RE: Running multiple walker metadynamics on Stampede2

From: Vermaas, Joshua (
Date: Tue Dec 03 2019 - 11:15:58 CST

Hi Sebastian,

I think has what you need. The usual ibrun command for NAMD would have one extra flag to specify the offset (the -o argument), which would be used to make sure that each instance of NAMD has its own distinct set of cores.


On 2019-12-02 21:50:09-07:00 wrote:

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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