<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>Dear Erik</DIV>
<DIV>Thanks for your explanation :)</DIV>
<DIV>regards</DIV>
<DIV>Delara<BR>--- On <B>Wed, 4/13/11, Erik Marklund <I><erikm@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: Erik Marklund <erikm@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, 2:02 PM<BR><BR>
<DIV id=yiv480741036>delara aghaie skrev 2011-04-13 11.26:
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<DIV>Hello</DIV>
<DIV>Previously I used gromacs/3.3 for my simulations of DPPc monolayer+Tip4P2005. I saw that it uses particle decomposition</DIV>
<DIV>Now I want to use versin 4.0.7 because I need tcoupl=v-rescale</DIV>
<DIV>This version does the domain decomposition which causes load imbalance.</DIV>
<DIV>with this version because of load imbalance and loss of performance the simulation needs longer time to run.</DIV>
<DIV>so the question:</DIV>
<DIV>what is the benefit of this domain decomposition. I think it causes the runs to be done slower !!!.</DIV>
<DIV> </DIV>
<DIV>thanks</DIV>
<DIV>D.aghaie</DIV></TD></TR></TBODY></TABLE></BLOCKQUOTE>Most 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.<BR><BR>Why go for 4.0.7, why not 4.5.4?<BR><BR><PRE class=yiv480741036moz-signature>--
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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
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