Running Array Jobs#
Job arrays allow you to run a group of identical/similar jobs. The Slurm script
is EXACTLY the same. The only difference between each sub-job is the environment
$SLURM_ARRAY_TASK_ID. So it can be a good idea if you want to do
some data level parallelization. E.g. let sub-job 1
process data chunk 1, sub-job 2 processes data chunk 2, … etc.
To do that, just add the following statement in your submission script, where
n is the number of jobs in the array:
An example of Slurm Array job script#
Or you can specify an array job at submission time, without modifying your submission script:
sbatch --array=1-20 job.script
In Slurm, the job array is implemented as a group of single jobs. E.g. if you
submit an array job with
#SBATCH --array=1-4. When the starting job is
ID=1000, the ids of all jobs are: 1000, 1001, 1002, 1003.
There is a limit of 1000 jobs per array. Slurm also has a bug where it will not allow array id’s above this limit, this can be worked around with a prefix in the script (e.g. for “1001-1020” use –array=01-20 and reference variables with a prefix 10$SLURM_ARRAY_TASK_ID)
A maximum number of simultaneously running tasks from the job array may be specified using a “%” separator. For example “–array=0-15%4” will limit the number of simultaneously running tasks from this job array to 4.