Hi Mark,<br><br>I originally specified my $NSLOTS as 4 in my original scripts (didn't include the header portion in my previous email). Are you saying that even though I specified 4 nodes as "-np 4", I'm still running my job on a single processor, based on the way I've written my script?<br>
<br>I'm pretty new to using GROMACS so I figured it would be faster for me to do a test run on the GROMACS 3.3.1 that's currently available on the cluster I'm using rather to compile the new version 4(?) that is out. Thanks for your recommendation though.<br>
<br>Lili<br><br><div class="gmail_quote">2009/8/2 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><a href="mailto:rainy908@yahoo.com" target="_blank">rainy908@yahoo.com</a> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Justin,<br>
<br>
You are correct about my attempt to run grompp using MPIRUN - it doesn't<br>
work. Actually I realized that I was using a version of Gromacs that wasn't<br>
compiled for MPI! Gromacs-3.3.1-dev is compiled for MPI, however. The<br>
submission script that worked is as follows:<br>
<br>
# Define locations of MPIRUN, MDRUN<br>
MPIRUN=/usr/local/topspin/mpi/mpich/bin/mpirun<br>
MDRUN=/share/apps/gromacs-3.3.1-dev/bin/mdrun<br>
<br>
cd /nas2/lpeng/nexil/gromacs/cg_setup<br>
<br>
# Run MD<br>
$MDRUN -v -nice 0 -np $NSLOTS -s md3.tpr -o md3.trr -c confout.gro -g<br>
md3.log -x md3.xtc<br>
<br>
..This was carried out after I ran grompp on a single node.<br>
</blockquote>
<br></div>
That still won't run a parallel mdrun. Justin indicated the correct approach.<br>
<br>
Also, unless you know a good reason for using a version of GROMACS 3(?) years old, use an up-to-date one. It'll be heaps faster.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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