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 ${tpr_filename}
does not have the file type suffix, or the integer suffix.
You'll need to actually tell us what you were trying that you found
didn't work if you want more help than this :-)
Mark
#!/bin/bash
## The time limit for the job. If it runs over this it will be killed.
## -lwalltime=0:05:0 would be five minutes.
#PBS -lwalltime=150:00:00
#PBS -W group_list=heroes
#PBS -q production_q
#PBS -lnodes=6:ppn=2
#$ -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
cd $PBS_O_WORKDIR
export PATH=/nfs/software/bin:$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:"
cat $PBS_NODEFILE
echo "///"
echo
jmdrun -printhostname -np $NUM_NODES -hostfile $PBS_NODEFILE $EXEC
echo
date
echo ending
exit;
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