Honfi001: /* apptainer pull */

2026-03-25T09:23:54Z

apptainer pull

← Older revision		Revision as of 11:23, 25 March 2026
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	'''Portability:''' An Apptainer container is a single <code>.sif</code> file. You can build it on your laptop, copy it to the cluster, share it with a collaborator, or archive it alongside a publication. It will run the same way everywhere Apptainer is installed.		'''Portability:''' An Apptainer container is a single <code>.sif</code> file. You can build it on your laptop, copy it to the cluster, share it with a collaborator, or archive it alongside a publication. It will run the same way everywhere Apptainer is installed.

	'''Reproducibility:''' A container captures the exact software environment used for an analysis — down to the specific library versions. This means an experiment can be repeated months or years later with the same ~~results~~, even if the host system has changed. When combined with a definition file (a text recipe that describes how the container was built), every step is documented and reproducible.		'''Reproducibility:''' A container captures the exact software environment used for an analysis — down to the specific library versions. This means an experiment can be repeated months or years later with the same environment, even if the host system has changed. When combined with a definition file (a text recipe that describes how the container was built), every step is documented and reproducible.

	== Loading Apptainer ==		== Loading Apptainer ==
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	module reset		module reset
	module load utilities Apptainer		module load utilities
			module load Apptainer
	</syntaxhighlight>		</syntaxhighlight>

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	=== Do Not Store Images in Your Home Directory ===		=== Do Not Store Images in Your Home Directory ===

	SIF files can easily be hundreds of megabytes or even several gigabytes in size. Store them on Lustre (e.g. in your scratch or project space) rather than in your home directory to avoid quota issues.		SIF files can easily be hundreds of megabytes or even several gigabytes in size. Store them on Lustre (e.g. in your scratch or project space) rather than in your home directory to avoid quota issues. Running images can be I/O intensive and this is not suitable for the home directory.

	== Basic Commands ==		== Basic Commands ==
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	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">
	apptainer pull ubuntu.sif docker://ubuntu:24.04		apptainer pull ubuntu.sif docker://ubuntu:18.04
	</syntaxhighlight>		</syntaxhighlight>

Honfi001: Created page with "= Introduction to Apptainer = == What is Apptainer? == Apptainer (formerly known as Singularity) is a container platform designed for High Performance Computing (HPC) environments. If you have heard of Docker, Apptainer solves a similar problem — it lets you package an application together with all of its dependencies (libraries, tools, configuration) into a single portable unit called a '''container'''. The key difference is that Apptainer was built from the ground..."

2026-03-25T09:18:12Z

Created page with "= Introduction to Apptainer = == What is Apptainer? == Apptainer (formerly known as Singularity) is a container platform designed for High Performance Computing (HPC) environments. If you have heard of Docker, Apptainer solves a similar problem — it lets you package an application together with all of its dependencies (libraries, tools, configuration) into a single portable unit called a '''container'''. The key difference is that Apptainer was built from the ground..."

New page

= Introduction to Apptainer =

== What is Apptainer? ==

Apptainer (formerly known as Singularity) is a container platform designed for High Performance Computing (HPC) environments. If you have heard of Docker, Apptainer solves a similar problem — it lets you package an application together with all of its dependencies (libraries, tools, configuration) into a single portable unit called a '''container'''. The key difference is that Apptainer was built from the ground up to run safely on shared multi-user systems like HPC clusters, where Docker cannot be used because it requires root privileges that would pose a security risk.

Some important differences between Apptainer and Docker:

{| class="wikitable"
|-
! !! Apptainer !! Docker
|-
| '''Privileges''' || Runs as a normal user — no root access needed || Requires root or membership in the <code>docker</code> group, which is effectively root
|-
| '''Image format''' || Single portable <code>.sif</code> file || Layered images stored in a daemon's internal storage
|-
| '''Integration with host''' || Seamless access to host filesystems, GPUs, and network by default || Isolated by default; explicit configuration needed to share resources
|-
| '''Designed for''' || HPC, scientific computing, shared multi-user systems || Cloud, microservices, development environments
|-
| '''Docker compatibility''' || Can pull and run Docker images directly || N/A
|}

=== Why Apptainer for Research? ===

Two features make Apptainer particularly valuable for scientific work:

'''Portability:''' An Apptainer container is a single <code>.sif</code> file. You can build it on your laptop, copy it to the cluster, share it with a collaborator, or archive it alongside a publication. It will run the same way everywhere Apptainer is installed.

'''Reproducibility:''' A container captures the exact software environment used for an analysis — down to the specific library versions. This means an experiment can be repeated months or years later with the same results, even if the host system has changed. When combined with a definition file (a text recipe that describes how the container was built), every step is documented and reproducible.

== Loading Apptainer ==

On the Anunna HPC cluster, Apptainer is available in the <code>utilities</code> module bucket. Load it with:

<syntaxhighlight lang="bash">
module reset
module load utilities Apptainer
</syntaxhighlight>

You can verify it is loaded by running:

<syntaxhighlight lang="bash">
apptainer --version
</syntaxhighlight>

== Best Practices ==

=== Set Your Cache Directory ===

Apptainer downloads container layers to a local cache before building SIF files. By default this cache lives under your home directory (<code>$HOME/.apptainer/cache</code>), which can quickly exceed your home quota — especially with large images.

Change the cache location to your scratch space by setting the <code>APPTAINER_CACHEDIR</code> variable. You will need to create the directory first:

<syntaxhighlight lang="bash">
mkdir -p $myScratch/Apptainer
export APPTAINER_CACHEDIR=$myScratch/Apptainer
</syntaxhighlight>

Consider adding the <code>export</code> line to your <code>~/.bashrc</code> so it is set automatically in every session.

=== Do Not Run Apptainer on the Login Nodes ===

Building and running containers can be resource-intensive. Always request a compute node (e.g. via <code>srun</code>) before running Apptainer commands. The login nodes are shared and should not be used for heavy workloads.

=== Do Not Store Images in Your Home Directory ===

SIF files can easily be hundreds of megabytes or even several gigabytes in size. Store them on Lustre (e.g. in your scratch or project space) rather than in your home directory to avoid quota issues.

== Basic Commands ==

Apptainer has five core commands you will use regularly:

=== <code>apptainer pull</code> ===

Downloads a container image from a remote registry and saves it as a <code>.sif</code> file.

<syntaxhighlight lang="bash">
apptainer pull ubuntu.sif docker://ubuntu:24.04
</syntaxhighlight>

=== <code>apptainer build</code> ===

The build command is used for converting images from one format to another. It can create a SIF from a definition file, convert a sandbox to a SIF, or convert between formats.

<syntaxhighlight lang="bash">
# Build from a definition file
apptainer build myimage.sif myrecipe.def

# Convert a sandbox directory to a SIF
apptainer build myimage.sif /path/to/sandbox/
</syntaxhighlight>

=== <code>apptainer exec</code> ===

Runs a single specific command inside a container and returns the output.

<syntaxhighlight lang="bash">
apptainer exec ubuntu.sif cat /etc/os-release
</syntaxhighlight>

=== <code>apptainer shell</code> ===

Opens an interactive shell inside the container, allowing you to explore and run commands as if you had logged into a different machine.

<syntaxhighlight lang="bash">
apptainer shell ubuntu.sif
</syntaxhighlight>

=== <code>apptainer run</code> ===

Executes the container's default action (its '''runscript'''). What this does depends on how the container was built.

<syntaxhighlight lang="bash">
apptainer run myimage.sif
</syntaxhighlight>

=== At a Glance ===

{| class="wikitable"
|-
! Command !! Purpose
|-
| <code>apptainer pull</code> || Download an image from a registry
|-
| <code>apptainer build</code> || Build an image from a definition file or sandbox
|-
| <code>apptainer exec</code> || Run a single command inside a container
|-
| <code>apptainer shell</code> || Open an interactive shell inside a container
|-
| <code>apptainer run</code> || Run the container's default action
|}

Tutorials/Apptainer-Introduction - Revision history

Honfi001: /* apptainer pull */