ok here the pbs file for the job<div><br></div><div><div>#!/bin/bash </div><div>#PBS -l nodes=1:ppn=1</div><div>#PBS -l walltime=00:01:59</div><div>#PBS -o output.out </div><div>#PBS -j oe</div><div>#PBS -N mdrun </div>
<div>WORK_HOME=/auto/hpc-08/knomura/choubey/GROMACS/test</div><div>cd $WORK_HOME</div><div>source /usr/usc/mpich/default/setup.sh</div><div>mdrun_mpi -v -s em -o em -c after_em -g emlog</div><div><br></div><div>Is my command line wrong? </div>
<br><div class="gmail_quote">On Tue, Sep 15, 2009 at 6:25 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div></div><div class="h5"><br>
<br>
Amit Choubey wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi everyone,<br>
<br>
I have the gromacs mpi version on my system and everything in the simulation works fine until i get to mdrun_mpi and when i use this executable the following pops error comes up<br>
<br>
MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry in /dev.<br>
<br>
Then i tried the to do mdrun_mpi -h on the terminal and the same thing comes out.<br>
<br>
MX:hpc-login2:mx_init:querying driver:error 5(errno=2):No MX device entry in /dev.<br>
<br>
Is this an installation problem? I am also not able to find the online manual for mpi version of gromacs, could someone send me the link?<br>
<br>
</blockquote>
<br></div></div>
Because MPI only applies to mdrun, so there's no need for a separate manual. All the information for mdrun applies to mdrun_mpi, except that it can be executed in parallel.<br>
<br>
It looks like there is either a problem with the MPI implementation of the machine, or you're calling the command wrong. If you can post your command line or the contents of whatever submission script you might be using, we might be able to implicate (or rule out) the latter.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Thank you,<br>
Amit <br>
<br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote></div><br></div>