AMBER Archive (2008)

Subject: RE: AMBER: Compile AMBER 9 on TACC Ranger super computer

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Aug 14 2008 - 19:38:30 CDT

Hi Lei,

Yes, sorry I made a small mistake in the qsub script - since I forgot it was
setup for bash shell.

It should read:
-----------------------------------

#!/bin/bash
#$ -V # Inherit the submission environment
#$ -cwd # Start job in submission directory
#$ -N testPMEMD # Job Name
#$ -j y # combine stderr & stdout into stdout
#$ -o $JOB_NAME.o$JOB_ID # Name of the output file (eg. myMPI.oJobID)
#$ -pe 2way 32 # Requests 2 cores/node, 32/16 = 2 nodes total (4
cpu)
#$ -q development # Queue name
#$ -l h_rt=00:45:00 # Run time (hh:mm:ss) - 0.5 hours
set -x #{echo cmds, use "set echo" in csh}
export AMBERHOME=~/amber9
cd $AMBERHOME/test
export DO_PARALLEL=ibrun
make test.pmemd

-----------------------------------

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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