Writing job scripts

Script structure

A well-structured sbatch script follows a consistent layout that makes it readable, maintainable, and less error-prone. Every script has four parts:

1. Shebang line — the interpreter directive
2. SBATCH directives — resource requirements and job configuration
3. Environment setup — module loading and variable definitions
4. Job execution — the actual commands to run

Complete template

#!/bin/bash

# Job identification
#SBATCH --job-name=my_job
#SBATCH --output=results_%j.out
#SBATCH --error=results_%j.err

# Resource allocation
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#SBATCH --mem=64GB
#SBATCH --time=02:00:00

# Queue selection
#SBATCH -p short-40core

# --- Environment setup ---
module purge
module load intel/oneAPI/2022.2
module load compiler/latest
module load mpi/latest

export OMP_NUM_THREADS=1
export I_MPI_PIN_DOMAIN=omp

echo "Job ID: $SLURM_JOBID"
echo "Running on nodes: $SLURM_JOB_NODELIST"
echo "Number of tasks: $SLURM_NTASKS"
echo "Start time: $(date)"

# --- Job execution ---
cd $SLURM_SUBMIT_DIR

mpirun ./my_app input.dat > computation.log

echo "Job completed at: $(date)"

Directive best practices

Group related directives with comments

# Job identification
#SBATCH --job-name=protein_folding
#SBATCH --output=folding_%j.out
#SBATCH --error=folding_%j.err

# Resource requirements
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=40
#SBATCH --mem-per-cpu=2GB
#SBATCH --time=12:00:00

# Job placement
#SBATCH -p long-40core

Use descriptive output names

#SBATCH --output=simulation_%x_%j.out
#SBATCH --error=simulation_%x_%j.err
# %x = job name, %j = job ID

Environment setup guidelines

• Always purge modules first — module purge ensures a clean environment and prevents conflicts.
• Set threading variables — e.g. export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK.
• Print job information — job ID, node list, working directory, and start time make debugging much easier.

Execution best practices

# Exit on any error
set -e

# Check inputs exist before starting
if [ ! -f "input.dat" ]; then
    echo "ERROR: input.dat not found"
    exit 1
fi

# Time the main computation
start_time=$(date +%s)
mpirun ./my_app input.dat
end_time=$(date +%s)
echo "Computation completed in $((end_time - start_time)) seconds"

Common directive reference