Job Arrays

Job arrays are the preferred way to submit many similar jobs, for instance, if you need to run the same program on a number of input files, or with different settings or run them with a range of parameters. Arrays are created with the -a start-finish sbatch parameter. E.g. sbatch -a 0-19 will create 20 jobs indexed from 0 to 19. There are different ways to index the arrays, which are described below.

The behavior of the jobs can then be tied to Slurm Environment variables, which tell the program, which part of the array they are.

Job Array Indexing, Stepsize and more

Slurm supports a number of ways to set up the indexing in job arrays.

  • Range: -a 0-5
  • Multiple values: -a 1,5,12
  • Step size: -a 0-5:2 (same as -a 0,2,4)
  • Combined: -a 0-5:2,20 (same as -a 0,2,4,20)

Additionally, you can limit the number of simultaneously running jobs with the %x parameter in there:

  • -a 0-11%4 only four jobs at once
  • -a 0-11%1 run all jobs sequentially
  • -a 0-5:2,20%2 everything combined. Run IDs 0,2,4,20, but only two at a time.

You can read everything on array indexing in the sbatch man page.

Slurm Array Environment Variables

The most used environment variable in Slurm arrays is $SLURM_ARRAY_TASK_ID. This contains the index of the job in the array and is different in every Job of the array. Other variables are:

    Total number of tasks in a job array. 
    Job array ID (index) number. 
    Job array's maximum ID (index) number. 
    Job array's minimum ID (index) number. 
    Job array's index step size. 
    Job array's master job ID number. 

Example Job Array

This is an example of a job array, creates a job for every file ending in “.inp” in the current workding directory:

#SBATCH -p medium
#SBATCH -t 01:00
# insert X as the number of .inp files you have -1 (since bash arrays start counting from 0)
# ls *.inp | wc -l
#SBATCH -a 0-X
#for safety reasons
shopt -s nullglob
#create a bash array with all files
#put your command here. This just runs the fictional "big_computation" program with one of the files as input
./big_computation ${arr[$SLURM_ARRAY_TASK_ID]}

In this case, you have to get the number of files beforehand (fill in the X). You can also automatically do that by removing the #SBATCH -a line and adding that information when submitting the job:

sbatch -a 0-$(($(ls ./*.inp | wc -l)-1))

The part in the parenthesis just uses ls to output all .inp files, counts them with wc and then subtracts 1, since bash arrays start counting at 0.

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