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On 23/09/2011 4:37 PM, Sumanth M. Kumar wrote:
<blockquote
cite="mid:CANPiPQ6NrU3j4Dq-LHRqBsCgZqJ1xLdzjHpOn6mp_GXSrqNAxA@mail.gmail.com"
type="cite">
<div>Hi everyone,</div>
<div> </div>
<div>I did a simulation in an amazon cluster with 7.5 GB memory
and 4 EC2 Compute Units (2 virtual cores with 2 EC2 Compute
Units each) and it was done with 0.5ns/day. Now Im running a
simulation in another amazon cluster of 7 GB of memory and 20
EC2 Compute Units (8 virtual cores with 2.5 EC2 Compute Units
each), but still the speed is same even if i use "mpirun -np 8"
with the mdrun, and finally its taking the same time as 2core
system, i.e. 0.5ns/day. I would like to know whether I should
make any changes during compilation? I had enabled mpirun while
compiling GROMACS. Do I need to make any changes, so that it
will consider all the 8 processors?</div>
</blockquote>
<br>
Virtual cores are useless for GROMACS because it saturates the
processor pipelines on its own (though Intel's hyperthreading from
5-6 years ago was an exception). You need real cores, and to
configure MPI to assign processes 1-to-1 to real cores. The details
will be up to you and your system admins. You don't need to do
anything with GROMACS other than configure with MPI.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CANPiPQ6NrU3j4Dq-LHRqBsCgZqJ1xLdzjHpOn6mp_GXSrqNAxA@mail.gmail.com"
type="cite">
<div> </div>
<div>Thank you very much.</div>
<div> </div>
<div>Sumanth<br>
<br clear="all">
<br>
-- <br>
</div>
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<div><span style="TEXT-TRANSFORM: none; BACKGROUND-COLOR:
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face="georgia,serif"><strong>Sumanth Kumar.M<br>
</strong> </font></span></div>
<div><span style="TEXT-TRANSFORM: none; BACKGROUND-COLOR:
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face="georgia,serif">On-the-Job Trainee<br>
Plant Molecular Biology Lab.<br>
Plant Breeding, Genetics and Biotechnology<br>
International Rice Research Institute<br>
DAPO-7777, Metro Manila<br>
Philippines<br>
Tel : <span> </span>+63- 9163129718</font></span><span
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email :<span> <a moz-do-not-send="true"
href="mailto:s.kumar@irri.org" target="_blank">s.kumar@irri.org</a></span></font></span></div>
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href="mailto:sumanthkumar07@gmail.com" target="_blank">sumanthkumar07@gmail.com</a></span></font></span></div>
<br>
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