The -np flag should be specified to the mpirun command (gromacs
determines it automatically).
It could also be a problem with your MPI library or queue system - I
have no idea why it is trying to start 3 processes...
Cheers,
Erik
On Aug 6, 2007, at 12:46 PM, Anupam Nath Jha wrote:
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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