See a complete tutorial on Singularity/Apptainer

Singularity is now called Apptainer, but in our cluster is still going by the singularity command.

From your terminal you can get the date with date, but it’s going to be a boring date:

date
# will print something like 'Wed 21 Jan 11:43:30 GMT 2026'

We need a better tool, that prints something like:

 ______________________________
< Wed Jan 21 11:42:59 UTC 2026 >
 ------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Instead of installing the program, we will run a container that contains it to have a first hands-on experience of a container

Downloading the container

Singularity containers are stored in images (files) that can be easily shared and copied. In general, you might simply download or copy a file to get a new Singularity container. Alternatively, we can get containers from online repositories - similar to Docker Hub.

# Since we need internet, let's go to the software node
ssh software

# Let's download an image for `lolcow`
singularity pull library://lolcow

# check what you just downloaded (should include lolcow_latest.sif)
ls -ltr | tail

Running a tool from the container

Each container has an entire system in it (potentially with a lot of tools). To execute a single tool (program) from a container we use this syntax:

singularity exec $IMAGE $COMMAND

# for example:
singularity exec lolcow_latest.sif  cowsay "NBI HPC!"

The command means run the cowsay "NBI HPC!" command, but using the tool from lolcow_latest.sif.

Executing the container

While exec allows to run any tool that is available inside the container, there is a special run command to execute a special script (if available) that is the entry point of the image.

We can confirm that lolcow has an entry point:

# Check what would be executed by the image itself
singularity inspect --runscript lolcow_latest.sif

# Run the script! Simply:
singularity run lolcow_latest.sif