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

delara aghaie d_aghaie at yahoo.com
Wed Apr 13 11:44:26 CEST 2011

Dear Erik
Thanks for your explanation :)
--- On Wed, 4/13/11, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

From: Erik Marklund <erikm 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, 2:02 PM

delara aghaie skrev 2011-04-13 11.26: 

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 !!!.
D.aghaieMost of the time it reduces communication of coordinates, which in turn can is one of the big bottlenecks in parallel MD. Domain decomposition makes sure that atoms which are close to eachother, and hence are likely to interact, are passed to the same core. With particle decomposition the atoms are statically asigned to the different cores, and the decomposition may not reflect how the aroms interact.

Why go for 4.0.7, why not 4.5.4?

Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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