Get your Jupyterhub box set up on Linode with a single go!

As a constantly evolving project, this has now been moved entirely onto Github, and is available here. In its current iteration, it does all sorts of cool things beyond Jupyterhub installation, including domain level installation of Python packages and other cool stuff. Give it a whirl! (Just make sure you change your name.)

At CBRD, a lot of the research work we do is done on remote machines. For various reasons, we like being able to spin up and wind down these boxes at will, and auto-configure them at short notice according to a few standard variables. Depending on the installation, then, we would have a perfectly set up box with all the features we want, focused around R, Python and as frontends, RStudio and Jupyterhub. There are a wide range of ways to configure boxes – Puppet, Chef cookbooks, Dockerfiles, and all that –, but for ease of use, we rely on simple shell files that can be run as Linode StackFiles.

Basic usage

The ResearchNode StackFile (GitHub・Linode) does six things:

  • Update system and add the CRAN repo as a source
  • Install R and RStudio
  • Install Python and JupyterHub
  • Install an opinionated set of system level packages (i.e. available to all users)
  • Configures ports and some other configuration items for the instance
  • Daemonises the RStudio server and JupyterHub to automatically start at failure and automatically start at reboot

When deployed using Linode from its StackFile, it allows for a wide range of configuration options, including ports for both Jupyter and RStudio, and a completely configured first user set up both on JupyterHub and RStudio. In addition, you can configure some install settings. A ‘barebones’ install option exists that allows for a minimum set of packages to be installed – this is useful for testing or if the desired configuration diverges from the ordinary structure. In addition, OpenCV, deep learning tools and cartography tools can be selectively disabled or enabled, as these are not always required.

User administration for Jupyterhub and RStudio

In general, user administration is by preset attached to PAM, i.e. the built-in Linux administration structure. JupyterHub has its own administration features, described here. RStudio, on the other hand, authenticates by user group membership. The two share the same usergroup, specified in the configuration (by default and convention, this is jupyter, but you can change it), and because users created by JupyterHub fall into that user group, creating users in JupyterHub automatically grants them access to RStudio. This is overall acceptable as we tend to use both, but there might be a safety concern there. If so, you can change the auth-required-user-group=$USERGROUPNAME setting to a defined usergroup in the /etc/rstudio/rstudio.conf.

Issues

There are some glitches that we’re trying to iron out:

  • Cartography and GIS tools glitch a little due to issues with PROJ.4.
  • GPU/CUDA support is not implemented as this is not customarily used or provided on Linodes
  • certbot and Let's Encrypt is not really supported yet, as our boxes are never directly public-facing, but you should most definitely find a way to put your server behind some form of SSL/TLS.
  • Currently, only Ubuntu 16.04 LTS is supported, as it’s the most widely used version. CRAN does not yet support more recent versions yet, but these will be added once CRAN support is added.
New to Linodes? Linode is a great service offering a simple, uncomplicated way to set up a Linux server, just how you want it! 👍🏻 In fact, I’ve been using Linode servers for over four years, and have only good experiences with them. I keep recommending them to friends, and they’re all happy! So if this post was helpful, and you’re thinking of signing up for a Linode, would you consider doing so using my affiliate link? I run this blog as a free service and pay for hosting out of pocket, and I don’t do advertisements (and never will!) or paid reviews of things (like what, paid Tyvek reviews? “Best Ebola PPE”? Nope.) – so really, it would make me so happy if you could help out this way.

As always, do let me know how things work out for you! Feel free to leave comments and ideas below. If you’re getting value out of using this script, just let me know.