Re: Running multiple walker metadynamics on Stampede2

From: Sebastian S (thecromicusproductions_at_gmail.com)
Date: Wed Dec 04 2019 - 21:44:38 CST

Hi Josh,

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
http://www.ks.uiuc.edu/Research/namd/2.12/ug/node69.html

Regards,

Sebastian

On Tue, Dec 3, 2019 at 12:15 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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.
>
> -Josh
>
>
>
> 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,
> Sebastian
> #!/bin/bash
> #$ -pe mpi-24 576 # Specify parallel environment and legal core size
>
> TASK=0
> rm -f ./hostfile
> cat $PE_HOSTFILE | while read -r line; do
> host=`echo $line|cut -f1 -d" "|cut -f1 -d"."`
> echo $host >> hostfile
> done
> hostfile="./hostfile"
>
> while IFS= read -r host
> do
> 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
>
> wait
> rm ./hostfile
>
>

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