Reproducible computational environments using containers
3 February 2020
This session aims to introduce the use of Docker containers with the goal of using them to effect reproducible computational environments. Such environments are useful for ensuring reproducible research outputs and for simplifying the setup of complex software dependencies across different systems. We will also briefly introduce the Singularity container environment which is compatible with Docker and designed for use on multi-user systems (such as HPC resources).
Trainer
Andy Turner
Andy Turner is a senior member of the RSE teams for the UK national
HPC services ARCHER and
Cirrus. He is also heavily involved in
advanced computing training at EPCC. Andy has a particular interest
in enabling new user communities to make use of HPC and the use of
novel user engagement to improve the HPC user experience. He has been
involved the HPC Carpentry initiative for the past two years.
Details
This course is free to all academics.
Pre-requisites
Attendees should bring their own laptop (Windows/Mac/Linux)
The prerequisites for this course are minimal and help/advice will be given on these topics if required by attendees. Ideally:
- You should have basic familiarity with using a command shell, and the lesson text will at times request that you "open a shell window", with an assumption that you know what this means.
- Under Linux or macOS it is assumed that you will access a bash/zsh shell (usually the default), using your Terminal application.
- Under Windows, Powershell and Git Bash should allow you to use the Unix instructions. We will also try to give command variants for Windows cmd.exe.
- As an item of setup, it is assumed that you have a directory named 'container-playground' that you are able to 'cd' to using your command shell, and are also able to find using your computer's graphical file browser (e.g., Finder on macOS or Windows Explorer). One way to achieve this is to create your 'container-playground' directory within your computer's Desktop directory.
- The lessons will sometimes request that you use a text editor to create or edit files in particular directories. It is assumed that you either have an editor that you know how to use that runs within the working directory of your shell window (e.g. nano), or that if you use a graphical editor, that you can use it to read and write files into the working directory of your shell.
Timetable
Course will run from 10:30 - 16:00
Details to follow
We will be providing tea and coffee both morning and afternoon throughout the workshop. Lunch will *not* be provided although there are places to eat in the area and the workshop location has space for eating a packed lunch.
Course Materials
Draft Slides and exercise material for this course.
Location
The course will be held at University of Durham, Durham
Registration
Please use the registration page to register for ARCHER courses.
Questions?
If you have any questions please contact the ARCHER Helpdesk.
