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<blockquote type=cite class=cite cite>We are a bunch of undergraduate
students and have put up a cluster of 16 IBM's using LAM for the purpose
of running GROMACS. During our simulation test runs we noticed that the
running time increases as the number of nodes in the LAM topology
increases. We couldn't diagonise the problem...plz
help.</blockquote><br>
How many atoms in this simulation?<br><br>
If you aren't already doing so, would be best to use the benchmark
simulation files on the web site for running your benchmarks, unless
there is something you have of particular interest to you.<br><br>
If there is a small number, then it isn't going to scale very well at all
since the system will spend most of the time trying to communicate with
the other nodes. Even with a large system I have found that GROMACS
scales poorly beyond a single box due to the slower speed of
communication over the networks. You can see this by looking at the
benchmark page on the web site too.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy<br>
Monash University<br>
381 Royal Parade<br>
Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083</html>