NAMD on Ranger at Teragrid

From: Zumot, Elia Nabil (enz1_at_pitt.edu)
Date: Thu Jun 10 2010 - 15:08:16 CDT

Hi all,

I'm trying to run NAMD on Ranger (TACC) at Teragrid for the first time.
Could you tell me if there is anything wrong (or not optimal) with the following job script?

#$ -A TG-MCB100108

#$ -N test

#$ -cwd

#$ -o output

#$ -q normal

#$ -V

#$ -l h_rt=01:00:00

#$ -pe 16way 64

 

export VIADEV_SMP_EAGERSIZE=64

export VIADEV_SMPI_LENGTH_QUEUE=256

export VIADEV_ADAPTIVE_RDMA_LIMIT=0

export VIADEV_RENDEZVOUS_THRESHOLD=50000

module unload mvapich2

module swap pgi intel

module load mvapich

cd $WORK

module load namd/2.7b2

ibrun -n 64 env VIADEV_RENDEZVOUS_THRESHOLD=50000 namd2 test.conf >& test.log

Thanks

Elia

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