From: Sebastian S (thecromicusproductions_at_gmail.com)
Date: Wed Dec 04 2019 - 21:44:38 CST
Thanks for your reply! I was actually wondering if there is something that
sends all the jobs to run at the same time, similar to the one for
replica exchange umbrella sampling presented here
On Tue, Dec 3, 2019 at 12:15 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
> Hi Sebastian,
> I think
> https://portal.tacc.utexas.edu/user-guides/stampede2#more-than-one-mpi-application-running-concurrently 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 owner-namd-l_at_ks.uiuc.edu 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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