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Running Docker images using Apptainer/Singularity#

Before you start#

Apptainer/Singularity is the most widely used container system for HPC. It is designed to execute applications at bare-metal performance while being secure, portable, and 100% reproducible. Apptainer is an open-source project with a friendly community of developers and users. The user base continues to expand, with Apptainer/Singularity now used across industry and academia in many areas of work.

Authentication#

You can use public images without being authenticated in the following cases:

Registry Image Type Login required
Dockerhub Public No
Dockerhub Private Yes, Dockerhub credentials

When using authentication, it's relative to the source you want to use (Dockerhub registry supported) and the authentication is saved per cluster.

Upload an image directly from Dockerhub to Apptainer/Singularity#

Optional (needed for private images only) 

$ apptainer registry login --username <username> docker://docker.io

Get the image from Dockerhub by specifying the image account (optional for official image) and name 

$ mkdir ~/myimages
$ cd ~/myimages
$ apptainer pull docker://docker.io/alpine:latest
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 63b65145d645 skipped: already exists  
Copying config 6a2bcc1c7b done  
Writing manifest to image destination
Storing signatures
2023/03/10 10:25:14  info unpack layer: sha256:63b65145d645c1250c391b2d16ebe53b3747c295ca8ba2fcb6b0cf064a4dc21c
INFO:    Creating SIF file...
$ ls
alpine_latest.sif 
$ srun --pty --qos debug -N 1 apptainer shell alpine_latest.sif 
Apptainer> cat /etc/alpine-release 
3.17.2
Apptainer> exit
$

Run the image on the clusters#

You can submit the following Slurm script with the sbatch command 

#!/bin/bash -l

#SBATCH --nodes 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --mem 1024
#SBATCH --qos debug

srun apptainer exec alpine_latest.sif ls /etc
You can check the Slurm output file:

sbatch apptainer.run 
Submitted batch job 2649847
$ ls
alpine_latest.sif  apptainer.run  slurm-2649847.out
$ cat slurm-2649847.out 
alpine-release
apk
conf.d
crontabs
...

Interactive Shell#

To have an interactive shell within your image, simply use this: 

$ srun --pty --qos debug -N 1 apptainer shell <filename>.sif