Job Parameters

Here's the meaning of useful parameters that we can add in the header of our job scripts. You can either add them on the header of a script or directly in the qsub command.

#$ -N NAME = Names our job in the cluster as specified in NAME
#$ -q QUEUE = Automatically sends our job to the specified queue in QUEUE, so we don't need to specify it in the qsub command.
#$ -M EMAIL = Sends notifications of the job status to the specified address in EMAIL, according to criteria below.
#$ -m beas = Send you email of job status (b)egin, (e)rror, (a)bort, (s)suspend.
#$ -e DIRNAME = redirects error logs to DIRNAME. Default is home directory
#$ -o DIRNAME = redirects standard output to DIRNAME. Default is home directory.
#$ -l hostname=HNAME = forces queue to submit job in the specified HNAME (cronus, rhea, etc...).

Sample header for hello_world.sh:

#!/bin/bash
#
#$ -N hello_world
#$ -M someaddress@uci.edu
#$ -m beas
#$ -q ttn.q

echo "hello world"

Another way to do it is by removing the #$ parameters of the header and run:

qsub -N hello_world -M someaddress@uci.edu -m beas -q ttn.q hello_world.sh

Log files

SGE automatically creates 2 log files in the default/specified folder, JOBNAME.eJOBID and JOBNAME.oJOBID. 'e' is for error messages and 'o' is for standard output.