Submitting a job

Last updated on 2026-10-26 | Edit this page

Overview

Questions

  • How do you ask Slurm for time and cores without starting the work on the login node?
  • What does a job array change, compared with four separate scripts?

Objectives

  • Write a batch script with a job name, a partition, a core count, a time limit, and an output file.
  • Explain why Snellius rounds a small request up to 16 cores on the rome partition.
  • Submit a script with sbatch and read its state with squeue.
  • Use SLURM_ARRAY_TASK_ID to give each array task a different input.
  • Cancel a job you submitted by mistake with scancel.

The script is the request

A batch script is a shell script with a header of #SBATCH lines. Slurm reads the header. The shell runs the rest, on a compute node, after the wait.

This is the Snellius shape. The file in the lesson is episodes/files/pi-snellius.sh.

BASH 

#!/bin/bash
#SBATCH --job-name=pi-one
#SBATCH --partition=rome
#SBATCH --cpus-per-task=16
#SBATCH --time=00:15:00
#SBATCH --output=pi-%j.out

module purge
module load 2025
export SAMPLE_COUNT=1000
python3 pi_one.py

%j in the output name becomes the job id. pi_one.py prints one line, samples=1000 hits… estimate=…=. It uses a fixed random sequence, so the same SAMPLE_COUNT always prints the same line. The program is in episodes/files/pi_one.py.

On Snellius the rome partition gives memory with the cores, and the smallest slice is 16 cores. A request for 1 core is rounded up to 16, and the project is charged for 16. Asking for 16 in the script matches what you will be charged.

On the course cluster the same nodes answer to rome and to thin_course, and a node has two cores. Ask for one core there. episodes/files/pi-course.sh is that script: --partition=thin_course and --cpus-per-task=1.

Submit from the directory that contains pi_one.py:

BASH 

sbatch pi-course.sh
squeue -u "$USER"

sbatch prints Submitted batch job and a number. squeue shows PD while the job waits and R while it runs. When it leaves the queue, read pi-<jobid>.out.

Callout

srun can start a step inside a job, or a short interactive allocation. sbatch is the command for a script you can resubmit. This lesson uses sbatch.

The directives you will see most often are in episodes/files/slurm-directives.tsv. The same rows are below.

directive meaning example where
–job-name a short name in the queue pi-one any Slurm cluster
–partition which group of nodes rome Snellius and the course cluster
–cpus-per-task cores for the one task 16 Snellius rome slice
–time wall clock limit 00:15:00 any Slurm cluster
–output file for the job text pi-%j.out any Slurm cluster
–array one index per task 0-3 any Slurm cluster

While you wait

A job in PD is waiting for resources. squeue -u "$USER" is enough during class. scancel JOBID removes a job you do not want. On Snellius, scontrol show job JOBID tells you why a job is still waiting. On the course cluster the reason is usually that someone else holds the two cores.

Do not resubmit because the first job is still PD. You will get two jobs, and then four.

Four lengths, one script

A job array runs the same script many times. SLURM_ARRAY_TASK_ID is 0, 1, 2, or 3 when you ask for --array=0-3. %A is the array id and %a is the task id, so each task gets its own output file.

episodes/files/pi-array.sh:

BASH 

#!/bin/bash
#SBATCH --job-name=pi-array
#SBATCH --partition=thin_course
#SBATCH --cpus-per-task=1
#SBATCH --time=00:10:00
#SBATCH --array=0-3
#SBATCH --output=pi-%A_%a.out

module purge
module load 2025
sizes=(1000 2000 4000 8000)
export SAMPLE_COUNT="${sizes[$SLURM_ARRAY_TASK_ID]}"
python3 pi_one.py

A faded header

BASH 

#SBATCH --job-name=________
#SBATCH --partition=________
#SBATCH --cpus-per-task=________
#SBATCH --time=________

On the course cluster the partition is thin_course or rome, and the core count is 1 for this program. On Snellius rome the core count for this lesson is 16.

Challenge

Predict the array index

sizes has four numbers: 1000, 2000, 4000, 8000. The header says --array=0-3. Which SAMPLE_COUNT does task 2 export? Write the number before you look at the solution.

Task 2 exports 4000. The index starts at 0, so task 0 is 1000, task 1 is 2000, task 2 is 4000, and task 3 is 8000. The output file for task 2 is pi-<arrayid>_2.out.

Challenge

Check the batch script

From the lesson directory:

BASH 

bash episodes/files/exercises/check-batch-script.sh

SH 

batch-script=ok

Then, if you are on the course cluster, submit the one-core script and the array. Copy pi_one.py into the directory you submit from, or submit from episodes/files.

BASH 

cd episodes/files
sbatch pi-course.sh
sbatch pi-array.sh
squeue -u "$USER"

The check runs bash -n on pi-snellius.sh and requires the five directives plus module load 2025. A missing --time line makes it exit with an error.

After sbatch, squeue shows one job and an array. When they finish, pi-<jobid>.out contains one samples=1000 line. The array writes four files. Task 0 prints samples=1000. You can also run SAMPLE_COUNT=1000 python3 pi_one.py on the login node for this tiny count if the queue is busy. 1000 samples is a login-node-sized test. The array sizes above 1000 belong in the job.

Key Points
  • A batch script is a shell script plus #SBATCH resource lines.
  • sbatch submits. squeue shows the wait. scancel removes a job.
  • On Snellius rome, ask for 16 cores because smaller requests are rounded up.
  • On the course cluster, ask for 1 core on thin_course or rome.
  • SLURM_ARRAY_TASK_ID selects the input for one task in an array.