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. This type of parallelism is usually called trivially parallel jobs.

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.

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:

  • SLURM_ARRAY_TASK_COUNT
    • Total number of tasks in a job array
  • SLURM_ARRAY_TASK_ID
    • Job array ID (index) number
  • SLURM_ARRAY_TASK_MAX
    • Job array’s maximum ID (index) number
  • SLURM_ARRAY_TASK_MIN
    • Job array’s minimum ID (index) number
  • SLURM_ARRAY_TASK_STEP
    • Job array’s index step size
  • SLURM_ARRAY_JOB_ID
    • Job array’s master job ID number

Example job array

The most simple example for using a job array is running a loop in parallel. A simple example is this:

Job array runing loop in parall
#!/bin/bash
#SBATCH -p medium
#SBATCH -t 10:00
#SBATCH -n 1
#SBATCH -c 4

module load python
for i in {1..100}; do
  python myprogram.py $i
done
#!/bin/bash
#SBATCH -p medium
#SBATCH -t 10:00
#SBATCH -n 1
#SBATCH -c 4
#SBATCH -a 1-100

module load python
python myprogram.py $SLURM_ARRAY_TASK_ID

The loop in the first example runs on the same node and in serial. More efficiently, the job array in the second tab unrolls the loop and if resources are available, runs all of the 100 jobs in parallel.

Example job array running over files

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

​
#!/bin/bash
#SBATCH -p medium
#SBATCH -t 01:00
#SBATCH -a 0-X
# insert X as the number of .inp files you have -1 (since bash arrays start counting from 0)
# ls *.inp | wc -l
 
#for safety reasons
shopt -s nullglob
#create a bash array with all files
arr=(./*.inp)
 
#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)) jobarray.sh

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.