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PBS qsub Quick Reference Guide


To submit a job to PBS, the following command is used:

$ qsub myscript

where myscript is a file that contains the qsub options for the given job.



These options are given in the form of

#PBS option[[=]value]

where some options may require values to be included.



Control the environment in which the script operates.

Directive Options Description
-A Project name Charge the specified project name.
-V NONE Export the environment.
-S Shell path Parse the job script using this shell.


Control standard output, error, and mail reporting.

Directive Options Description
-m b Send mail when the job begins execution.
-m e Send mail when the job finishes.
-e File Define standard error file.
-o File Define standard output file.
-M E-mail address(es) Send mail to address(es).
-j oe Send stdout and stderr to the same file.


Specify how and where to run a job.

Directive Options Description
-N Name Name of the job
-q Name Name of the queue
-r y Specifies that the job is rerunable.


Specify resource limits to run a job.

Directive Description
-l ncpus=# Number of cores to be used.

Specify the maximum run length of the job.

Directive Description
-l walltime=# Maximum wall-clock time.

Note that times may be specified in the form [[hours:]minutes:]seconds or as an integer number of seconds. The following table provides examples of valid times:

Time Explanation
120 120 seconds
12:00:00 12 Hours, 0 minutes, and 0 seconds


Specify the dependencies on other jobs. In PBS, the dependencies are specified with the following syntax:

#PBS -W depend=dependency_expression

where dependency_expression is a comma-delimited list of one or more dependencies. Each dependency is of the form

type:jobid[:jobid...]

where type is one of the directives listed below, and jobid[:jobid...] is a list of one or more job IDs upon which the dependency exists.

Directive Description
after Execute current job after listed jobs have begun.
afterok Execute current job after listed jobs have terminated without error.
afternotok Execute current job after listed jobs have terminated with an error.
afterany Execute current job after listed jobs have terminated for any reason.
before Listed jobs can be run after current job begins execution.
beforeok Listed jobs can be run after current job terminates without error.
beforenotok Listed jobs can be run after current job terminates with an error.
beforeany Listed jobs can be run after current job terminates for any reason.

See the qsub man page for more information.

Last update: January 22, 2010

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