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<div style="">During your installation, if you use --program-suffix=_mpi, so the mdrun_mpi will work.<br>
I suggest you to check the nodes of the cluster, probably try pbsnodes, on a master node no job may be run.
<br>
Note that I do not know much about your information, so the (guessing) suggestion maybe not fit for your problems, just cause I once confused about why mine 4cpus barely used before too.<br>
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Best,<br>
<br>
lina<br>
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<div style="direction: ltr;" id="divRpF604005"><font size="2" color="#000000" face="Tahoma"><b>From:</b> gmx-users-bounces@gromacs.org [gmx-users-bounces@gromacs.org] on behalf of Carsten Kutzner [ckutzne@gwdg.de]<br>
<b>Sent:</b> Thursday, July 08, 2010 4:04 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] mpi run<br>
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<div>Hi Mahmoud,
<div><br>
</div>
<div>for anyone to be able to help you, you need to provide</div>
<div>a lot more information, at least:</div>
<div>- which mpi library are you using?</div>
<div>- how did you compile and/or install Gromacs?</div>
<div>- what commands do you use to run mdrun and what was</div>
<div>the output of it?</div>
<div><br>
</div>
<div>Best,</div>
<div> Carsten</div>
<div><br>
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<div>
<div>On Jul 8, 2010, at 9:41 AM, nanogroup wrote:</div>
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Dear GMX Users,<br>
<br>
I have a PC with 4 CPU, but the Gromacs only use one CPU.<br>
<br>
the command of mpiru works on linux; however, the command of mdrun_mpi does not work.<br>
<br>
Would you please help me how to set up the mdrun_mpi in Gromacs 4.0.4<br>
<br>
Many thanks,<br>
Mahmoud<br>
<br>
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<div><span class="Apple-style-span" style=""><span class="Apple-style-span" style="">
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--</div>
<div>Dr. Carsten Kutzner</div>
<div>Max Planck Institute for Biophysical Chemistry</div>
<div>Theoretical and Computational Biophysics</div>
<div>Am Fassberg 11, 37077 Goettingen, Germany</div>
<div>Tel. +49-551-2012313, Fax: +49-551-2012302</div>
<div><a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne" target="_blank">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a></div>
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