Containers on HPC and Cloud with Singularity


You’ll need a laptop with a web browser and a terminal. See also the Setup page.

You might want to brush up on the fundamentals of the Linux Shell for HPC.


This tutorial has been designed in a modular way. Episodes can be thought as categorised as follows:

Once you’ve gone through Episodes 1-5, there are almost no further dependencies. You can go on and pick whichever you are interested in, and you will be able to follow through.

A webinar series for episodes 1 to 11 is now available on the Pawsey Centre Youtube channel! Playlist here.
You can download the webinar slides here.

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00:00 1. Introduction to containers
00:10 2. Basics of Singularity
00:50 3. Share files with the host: BLAST, a bioinformatics demo
01:10 4. Build and share your own container image
01:30 5. Inside a build definition file
01:50 6. Building images with Docker
02:10 7. GUI enabled web applications: RStudio in a container
02:30 8. Making Python not awful with containers
02:50 9. Computational Fluid Dynamics with MPI containers
03:10 10. Set up writable containers: another bio example with Trinity
03:30 11. Molecular dynamics with GPU containers
03:45 12. Reproducible scientific workflows
04:00 13. GUI applications using X11 windows: the Gnuplot example
04:15 14. Streamline the user experience: bash wrappers and modules
04:45 15. Setup Singularity on your machine
05:00 16. Overview of Docker
05:30 17. Run multi-component web services with Docker Compose
05:45 18. Other notable container tools
06:00 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.