Using Apptainer containers to run commands

Overview

Teaching: 10 min
Exercises: 5 min

Questions

• How do I run different commands within a container?

• How do I access an interactive shell within a container?

Objectives

• Learn how to run different commands when starting a container.

• Learn how to open an interactive shell within a container environment.

Running specific commands within a container

We saw earlier that we can use the apptainer inspect command to see the run script that a container is configured to run by default. What if we want to run a different command within a container?

If we know the path of an executable that we want to run within a container, we can use the apptainer exec command. For example, using the hello-world.sif container that we’ve already pulled from Apptainer Hub, we can run the following within the test directory where the hello-world.sif file is located:

$ apptainer exec hello-world.sif /bin/echo Hello World!

Hello World!

Here we see that a container has been started from the hello-world.sif image and the /bin/echo command has been run within the container, passing the input Hello World!. The command has echoed the provided input to the console and the container has terminated.

Note that the use of apptainer exec has overriden any run script set within the image metadata and the command that we specified as an argument to apptainer exec has been run instead.

Basic exercise: Running a different command within the “hello-world” container

Can you run a container based on the hello-world.sif image that prints the current date and time?

Solution

$ apptainer exec hello-world.sif /bin/date

Wed Apr 17 15:32:16 CDT 2024

The difference between apptainer run and apptainer exec

Above we used the apptainer exec command. In earlier episodes of this course we used apptainer run. To clarify, the difference between these two commands is:

• apptainer run: This will run the default command set for containers based on the specfied image. This default command is set within the image metadata when the image is built (we’ll see more about this in later episodes). You do not specify a command to run when using apptainer run, you simply specify the image file name. As we saw earlier, you can use the apptainer inspect command to see what command is run by default when starting a new container based on an image.

• apptainer exec: This will start a container based on the specified image and run the command provided on the command line following apptainer exec <image file name>. This will override any default command specified within the image metadata that would otherwise be run if you used apptainer run.

Opening an interactive shell within a container

If you want to open an interactive shell within a container, Apptainer provides the apptainer shell command. Again, using the hello-world.sif image, and within our test directory, we can run a shell within a container from the hello-world image:

$ apptainer shell hello-world.sif

Apptainer> whoami
[<your username>]
Apptainer> ls
hello-world.sif
Apptainer> 

As shown above, we have opened a shell in a new container started from the hello-world.sif image. Note that the shell prompt has changed to show we are now within the Apptainer container.

Discussion: Running a shell inside a Apptainer container

Q: What do you notice about the output of the above commands entered within the Apptainer container shell?

Q: Does this differ from what you might see within a Docker container?

Use the exit command to exit from the container shell.

Key Points

• The apptainer exec is an alternative to apptainer run that allows you to start a container running a specific command.

• The apptainer shell command can be used to start a container and run an interactive shell within it.