RE: [NAMD] Running REUS in many nodes

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Nov 20 2018 - 16:51:32 CST

Hi Sebastian,

This is a submission script from work I've done recently on stampede, asking for 71 windows each on their own node. Adjust as needed:

#!/bin/bash
#SBATCH --job-name=jobname
#SBATCH --nodes=71
#SBATCH --ntasks=923
#SBATCH --time=3:00:00
#SBATCH --partition=normal
#SBATCH --mail-type=ALL
#SBATCH --mail-user=joshua.vermaas_at_nrel.gov
#SBATCH -A FILLMEIN
cd /the/correct/directory/where/namd/should/run/from
ibrun /work/00288/tg455591/NAMD_LATEST_Linux-KNL-MPI-smp-Stampede/namd2 +ppn 4 +pemap 0-51 +commap 53-65 +replicas 71 run0.namd +stdout %d/run0.%d.log

In principle, you could also use the module version of NAMD (module load namd, follow the help it offers you), as I believe that is also a MPI+SMP build of NAMD.

-Josh

On 2018-11-20 15:17:48-07:00 owner-namd-l_at_ks.uiuc.edu wrote:

Hi everyone,
I'd like to perform some replica exchange umbrella sampling simulations
using Stampede. For this, I would like to use 25 nodes and run each
replica in one full node. For example, if I would like to run the tutorial from https://www.ks.uiuc.edu/Training/Tutorials/science/umbrella/1%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C1%7C636783490676711032&sdata=WAc01JkBf8EvFpOSkLErCaiiemYXjG6CnxviHRYHb3Y%3D&reserved=0>
what should I do? I usually use the runbatch_latest_knl code to
run regular simulations on a single node.
Thanks a lot and happy Thanksgiving,
Sebastian

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