1. Introduction to Apptainer

Lesson Objectives

• Know about the apptainer command in the terminal
• Know about run, exec, shell, pull and build commands

Questions

• What is Apptainer, and how do I access it on Mahuika?
• What are the main commands I will use to work with containers?

How to start using Apptainer on Mahuika

Apptainer is loaded on Mahuika by default. If you type in

apptainer --version

into the terminal, you will get:

user.name@computer-name:~$ apptainer --version
apptainer version 1.4.2-1.el9

You will see the version of Apptainer available to you on Mahuika.

If you type in apptainer --help into the terminal, you will see all the options available to you:

user.name@computer-name:~$ 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 <command> [<subcommand>]
  $ apptainer help build
  $ apptainer help instance start

We will start by looking at the 5 most used commands in Apptainer. These are:

1. run: Run a specific command as designed by the creator of the container.
2. exec: Execute a custom command that you want to run on the container.
3. shell: Perform tasks on the container interactively.
4. pull: Pull (download) a container from the cloud.
5. build: Construct a container from a definition (def) file.

Some others that we will also look at (but are less essential) are:

• inspect: To check out features of your container, including the %runscript and def file.
• cache: To check out and remove files in the Apptainer cache.
• test: Allows the user to test the container as designed by the creator of the container.
• run-help: Allows the creator to provide notes to help explain how to use the container.

Keypoints

• Apptainer is available on Mahuika by default — you can check this with apptainer --version.
• Use apptainer --help to list all the commands and options available to you.
• Know the 5 most used commands in Apptainer: run, exec, shell, pull, and build.
• Be aware of some other useful commands you will meet later: inspect, cache, test, and run-help.