From HPC

qsub

qsub is the part of the Sun Grid Engine that allows you to submit you work to the cluster job queue. There are many command options for it i.e. setting up the enviroment, job name, array jobs, email alerts etc.

The two import switches to use are -cwd (makes the job start from the current working directory) and -V (makes the job run with the current enviroment variables)

qsub options program

Example

qsub -cwd -V myprog

Options

-V (set enviroment variables to those when job is submitted)
-cwd (run the job from current working directory)
-N name (sets name of job) 
-M email@address (set email address for job notifaction
-m options (when to send email notification)
   b (begining of job)
   e (end of job)
   a (abortion of job)
   n (never email)
   s (suspention of job)
   example -m a,s,e
-t start-end:step Array job will run job the number of times between start-end (i.e. 1-5), :step is option and is the step increment (1-6:2 would be 1 2 4 6). To use the sequence number in your script use the environment variable $SGE_TASK_ID