[gmx-users] how to run parallel jobs in gromacs

[Anupam Nath Jha]

Dear all

i am new in gromacs. i have installed gromacs-3.3.3 in our cluster(mpi is
already there) with parallel version (using the following command):


make clean
./configure --enable-mpi --disable-nice --program-suffix="_mpi"
make mdrun
make install-mdrun

it went fine.

but when i ran the command -
qsub pbs_submit

it's the pbs_submit file:

#This is a PBS script for Parallel Jobs
#!/bin/bash -f
#PBS -l nodes=2:ppn=2
#PBS -o /home/anupam/MD/lyd
#PBS -e /home/anupam/MD/lyd
#PBS -q default

cd /home/anupam/MD/lyd
mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr
mpirun mdrun_mpi -v -deffnm -np 4 em

but it's not doing anything,except writing this:

totalnum=3  numhosts=2
there are not enough hosts on which to start all processes
totalnum=3  numhosts=2
there are not enough hosts on which to start all processes



can you help me out?

thanks in adavnce
anupam



-- 
Science is facts; just as houses are made of stone, so is science is made of
facts; but a pile of stones is not a house, and  a collection of facts is not
necessarily sciece.

Anupam Nath Jha
Ph. D. Student
Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
IISc,Bangalore-560012
Karnataka
Ph. no.-22932611



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