Jobscript

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General

A jobscript can be used to submit the job you wish to execute to a Batch-Scheduler. It is very similar to a sh-file and generally uses the same format, but is more powerful. Besides shell commands, you can use so-called magic cookies, e.g. #BSUB for LSF systems. This allows you to specify a lot of parameters, e.g. the time and memory your application requires or - if your code runs in parallel - the number of compute slots to employ.



Structure

Like a regular sh-file, your jobscript should start with a shebang (#!), e. g. in case you are using zsh:

#!/usr/bin/env zsh

Usually, this first line is followed by several directives using magic cookies, that are explained in more depth in the next section. The third part of a jobscript consists of shell commands, for example, to change to your working directory, to load the needed Modules and to execute your application.

Magic Cookies

The magic cookie differs from Batch-Scheduler to Batch-Scheduler. Click here to figure out which one you are going to need. Depending on your batch system, these pages provide more information on how to use magic cookies in your jobscript: LSF, SLURM, Torque.

One advantage of jobscripts is that the parameters that are prefixed with magic cookies are treated like comments. So you can run your jobscript as an sh-file without the Batch-Scheduler and if that works, still adjust and correct the lines with magic cookies destined for the Batch-Scheduler.

Job Submission

Depending on your Batch-Scheduler, proceed to one of the links below to find out how to submit your job to a batch system that controls the resources for computation: LSF, SLURM, Torque.

Note that all incoming jobs (defined in a jobscript) are added to a queue. The Batch-Scheduler decides at what time a certain job is executed. The waiting time depends on various factors, e. g. the time and memory you asked for in your jobscript. The rule of thumb is: the more resources your job needs, the longer it will be queued.

You can always check the current status of your submitted jobs and their ids with shell commands that are also explained on the pages linked above.

References

Jobscript examples