Using the computational chemistry software package Quantum ESPRESSO
Edit me

Running Quantum ESPRESSO on the cluster

Part 1: Setting Up Your Workspace

Create a Working Directory

Your home directory is limited to 5GB, so you need to use the shared storage for larger datasets.

mkdir /data/datasets/$USER
cd /data/datasets/$USER

This directory has significantly more capacity for your computational work.

Part 2: Interactive Computing with srun

Allocate Compute Resources

Use srun to request an interactive shell on a compute node. This gives you direct access to Intel CPUs and T4 GPUs.

srun -t 12:00:00 -p standard --pty /bin/bash

Parameters explained:

  • -t 12:00:00 — Request 12 hours of compute time
  • -p standard — Use the standard partition
  • --pty /bin/bash — Launch an interactive bash shell

You’ll now have a shell prompt on a compute node.

Load Required Software

Step 1: Load Spack environment

Spack is a package manager that manages software installations. Load it first:

source /data/software/packages/spack/setup-env.sh

Step 2: Load NVHPC compiler suite

spack load nvhpc@24.1

Step 3: Load Quantum ESPRESSO

spack load quantum-espresso /3qnajq7

Run Quantum ESPRESSO

Now you can execute Quantum ESPRESSO calculations:

mpirun pw.x < inputfile

Replace inputfile with your actual input file.

Part 3 (Optional): Batch Processing with sbatch

For longer or multiple jobs, use sbatch instead of interactive mode. This submits jobs to the queue without requiring you to stay connected.

Move to your workspace

Create it if it doesn’t exist:

cd /data/datasets/$USER

Create a Batch Script

Create a file named job.sh:

#!/bin/bash
#SBATCH -t 12:00:00
#SBATCH -p standard
#SBATCH -J qe_job
#SBATCH -o output.log
#SBATCH -e error.log

source /data/software/packages/spack/setup-env.sh
spack load nvhpc@24.1
spack load quantum-espresso /3qnajq7

cd /data/datasets/$USER
mpirun pw.x < inputfile

Script parameters:

  • #SBATCH -t 12:00:00 — Walltime limit (12 hours)
  • #SBATCH -p standard — Partition to use
  • #SBATCH -J qe_job — Job name
  • #SBATCH -o output.log — Standard output file
  • #SBATCH -e error.log — Error output file

Submit Your Job

sbatch job.sh

Check job status:

squeue -u $USER

View results in output.log and error.log once the job completes.