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

Peter Lai pcl at uab.edu
Wed Apr 13 13:44:31 CEST 2011

You can always try mdrun -dlb yes whch will turn on dynamic load balancing from the beginning..
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of delara aghaie [d_aghaie at yahoo.com]
Sent: Wednesday, April 13, 2011 4:41 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 2nd question related to load imbalance

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://us.mc1301.mail.yahoo.com/mc/compose?to=spoel@xray.bmc.uu.se>    http://folding.bmc.uu.se<http://folding.bmc.uu.se/>
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