version 4.5.4 is even better. In addition it contains new features and bugfixes.

-- David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
-- gmx-users mailing list    gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110413/f73627f1/attachment.html>

More information about the gromacs.org_gmx-users mailing list