Quantum Espresso Tutorial

Basics

To run Quantum Espresso on the cluster, you must first load the Open MPI module and the Quantum Espresso module using the commands:

module load openmpi
module load qe

To load a specific version of the modules, add the version number to the load command.

module load openmpi/gcc
module load qe/gcc/6.2.0

When running Quantum Espresso jobs, it is advised that users create a new directory located in /data to store the data in, and a new directory in /local to run the job in.

Most Quantum Espresso input files require the assistance of pseudo-potential files, which contain approximation for the simplified description of complex systems such as periodic elements. It is recommended that these files are stored in a directory named /pseudo. The file path of these pseudo-potential files are generally referenced at the beginning of a QE input file in the &control section, as seen below:

&control
prefix='silicon',
pseudo_dir = 'pseudo/',
outdir='output/'
module load qe/gcc/6.2.0

You can also specify a directory for the output to be saved to in this &control section. If the directory does not exist, it will be created when the program is run, and output files will be saved there.

Running Quantum Espresso through a job script

1. Create a QE input file, with the extension *.in. This repository provides a simple script, si.scf.in, and it’s helper script Si.pz-vbc.UPF, which performs self-consistent calculations for Silicon in the diamond structure.

2.Ensure the helper script is located in a directory named /pseudo

3. Prepare the submission script, which is the script that is submitted to the Slurm scheduler as a job in order to run the QE script. This repository provides the script job.sh as an example.

job.sh

#!/bin/bash

#SBATCH --job-name=qe_test
#SBATCH -o qe_out%j.out
#SBATCH -e qe_err%j.err
#SBATCH -N 2
#SBATCH --ntasks-per-node=4
#SBATCH -p no-kill

echo -e '\n submitted Quantum Espresso job'
echo 'hostname'
hostname

# loads Open MPI and Quantum Espresso modules
module load openmpi/gcc
module load qe

# run Quantum Espresso using Open MPI's mpirun
# results will be printed to output.file
mpirun pw.x < pwscf.in
			

4. Submit the job using sbatch job.sh

5. Examine the results.