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On 31/10/2011 12:28 PM, Sanku M wrote:
<blockquote
cite="mid:1320024532.37912.YahooMailNeo@web114417.mail.gq1.yahoo.com"
type="cite">
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<div>Hi,</div>
<div> I just compiled gromacs 4.5.4 in a cluster. But, I find
that if I try to make use of threading introduced in gromacs
4.5.x series, it does not work. </div>
<div> After issuing command like mdrun -v -s , I expected that
for my 8-core processor which is not running any other jobs,
the threading will show one job with 800 % cpu usage. But, it
is showing 100 % cpu usage hence using only 1 of the 8
processors. I was wondering whether there is any command line
I need to use to ensure the gromacs understands that there is
8 processors in a core and force make full use of the entire
machine.</div>
<div><br>
</div>
<div>I have tried the same thing in another different cluster
where I found that threading works with showing 800 % cpu
usage . But, for this cluster , the threading does not work.</div>
</div>
</blockquote>
<br>
These metrics are unreliable unless you have documentation stating
what 800% vs 100% means, and that you have 8 physical cores -
virtual cores are not useful for GROMACS, because they derive their
benefit from overlapping downtime on one process (e.g. accessing
memory) with compute time on another and GROMACS does not have
significant downtime.<br>
<br>
If you have compiled with threading, then the top of the .log file
reports how many threads GROMACS has automatically determined to
use. You should then look at performance of runs over several
minutes to determine what speed-up is occurring.<br>
<br>
Mark<br>
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