[gmx-users] Re: Running Gromacs in Clusters

[Dr. Vitaly Chaban]

> 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?
>

1. You may try explicit adding " --hostfile $PBS_NODEFILE" as the
argument for your MPIRUN,

2. Also, some setups do not work (I do not know why), if you
explicitly specify PPN=XXX (or ncpus=24 in the above instance)

-- 
Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark