Honfi001 at 09:11, 12 March 2026

2026-03-12T09:11:44Z

← Older revision		Revision as of 11:11, 12 March 2026
Line 3:		Line 3:
	== Getting Started ==		== Getting Started ==

	First, make sure your module environment is clean and Apptainer is loaded:		First, grab an interactive session in a compute node.

			Then make sure your module environment is clean and Apptainer is loaded:

	<syntaxhighlight lang="bash">		<syntaxhighlight lang="bash">

Honfi001: Add message about storing image in lustre

2026-03-12T09:09:41Z

Add message about storing image in lustre

New page

= Pulling Apptainer Images =

== Getting Started ==

First, make sure your module environment is clean and Apptainer is loaded:

<syntaxhighlight lang="bash">
module reset
module load utilities Apptainer
</syntaxhighlight>Also, please make sure to store image and in your lustre folders.

== Your First Pull ==

Let's start by pulling a simple "hello world" container image:

<syntaxhighlight lang="bash">
apptainer pull ./hello-world.sif shub://vsoch/hello-world
</syntaxhighlight>

That is a lot happening in one line, so let's break it down piece by piece:

{| class="wikitable"
|-
! Part !! What it means
|-
| <code>apptainer pull</code> || The Apptainer command to download a container image.
|-
| <code>./hello-world.sif</code> || The output filename. This is where Apptainer will save the downloaded image. The <code>.sif</code> extension stands for '''Singularity Image Format''' — Apptainer's own container format. The <code>./</code> means "save it in my current directory".
|-
| <code>shub://vsoch/hello-world</code> || The source to pull from. <code>shub://</code> tells Apptainer to look at [https://singularity-hub.org Singularity Hub], a public registry for container images. <code>vsoch/hello-world</code> is the user and image name, much like a path on GitHub.
|}

Once the command finishes, you will have a file called <code>hello-world.sif</code> in your current directory. You can verify this:

<syntaxhighlight lang="bash">
ls -lh hello-world.sif
</syntaxhighlight>

This <code>.sif</code> file is your container — a single, portable file that contains an entire operating system and software environment. You can copy it, move it, or share it just like any other file.

== Running the Container ==

The simplest way to use a container is with <code>apptainer run</code>. This executes whatever default action the container was built to perform:

<syntaxhighlight lang="bash">
apptainer run ./hello-world.sif
</syntaxhighlight>

You should see a friendly output from the container. That is it — you just ran software inside a container.

== Opening a Shell Inside the Container ==

Instead of running the container's default action, you can open an interactive shell inside it. This lets you look around and explore the container's environment as if you had logged into a different machine.

<syntaxhighlight lang="bash">
apptainer shell ./hello-world.sif
</syntaxhighlight>

You will notice your prompt changes (usually to <code>Apptainer></code>), indicating that you are now "inside" the container. Type <code>exit</code> when you want to leave.

=== The Container is Not Fully Isolated (by Default) ===

Here is something important that surprises many beginners: by default, Apptainer does '''not''' fully isolate the container from the host system. Your home directory and parts of the host filesystem are still visible inside the container.

Try this while inside the shell:

<syntaxhighlight lang="bash">
apptainer shell ./hello-world.sif
</syntaxhighlight>

Then, from inside the container:

<syntaxhighlight lang="bash">
Apptainer> mkdir ~/test-from-container
Apptainer> ls ~/test-from-container
Apptainer> exit
</syntaxhighlight>

Now, back on the host:

<syntaxhighlight lang="bash">
ls ~/test-from-container
</syntaxhighlight>

The directory is there — on your '''real''' filesystem. The container was able to create it because your home directory was mounted inside the container by default. This is by design: it makes it easy to work with your own files, but it means the container is not completely separate from the host.

=== Full Isolation with <code>--containall</code> ===

If you want the container to be fully isolated from the host system — no access to your home directory, no shared environment variables, no host filesystems — use the <code>--containall</code> flag (or its short form <code>-C</code>):

<syntaxhighlight lang="bash">
apptainer shell --containall ./hello-world.sif
</syntaxhighlight>

Now try the same thing from inside:

<syntaxhighlight lang="bash">
Apptainer> mkdir ~/test-isolated
Apptainer> exit
</syntaxhighlight>

Back on the host:

<syntaxhighlight lang="bash">
ls ~/test-isolated
</syntaxhighlight>

This time, the directory does '''not''' exist on your host. The container was completely isolated — anything it created lived only inside the container's temporary environment and was discarded when you exited.

Use <code>--containall</code> (or <code>-C</code>) when you want a clean, reproducible environment that does not interfere with (or depend on) the host system.

== Running a Specific Command with <code>exec</code> ==

Sometimes you do not want a full interactive shell — you just want to run a single command inside the container and get the output. That is what <code>apptainer exec</code> is for.

For example, let's check which operating system is inside this container:

<syntaxhighlight lang="bash">
apptainer exec ./hello-world.sif cat /etc/lsb-release
</syntaxhighlight>

You should see output similar to:

<syntaxhighlight lang="text">
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=14.04
DISTRIB_CODENAME=trusty
DISTRIB_DESCRIPTION="Ubuntu 14.04.6 LTS"
</syntaxhighlight>

The container is running '''Ubuntu 14.04''' — regardless of what operating system your host machine is running. This is the power of containers: you can run software built for a completely different OS environment without any conflicts.

The pattern for <code>exec</code> is:

<code>apptainer exec ''[options]'' ''container.sif'' ''command'' ''[arguments]''</code>

== Summary ==

You now know the three main ways to interact with a pulled Apptainer container:

{| class="wikitable"
|-
! Command !! What it does
|-
| <code>apptainer run container.sif</code> || Runs the container's default action
|-
| <code>apptainer shell container.sif</code> || Opens an interactive shell inside the container
|-
| <code>apptainer exec container.sif ''command''</code> || Runs a single specific command inside the container
|}

And one important flag to remember:

{| class="wikitable"
|-
! Flag !! What it does
|-
| <code>--containall</code> (or <code>-C</code>) || Fully isolates the container from the host (no shared home directory, no host environment)
|}

Tutorials/Apptainer-PullingImages - Revision history

Honfi001 at 09:11, 12 March 2026

Honfi001: Add message about storing image in lustre