Using Containers

You can interact with SIF containers in different ways. The following sections show how to interact with images.

For demonstration, a SIF container ubuntu.sif that was built in Building Containers page will be used.

For more information, refer to the Apptainer Documentation.

Running Containers

The %runscripts section of a def file is user defined script that defines the actions a container should perform when you run it. For example the %runscripts section of the def file ubuntu.def looks like:

    python /opt/

This will be triggered when the run command is used. For example, to run the ubuntu.sif container, run:

apptainer run ubuntu.sif

This will run the lines specified in the runscript section python /opt/ Output:

[0, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1]
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]

The output shows the output of the python script

If the runscript accepts arguments, you can pass arguments to the run command.

You can also run SIF containers as an executable file. This behaves as the run command. For example, to run the ubuntu.sif container, you simply run:


The output is the same of the run command.

Executing Containers

To execute a custom command within a SIF container, you can use the exec command. For example, to execute the command echo "Hello Discovery!" using the ubuntu.sif container, run:

apptainer exec ubuntu.sif  echo "Hello Discovery"


Hello Discovery!


Apptainer allows you to spawn a new shell within your container and interact with it as a small virtual machine. This can be done using the shell command.

$ apptainer shell ubuntu.sif

This shows that you’re inside the container and you can run shell commands.

Apptainer> uname

SLURM Submission Script

You can also integrate the containers into a SLURM submission script. For more information, refer to the Slurm Commands page. For example, to submit a job that runs the ubuntu.sif container, you need first to create a job script, named with the following content.


## Slurm Directives
#SBATCH --job-name=test_container
#SBATCH --output=test_container-%j.out
#SBATCH --ntasks=2
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=5G
#SBATCH -p normal
#SBATCH --time 00:10:00

## Load modules

## Run the program using use 'srun'.
srun apptainer run ubuntu.sif

Here, 1 CPU with 5 G memory per CPU and 10 minutes of Walltime was requested for the task (Job steps). The container will run only once (`--ntasks=1'). If the --ntasks is set to two, this means that the python program will be executed twice.

To submit the created job, you simply run:


After the job is complete, you can check the output file, which shows that the ubuntu.sif container run once.

$ cat test_container_-54391.out
[0, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1]
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]