Introduction

This repository provides tools for managing the MatML ecosystem, including building of Docker images.

Available Docker Images

All docker images are at the Materials Virtual Lab Docker Repository.

Running code

Assuming you have your script script.py in the current directory, you can run it using:

docker run --name test -v .:/work -t materialsvirtuallab/matml python /work/script.py

If you need to get a file out of your docker container, use:

docker cp test:<filename> .

Running on HPC such as Expanse or NERSC

SDSC and NERSC uses singularity. You will first need to build a singularity image from the docker images.

Building the SIF

SSH to the cluster and start an interactive session with enough memory, e.g.:

srun -N 1 -n 1 -c 4 --mem 50G -p condo -q condo -A <allocation> -t 4:00:00 --pty /bin/bash

or if you are using the hotel queue:

srun -N 1 -n 1 -c 4 --mem 50G -p hotel -q hotel -A <allocation> -t 4:00:00 --pty /bin/bash

Next pull the docker container.

module load singularitypro
singularity pull --disable-cache docker://materialsvirtuallab/matml

You should see a matml_latest.sif file in your directory. Exit the interactive shell.

Running jobs using the SIF container

You can now run a job using the SIF container. An example script is given below:

#!/bin/bash
#SBATCH --job-name="singularity"
#SBATCH -t 00:05:00
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH -o sing.out
#SBATCH -e sing.err
##SBATCH -p hotel
#SBATCH --qos hotel
#SBATCH -A <allocation>
#SBATCH --export=ALL

export OMP_NUM_THREADS=1

module load singularitypro

IMAGE=/tscc/nfs/home/shyuep/test_singularity/matml_latest.sif

singularity exec $IMAGE python script.py