[gmx-users] Running Gromacs in Clusters

[Erik Marklund]

Hi,

I looked at one of my old pbs jobs and noted that the following line works for me:
#PBS -l nodes=X:ppn=Y
where X is the number of nodes and ppn is the number of cores per node. Perhaps your batch system uses a different "dialect".

What errors do you get when you aim for more than one node?

Furthermore, are you using virtual sites and constraints for your simulations? If not then you might be able to increase your simulation speed manifold.

Erik

7 nov 2012 kl. 17.50 skrev 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/*
> --
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html