Singularity image

A Singularity recipe is included with OMUSE. When building it, the result is a Singularity image which is a portable way to test OMUSE and the included models.

The image includes Jupyter for interactive Python notebooks and the following OMUSE models:

• cdo
• dales
• qgcm (hogg2006,ocean_only,hogg2006_20km)
• qgmodel
• swan

Building the image:

sudo singularity build omuse.img Singularity

Create a directory which the container can use at runtime for storing notebooks:

mkdir run

Launch the container to start Jupyter server inside:

singularity run --contain -B examples:/opt/notebooks,run:/run/user omuse.img

Then visit the reported localhost:8888 with a browser.

In the singularity command above, the –contain option disables mounting your home directory whereas the -B option specifies paths that will be mounted inside the container, in this case the examples distributed with OMUSE. If you have a folder with notebooks using OMUSE, you can mount this instead of the examples directory to execute them with the singularity container. The container above can also be used to run a regular python script that uses OMUSE functionality by piping the contents to the container python command:

cat myscript.py | singularity exec --contain omuse.img python3

Finally, it is also possible to launch a shell inside the container:

singularity shell --contain -B run:/run/user omuse.img

to execute your python code with all OMUSE dependencies findable. We advise to use the –contain option whenever you have OMUSE installed on your host system in $HOME/.local .