Usage of MINIME.LBL.GOV

GridEngine

Submitting Jobs

Requirements to submitting a job to the GridEngine:

Custom (non-system) Binaries must reside in a publically accessiable location (like /home/$USERNAME) to all nodes.
Script must be written to include all full paths to binaries and datasets from the perspective of '/'.

A generic script can be made as follows:

#!/bin/sh
#
# Script to parallelize encoding of MP3's
#
#$ -N Job Name
MP3=$1
date
/home/gmkurtzer/bin/bladeenc -q -outdir=/home/gmkurtzer/mp3s/ $MP3
date

Assuming you saved this script as '/home/gmkurtzer/queue.sh', you can submit the job with the command:

$ qsub /home/gmkurtzer/queue.sh

And can make it consume both CPU's by:

$ qsub -l CPU=2 /home/gmkurtzer/queue.sh

note: This does not mean that this job will run in parallel, rather it will tell the schedualler to mark both slots as full!

Monitoring Jobs

The command 'qstat' is the tool you should use to monitor the jobs that are in the queue and running. Here is some example usage:

Listing all queues:

$ qstat -f

Getting more information on a specific queue:

# qstat -j [JOB ID]