HPC Software – Virtualisation and Containers

Singularity/Apptainer

Singularity is a container platform. It allows you to create and run containers that package up pieces of software in a way that is portable and reproducible. You can build a container using Singularity on your laptop, and then run it on many of the largest HPC clusters in the world, local university or company clusters, a single server, in the cloud, or on a workstation down the hall. Your container is a single file, and you don’t have to worry about how to install all the software you need on each different operating system and system.

SingularityCE (Singularity Community Edition) and Apptainer are branches/children of the deprecated Singularity. SingularityCE is maintained by Sylabs while Apptainer is maintained by the Linux Foundation. By and large the two are interoperable with slightly different feature sets. The Ada Lovelace HPC system uses Apptainer, it is loaded by default as part of the OS when starting a session on the HPC.

Docker

Docker containers are a popular form of container. Unfortunately, due to its need for root access it’s not compatible on a lot of HPC systems. However, while the software isn’t compatible many of the file can be converted or imported into Singularity file that can be run using Apptainer. 

Apptainer on the cluster

To use Apptainer on the cluster, it is recommended to first start an Open OnDemand. Then you simply run apptainer:

While the example uses apptainer as the command, singularity commands can also be used

[decostal@ada ~]$ apptainer --version
apptainer version 1.4.2-1.el9

when using singularity commands and the system will still apply them to apptainer;

[decostal@ada ~]$ singularity --version
apptainer version 1.4.2-1.el9

Downloading images to run in apptainer

Pull

There are many ways to use apptainer, the most common of which is using docker files and converting them to .sif file for use with singularity due to the reasons mentioned above. When downloading these docker files from the internet to the system there are a few options in commands and what they do;

Pull – Makes a copy of the docker image in .sif format. 

apptainer pull docker://biobakery/workflows

This will make a .sif file called ‘workflows_latest.sif’ from the biobakery docker image. When using the ‘pull’ command it will always make an image of the latest version available. This is fine when starting out or if you can control the system it’s on but can cause issues for reproducibility. 

Build

Build – Makes a copy of the docker image in .sif format, allows you to specify which version of the image and save it under a custom name. Here is the structure of the command and an example for biobakery;

apptainer build <desired_name_of_sif_file> docker://<address/of/image>:<version>

apptainer build biobakery_workflows.sif docker://biobakery/workflows:latest

After your apptainer file is created you can then access the shell with

apptainer shell biobakery_workflows.sif

or run commands directly to the shell with

apptainer exec biobakery_workflows.sif humann --help

Sandbox

You can also add the –sandbox flag when building a new apptainer image. when using the build command don’t add .sif to the file and use the sandbox flag as seen below. You may get some errors when building a sandbox file from docker. It shouldn’t affect the functionality. 

apptainer build --sandbox biobakery_workflows/ docker://biobakery/workflows

You can then use the –writable flag with the shell command to enter the container shell and install software

apptainer shell --writable biobakery_workflows/

You can then use the app get command to install more programs inside the apptainer, once you’re done you can use the build command on the undefined file and rename it with the .sif extension 

apptainer build biobakery_workflows.sif biobakery_workflows/

Definition File

You can also make a definition file and run it on the HPC. This makes the system download the base file and then run the install commands as part as a predefined process. This is great for reproducibility 

Apptainer Documentation

[decostal@ada ~]$ apptainer --help

Linux container platform optimized for High Performance Computing (HPC) and
Enterprise Performance Computing (EPC)

Usage:
  apptainer [global options...]

Description:
  Apptainer containers provide an application virtualization layer enabling
  mobility of compute via both application and environment portability. With
  Apptainer one is capable of building a root file system that runs on any
  other Linux system where Apptainer is installed.

Options:
      --build-config    use configuration needed for building containers
  -c, --config string   specify a configuration file (for root or
                        unprivileged installation only) (default
                        "/etc/apptainer/apptainer.conf")
  -d, --debug           print debugging information (highest verbosity)
  -h, --help            help for apptainer
      --nocolor         print without color output (default False)
  -q, --quiet           suppress normal output
  -s, --silent          only print errors
  -v, --verbose         print additional information
      --version         version for apptainer

Available Commands:
  build       Build an Apptainer image
  cache	      Manage the local cache
  capability  Manage Linux capabilities for users and groups
  checkpoint  Manage container checkpoint state (experimental)
  completion  Generate the autocompletion script for the specified shell
  config      Manage various apptainer configuration (root user only)
  delete      Deletes requested image from the library
  exec        Run a command within a container
  help        Help about any command
  inspect     Show metadata for an image
  instance    Manage containers running as services
  key         Manage OpenPGP keys
  keyserver   Manage apptainer keyservers
  oci         Manage OCI containers
  overlay     Manage an EXT3 writable overlay image
  plugin      Manage Apptainer plugins
  pull        Pull an image from a URI
  push        Upload image to the provided URI
  registry    Manage authentication to OCI/Docker registries
  remote      Manage apptainer remote endpoints
  run         Run the user-defined default command within a container
  run-help    Show the user-defined help for an image
  search      Search a Container Library for images
  shell       Run a shell within a container
  sif         Manipulate Singularity Image Format (SIF) images
  sign        Add digital signature(s) to an image
  test        Run the user-defined tests within a container
  verify      Verify digital signature(s) within an image
  version     Show the version for Apptainer

Examples:
  $ apptainer help  []
  $ apptainer help build
  $ apptainer help instance start


For additional help or support, please visit https://apptainer.org/help/

If you encounter any issues using Apptainer, please reach out to ersearch@cqu.edu.au