Prerequisites
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.
Like this tutorial? Star it on Github (button on top right)!
| Setup | ||
| 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.