From FarmShare

This is meant to be a script you can copy and adapt to get up and running quickly. A similar one appears at the bottom of the man page for 'qsub'.

#!/bin/bash
# the above line is called a 'hashbang' and sets which shell you run under; you probably want bash

#
# set the name of the job; this will appear in the job listing
#$ -N example_job
#

#
# set the maximum memory usage (per slot)
#$ -l mem_free=3G
#

#
# set the number of slots, replace '1' with a larger number if needed
#$ -pe shm 1
#

#
# set the maximum run time, hh:mm:ss, default is 48hrs on FarmShare
#$ -l h_rt=12:00:00
#

#
# send mail when job ends or aborts
#$ -m ea
#

#
# specify an email address
#$ -M $USER@stanford.edu
#

# check for errors in the job submission options
#$ -w e
#

# pass the current environment variables
#$ -V
#

/full/path/to/command arg1 arg2 arg3 ...

#make sure that the command above actually doesn't use more memory or CPU than you specified.

Of course, you can just use the equivalent command line:

 qsub -S /bin/bash -N example_job -l mem_free=3G -pe shm 1 -m ea -M $USER@stanford.edu -w e -V /full/path/to/command arg1 arg2 arg3

You may need to also have '-b y' if the command is a binary and not a script.