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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