From: Niklaus Johner (niki.johner_at_gmail.com)
Date: Wed Feb 27 2013 - 14:27:34 CST
Hi,
Here is an example of submission script for namd on stampede. This is using the official namd build of stampede.
Best,
Niklaus
#!/bin/bash
#----------------------------------------------------
# Example SLURM job script to run MPI applications on
# # TACC's Stampede system.
# #
# # $Id: job.mpi 1580 2013-01-08 04:10:50Z karl $
# #----------------------------------------------------
#
#SBATCH -J jobname # Job name
#SBATCH -o myjob.%j.out # Name of stdout output file (%j expands to jobId)
#SBATCH -p normal # Queue name
#SBATCH -N 8 # Total number of nodes requested (16 cores/node)
#SBATCH -n 128 # Total number of mpi tasks requested
#SBATCH -t 24:00:00 # Run time (hh:mm:ss) - 24 hours
#SBATCH -A ??? # <-- Allocation name to charge job against
#SBATCH --mail-user=...
#SBATCH --mail-type=ALL
#SBATCH --dependency=afterok:138201 #equivalent of -hold_jid
# Launch the MPI executable named "input.int"
module load namd/2.9
module swap mvapich2 impi/4.1.0.024
export MKL_MIC_ENABLE=1
export I_MPI_EAGER_THRESHOLD=262144
ibrun tacc_affinity namd2 1nput.in >& output.out
Niklaus Johner
Weill Cornell Medical College
Harel Weinstein Lab
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065
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