Complex submissions

In Submitting your job using SGE we looked at the following script;

   
#specify the shell type
#$ -S /bin/sh

#run in the current working directory
#$ -cwd

#specify that the job will be killed if it uses over 40G or total memory or run for more than 24hours.
#indicate that the program should run for 1 hour and use 20G of total memory
#$ -l s_vmem=20G h_vmem=40G s_rt=360 h_rt=3600

#specify the number of cores required
#$ -pe mpich 1

#specify which queue you wish to use
#$ -q amd.q

#run a program command to print hostname and uptime
hostname && uptime
    

Most of this was not really required for the actual job (e.g. getting the hostname and uptime from each machine). However it is good practice to include limits for sun grid engine to work well.

Sun Grid Engine and Limits