What are job arrays?

A resource manager or scheduler that support job arrays typically exposes a task identifier to the job script as an environment variable. This is simply a number out of a range specified when the job is submitted.

For the resource managers and schedulers supported by atools, that would be * PBS_ARRAYID for PBS torque, * MOAB_JOBARRAYINDEX for Adaptive's Moab, and * SGE_TASKID for SUN Grid Engine (SGE), * SLURM_ARRAY_TASK_ID for Slurm workload manager.

Typically, this task identifier is then use to determine, e.g., the specific input file for this task in the job script:


Submitting arrays jobs is quite simple. For each of the supported queue systems and schedulers, one simply adds the -t <int-range> options to the submission command, qsub for PBS torque and SUN grid engine, msub for Moab, e.g., for PBS torque:

$ qsub  -t 1-250  bootstrap.pbs

The submission command above would create a job array of 250 tasks, and for each the PBS_ARRAYID environment variable would be assigned a unique value between 1 and 250, inclusive.

Although job arrays provide sufficient features for simple scenarios, it quickly becomes a nuisance for more sophisticated problems, especially in parameter exploration type computations. atools aims to eliminate as much as possible of the boiler plate code you have to write over and over again.