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On 11/06/2012 3:06 PM, delara aghaie wrote:
<blockquote
cite="mid:1339391204.42158.YahooMailNeo@web28703.mail.ir2.yahoo.com"
type="cite">
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<div><span>Dear Gromacs users</span></div>
<div><span>I have checked something today and it seems starnge
to me. Doing the Justin lyzozyme tutorial, I checked the
performance of our parallel system. Subimitting the job on 8
processors of one node, I get<span style="color: rgb(255, 0,
255);"> </span><span style="text-decoration: underline;
font-weight: bold; background-color: rgb(255, 255, 255);
color: rgb(255, 0, 255);">0.86 ns/day</span><span
style="color: rgb(255, 0, 255);"> </span>which seems to
be very weak performance. Do you have any idea about the
ns/day performance of 8 processors for the same lyzozyme
system?</span></div>
<br>
</div>
</blockquote>
<br>
When starting a new discussion, please do not reply to an existing
email. This confuses the mailing list archive.<br>
<br>
Parallel algorithms are not magic - they are engineered to provide
benefits under a range of conditions. Simply observing the rate on
one system at a number processors can give no real idea whether you
are getting value for running in parallel. This will depend on the
size of your simulation system and the attributes of your hardware.
There is lots of output in the .log file about how the parallel
calculation is running, and you will need to have read and
understood a fair bit of chapter 3 of the manual (particularly the
last sections) for that to make sense.<br>
<br>
Mark<br>
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