Batch Queuing

We do not allow any user jobs (Testing/Production) on frontend under any circumstances

Grendel uses the SGE queuing system. All jobs which run more than 2 minutes and all multiprocessor jobs should be submitted to SGE.

Instead of an interactive command like

./myjob
use
qsub job_script

e.g.: qsub test.sh
The components of this command are:

test.sh -> job_script: is not the actual job but the script that runs the user jobs.

Usually you will want to use a command script with qsub. The sample/test command script for the previous example would be

#!/bin/sh	[or tcsh]
#$ -V	[Use current environment setting in batch job]
#$ -cwd	[Use current directory as the job's working directory]
#$ -S /bin/bash	[Use shell as shell for the batch session]
#$ -N testjob	[Names the job job_name]
#$ -o $JOB_NAME.o$JOB_ID	[Direct job output to output_file]
#$ -e $JOB_NAME.e$JOB_ID	[Direct job error to error_file]
#$ -q normal	[Submits to queue designated by queue_name]
#$ -pe fill 8	[Executes job via the Parallel Environemnt]
hostname

For the detailed tutorial download this tutorial - Submit and Run Jobs on Grendel