Apptainer (Singularity)

Apptainer (opens new window), previously known as Singularity, provides application containers for Linux that is also compatible with Docker.

• Install with Conda
• Common practices and commands
  • Pull Docker image
  • Run Docker image
  • Listing running containers
  • Stop running container
  • Where are the images stored ?
  • Temporary file storage

Install with Conda

Requirements

• Conda (miniconda), see our Conda tutorial for more details.
• Conda channels: conda-forge, bioconda

Add the conda-forge channel

You will need the conda-forge channel to install Apptainer. If you have not set channels yet make sure to add it:

conda config --add channels conda-forge

Install Apptainer (Singularity) in conda environment

Create environment and install Apptainer (Singularity):

conda create -n apptainer -c conda-forge "apptainer"

Activate your apptainer environment and try running Apptainer:

conda activate apptainer

apptainer --help

Common practices and commands

All information is collected from the official Apptainer documentation (opens new window).

Pull Docker image

You can use the pull (opens new window) and build (opens new window) commands to download pre-built images from an external resource like the Container Library (opens new window) or Docker Hub (opens new window).

#-- Example 
apptainer pull docker://godlovedc/lolcow

#-- Example
apptainer build  -B $TMPDIR lolcow.sif docker://godlovedc/lolcow

Run Docker image

For demonstration, let’s use an easy (though somewhat useless) example of lolcow.sif (opens new window) image from Docker:

apptainer pull docker://godlovedc/lolcow
#-- The above command will save the alpine image from the Container Library as lolcow.sif

To start an instance, you should follow below pattern:

apptainer instance start -B $TMPDIR      <image>    <instance-name>

apptainer instance start -B $TMPDIR lolcow.sif instance1

This command causes Apptainer to create an isolated environment for the container services to live inside.

Listing running containers

One can confirm that an instance is running by using the instance list command like so:

apptainer instance list

INSTANCE NAME    PID        IP    IMAGE
instance1        3661427          /mnt/scratch/tmp/rootfs-728963423/root

Stop running container

When you are finished with your instance you can clean it up with the instance stop command as follows:

apptainer instance stop instance1

Where are the images stored ?

By default, Apptainer will create a set of folders in your $APPTAINER_CACHEDIR directory for docker layers, Cloud library images, and metadata, respectively:

$APPTAINER_CACHEDIR/cache/library
$APPTAINER_CACHEDIR/cache/oci
$APPTAINER_CACHEDIR/cache/oci-tmp

Temporary file storage

By default, Apptainer won't recognize lab tmp storage. You can apply lab tmp storage location /mnt/scratch/tmp to a container using -B $TMPDIR variable

#-- Example
apptainer shell -B $TMPDIR docker://ubuntu