[gmx-users] Running Gromacs in Clusters

[Marcelo Depolo]

Hi Erik,


That's good news! But i've got problems using more than one node per
simulation (24 cores per node in my cluster). I don't know if it's a
parallelization
script problem or anything else. I'm using PBS scripts like this:

*#!/bin/bash

#PBS -N Gromacs
#PBS -lselect=1:ncpus=24
#PBS -m ae
#PBS -M marcelo at xxxxx

date

cd $PBS_O_WORKDIR

source  /usr/share/modules/init/bash

source $HOME/gromacs

module load mpi-lam7

HOSTLIST=`cat $PBS_NODEFILE  |paste -s -d ","`
cat $PBS_NODEFILE
lamboot $PBS_NODEFILE
mpirun -np 24 $HOME/bin/mdrun -e prt.edr -v -s prt.tpr -o prt.trr -c
prt.gro -g

date*

I have tried to raise the number of nodes, of cores and both. I've got
nothing.
Do you have any suggestions?
-- 
Marcelo Depólo Polêto
Departamento de Bioquímica e Biologia Molecular
Universidade Federal de Viçosa - UFV
*Website: http://opensourcebioinformatics.com/site/*