Running Array Jobs
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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 variable, $SLURM_ARRAY_TASK_ID. So it can be a good
idea if you want to do some data level parallelization. E.g. let sub-job
1 (SLURM_ARRAY_TASK_ID=1) process data chunk 1, sub-job 2 processes
data chunk 2, ... etc.
To do that, just add the following statement in your submission script,
where n is the number of jobs in the array:
#SBATCH --array=1-n
An example of Slurm Array job script
#SBATCH --array=1-20
Or you can specify an array job at submission time, without modifying your submission script:
sbatch --array=1-20 job.script
In Slurm, the job array is implemented as a group of single jobs. E.g.
if you submit an array job with #SBATCH --array=1-4. When the starting
job is ID=1000, the ids of all jobs are: 1000, 1001, 1002, 1003.
There is a limit of 1000 jobs per array. Slurm also has a bug where it
will not allow array id's above this limit, this can be worked around
with a prefix in the script (e.g. for "1001-1020" use --array=01-20
and reference variables with a prefix 10$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.