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delara aghaie skrev 2011-04-13 11.26:
<blockquote cite="mid:646075.14902.qm@web130103.mail.mud.yahoo.com"
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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>
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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="moz-signature" cols="72">--
-----------------------------------------------
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
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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