[gmx-users] Replica exchange shell script

Mark Abraham Mark.Abraham at anu.edu.au
Sun Feb 26 05:07:51 CET 2006

Sukit Leekumjorn wrote:
> Dear GMX users;
> I have a question about running replica exchange MD on parallel 
> machines.  Current, I am able to run a single job in parallel using 
> Gromacs 3.3 official version.  To submitted and run this job I have to 
> have a shell script.  My question is  how to write a shell script to 
> submitted a job in parallel using REMD.  Below is the shell script that 
> I use to submitted a job running with 12 nodes.  I have seen several 
> emails on replica exchange but none had mentioned using a shell script.  
> I have four md#.tpr files "grompp" at different temperatures (did not 
> use -np option) and I want to run using 4 nodes.  I tried to modify the 
> line "export EXEC=" line to match what others have posted on mailing 
> list but it does not seem to work.  If anyone had experience with this, 
> please give me some insight on how to summited REMD job in parallel 
> using a shell script.

Your script looks basically fine. I use a perl script called by a PBS 
shell script to do both system setup and MD. The actual mdrun command I 
use is

${mdrun} -multi -np $ENV{'PBS_NCPUS'} -v -replex ${exchange_frequency} 
-s ${tpr_filename} -o ${tpr_filename} -c ${tpr_filename} -g 
${tpr_filename} -e ${tpr_filename} -stepout 500

where ${xxx} are sensible variable contents. Obviously ${tpr_filename} 
does not have the file type suffix, or the integer suffix.

You'll need to actually tell us what you were trying that you found 
didn't work if you want more help than this :-)


> #!/bin/bash
> ## The time limit for the job.  If it runs over this it will be killed.
> ## -lwalltime=0:05:0 would be five minutes.
> #PBS -lwalltime=150:00:00
> #PBS -W group_list=heroes
> #PBS -q production_q
> #PBS -lnodes=6:ppn=2
> #$ -notify
> #PBS -A jobx
> #PBS -N pe128_330
> NUM_NODES=`cat $PBS_NODEFILE | wc -l | sed "s/ //g"`
> ## Get in to the directory qsub was run from
> export PATH=/nfs/software/bin:$PATH
> export FF=/nfs/storage1/users/gromacs3.3_022006/bin
> export EXEC="$FF/mdrun_3.3_gcc_mpi -s 1pe330_2.tpr -np 12 -deffnm 1pe330_2"
> echo starting
> date
> echo "/// Running on:"
> echo "///"
> echo
> jmdrun -printhostname -np $NUM_NODES -hostfile $PBS_NODEFILE $EXEC
> echo
> date
> echo ending
> exit;
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