<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>Dear Dr. van der Spoel</DIV>
<DIV>many thanks for your explanations.</DIV>
<DIV>I want to know how I can overcome the performance loss due to load imbalance?</DIV>
<DIV>Thanks</DIV>
<DIV>regards</DIV>
<DIV>Delara<BR>--- On <B>Wed, 4/13/11, David van der Spoel <I><spoel@xray.bmc.uu.se></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: David van der Spoel <spoel@xray.bmc.uu.se><BR>Subject: Re: [gmx-users] 2nd question related to load imbalance<BR>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>Date: Wednesday, April 13, 2011, 2:01 PM<BR><BR>
<DIV class=plainMail>On 2011-04-13 11.26, delara aghaie wrote:<BR>> Hello<BR>> Previously I used gromacs/3.3 for my simulations of DPPc<BR>> monolayer+Tip4P2005. I saw that it uses particle decomposition<BR>> Now I want to use versin 4.0.7 because I need tcoupl=v-rescale<BR>> This version does the domain decomposition which causes load imbalance.<BR>> with this version because of load imbalance and loss of performance the<BR>> simulation needs longer time to run.<BR>> so the question:<BR>> what is the benefit of this domain decomposition. I think it causes the<BR>> runs to be done slower !!!.<BR>> thanks<BR>> D.aghaie<BR>> <BR>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.<BR><BR>-- David van der Spoel, Ph.D., Professor of Biology<BR>Dept. of Cell & Molec. Biol., Uppsala University.<BR>Box 596, 75124 Uppsala, Sweden.
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