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On 29/03/2012 12:25 PM, cuong nguyen wrote:
<blockquote
cite="mid:CAMj9MadNw3Z7L3_QPChd5EhJo2z+HA0F6R2vdkvqaCa-OWBYwQ@mail.gmail.com"
type="cite">Thanks Erik, <br>
In case I run my simulations on 4 nodes, please let me know what
do I have to add to the command to start "MPI"? I have used the
commands:<br>
<i>grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p
topol.top<br>
mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e
NVT_50ns -g NVT_50ns -v</i><br>
however, the speed was still the same.<br>
</blockquote>
<br>
You need to find out what MPI you have installed and consult the
available documentation for that. We cannot help you with that.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAMj9MadNw3Z7L3_QPChd5EhJo2z+HA0F6R2vdkvqaCa-OWBYwQ@mail.gmail.com"
type="cite">Best regards,<br>
<br>
Cuong<br>
<br>
<div class="gmail_quote">2012/3/15 Erik Marklund <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">If you are to run on a
single node, then there's no need for mpi nowadays. mdrun
uses all cores it can find anyway. If you need to split your
calculation over many machines, however, you will need mpi.
<div>
<br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Erik<br>
<div><br>
<div>
<div>15 mar 2012 kl. 04.50 skrev cuong nguyen:</div>
<br>
<blockquote type="cite">
<div>
<div class="h5">
<div>Dear Gromacs users,</div>
<div> </div>
<div>I prepare to run my simulations on the
supercomputer on single node with 64 CPUs.
Although I have seen on Gromacs Mannual
suggesting to use MPI to parellel, I still
haven't understood how to use this application
and which commands I have to use. Please help
me to deal with this?</div>
<div> </div>
<div>Many thanks and regards,</div>
<div> </div>
<div>Cuong</div>
<div> </div>
<br>
</div>
</div>
<div class="im">
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<div>-----------------------------------------------</div>
<div>Erik Marklund, PhD</div>
<div>Dept. of Cell and Molecular Biology,
Uppsala University.</div>
<div>Husargatan 3, Box 596, 75124
Uppsala, Sweden</div>
<div>phone: <a moz-do-not-send="true"
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</div>
<br>
<br clear="all">
<br>
-- <br>
<div>Nguyen Van Cuong</div>
<div>PhD student - Curtin University of Technology</div>
<div>Mobile: (+61) 452213981</div>
<div> </div>
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