[gmx-developers] Problem submitting GROMACS script

[rainy908 at yahoo.com]

Hi,

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:

-catch_rsh
/opt/gridengine/default/spool/compute-0-32/active_jobs/176501.1/pe_hostfile
compute-0-32
compute-0-32
compute-0-32
compute-0-32
Got 4 slots.
compute-0-32
compute-0-32
compute-0-32
compute-0-32
OSU MVAPICH VERSION 0.9.5-SingleRail
Can't read MPIRUN_HOST
# Cleaning local host (compute-0-32) for lpeng (lpeng)... done.


My submission script is:

# Define locations of MPIRUN, MDRUN, and grompp
MPIRUN=/usr/local/topspin/mpi/mpich/bin/mpirun
MDRUN=/share/apps/gromacs-3.3.1/bin/mdrun-mpi
grompp=/share/apps/gromacs-3.3.1/bin/grompp

cd /nas2/lpeng/nexil/gromacs/cg_setup

# Running Gromacs: read TPR and write output to /nas2 disk
$MPIRUN -v -machinefile $TMPDIR/machines -np $NSLOTS $grompp -f md.mdp -c
confout.gro -o md3.tpr -n index.ndx

# Run MD
$MDRUN -v -nice -np $NSLOTS -s md3.tpr -o md3.trr -c confout.gro -g md3.log
-x md3.xtc


Does anyone have any insight on what the problem could be?  Is the problem
with the MPI or the submission script?

Thanks,
Lili
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