Re: [NAMD] Running REUS in many nodes

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Tue Nov 20 2018 - 18:40:55 CST

Thank you very much, Josh! I'll play with that one

On Tue, Nov 20, 2018 at 5:51 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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/
> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FTraining%2FTutorials%2Fscience%2Fumbrella%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C60f3fd93c3b14a8f0df308d64f35ff61%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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