From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Nov 20 2018 - 16:51:32 CST
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:
#SBATCH -A FILLMEIN
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.
On 2018-11-20 15:17:48-07:00 owner-namd-l_at_ks.uiuc.edu wrote:
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: Mon Dec 31 2018 - 23:21:33 CST
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/
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,
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:33 CST