Justin,<br><br>You are correct about my attempt to run grompp using MPIRUN - it doesn't work. Actually I realized that I was using a version of Gromacs that wasn't compiled for MPI! Gromacs-3.3.1-dev is compiled for MPI, however. The 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 md3.log -x md3.xtc<br>
<br>..This was carried out after I ran grompp on a single node.<br><br><div class="gmail_quote">2009/7/31 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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><div></div><div class="h5"><br>
<br>
<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;">
Hi,<br>
<br>
I'm trying to carry out an MD simulation on 4 processors but am having trouble with the MPI ("Can't read MPIRUN_HOST"). My error is:<br>
<br>
-catch_rsh /opt/gridengine/default/spool/compute-0-32/active_jobs/176501.1/pe_hostfile<br>
compute-0-32<br>
compute-0-32<br>
compute-0-32<br>
compute-0-32<br>
Got 4 slots.<br>
compute-0-32<br>
compute-0-32<br>
compute-0-32<br>
compute-0-32<br>
OSU MVAPICH VERSION 0.9.5-SingleRail<br>
Can't read MPIRUN_HOST<br>
# Cleaning local host (compute-0-32) for lpeng (lpeng)... done.<br>
<br>
<br>
My submission script is:<br>
<br>
# Define locations of MPIRUN, MDRUN, and grompp<br>
MPIRUN=/usr/local/topspin/mpi/mpich/bin/mpirun<br>
MDRUN=/share/apps/gromacs-3.3.1/bin/mdrun-mpi<br>
grompp=/share/apps/gromacs-3.3.1/bin/grompp<br>
<br>
cd /nas2/lpeng/nexil/gromacs/cg_setup<br>
<br>
# Running Gromacs: read TPR and write output to /nas2 disk<br>
$MPIRUN -v -machinefile $TMPDIR/machines -np $NSLOTS $grompp -f md.mdp -c confout.gro -o md3.tpr -n index.ndx<br>
<br>
# Run MD<br>
$MDRUN -v -nice -np $NSLOTS -s md3.tpr -o md3.trr -c confout.gro -g md3.log -x md3.xtc<br>
<br>
</blockquote>
<br></div></div>
The problem could be that you're trying to run grompp using mpirun (which you shouldn't), and then trying to run a parallel job with mdrun without invoking mpirun.<br>
<br>
Probably something like:<div class="im"><br>
<br>
$grompp -f md.mdp -c confout.gro -o md3.tpr -n index.ndx<br>
<br></div>
$MPIRUN -v -machinefile $TMPDIR/machines -np $NSLOTS $MDRUN -v -nice -np $NSLOTS -s md3.tpr -o md3.trr -c confout.gro -g md3.log -x md3.xtc<br>
<br>
is more appropriate. Without knowing the specifics of your system, a guess is about all I can give.<br>
<br>
-Justin<br>
<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">
<br>
Does anyone have any insight on what the problem could be? Is the problem with the MPI or the submission script?<br>
<br>
Thanks,<br>
Lili<br>
<br>
<br></div>
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</blockquote>
<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>
========================================<br>
</blockquote></div><br><br clear="all"><br>