Running multiple walker metadynamics on Stampede2

From: Sebastian S (
Date: Mon Dec 02 2019 - 22:43:09 CST

Hi everyone,

I will be trying to run some multiple walker metadynamics simulations on
Stampede2 and wanted to know if there's an easy way of doing this.
I'm already able to run these simulations on my local cluster by using an
sh script (see below) but have no idea of how to do it on Stampede. Any
help would be appreciated!
As an example, let's say I want to run 24 replicas with namd files
testres.rep1.namd to testres.tep24.namd.

Since now thanks,


#$ -pe mpi-24 576 # Specify parallel environment and legal core size

rm -f ./hostfile
cat $PE_HOSTFILE | while read -r line; do
  host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
  echo $host >> hostfile

while IFS= read -r host
  let "TASK+=1"
  /usr/kerberos/bin/rsh -F $host -n "uname -a; echo $TASK; cd XXX; pwd;
module load namd; mpirun -np 24 namd2 testres.rep$TASK.namd >
 s$TASK.0.log ; exit" &
  sleep 20
done < $hostfile

rm ./hostfile

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