Re: NAMD on ranger.tacc

From: George M Giambasu (giambasu_at_gmail.com)
Date: Tue Jan 24 2012 - 12:22:42 CST

Here is what I use to run namd2.7 on ranger. I have not observed any
performance issues with this script.

George

#$ -S /bin/bash
#$ -A XXXXXXXXX   # replace with your TG account #
#$ -V    # pass current environment variables
#$ -cwd    # script will run from the directory that the job was
submitted from
#$ -N NAMD    
#$ -pe 16way 512    # 16 cores per node, 4 nodes, 64 cores total
#$ -q normal    
#$ -l h_rt=24:00:00 # 1 hour walltime

module unload mvapich
module swap pgi intel/10.1
module load mvapich-old/1.0.1
module load fftw2

export VIADEV_SMP_EAGERSIZE=64
export VIADEV_SMPI_LENGTH_QUEUE=256
export VIADEV_RENDEZVOUS_THRESHOLD=50000
export VIADEV_ADAPTIVE_RDMA_LIMIT=0

ibrun tacc_affinity /path/to/namd2 md2_prod_2.inp > eq_9.inp.log

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