JupyterHub deployment for the compmodels class

This repository contains an Ansible playbook for launching JupyterHub for the Computational Models of Cognition class at Berkeley.

The setup is a bit complex, so this readme will try to break it down and explain everything that's going on. If you want to jump right into the details of how to deploy, see first the installation instructions and then the section on deploying.

Overview

To understand what's going on behind the scenes, it is probably helpful to know what happens when a user accesses the server.

First, they go to the main url for the server.
This url actually points to a proxy server which authenticates the SSL connection, and proxies the connection to the JupyterHub instance running on the hub server.
The hub server is both a NFS server (to serve user's home directories) and the JupyterHub server. JupyterHub runs in a docker container called "jupyterhub".
Users see a JupyterHub login screen. When they click login, they are authenticated. When they access their server, JupyterHub creates a new docker container on one of the node servers running an IPython notebook server. This docker container is called "jupyter-username", where "username" is the user's username.
As users open IPython notebooks and run them, they are actually communicating with one of the seven node servers. The URL still appears the same, because the connection is first being proxied to the hub server via the proxy server, and then proxied a second time to the node server via the JupyterHub proxy.
Users have access to their home directory, because each node server is also a NFS client with the filesystem mounted at /home.

Proxy server

The proxy server runs nginx (pronounced "engine x"), which is a reverse HTTP proxy, in a docker container called "nginx". It proxies all connections from the main URL to port 8000 on the hub server.

You can verify that the proxy is running with docker ps. If you need to access logs for the proxy server, you can run docker logs --tail=10 nginx, and adjust the tail length as needed.

Static files

nginx proxies to the hub server, but it also serves the static notebook files directly to save on the number of files that need to be accessed. To do this, it mounts a volume from the jupyter/systemuser container, which contains all the necessary notebook files. However, this also means that if the user server docker images are updated on the node servers, that the jupyter/systemuser container must also be updated on the proxy server or you may see weird errors because the clients are requesting files that the proxy server has an old version of, or doesn't have at all. See the docker documentation on data volume containers for more details on how this works.

Hub server

The hub server fulfills two functions: it is both the NFS server, hosting all user's home directories, and it is the JupyterHub server.

NFS

NFS is the Network File System. It requires there to be a host server, where the files actually exist, and then any number of client servers that mount the NFS filesystem. Once the filesystem is mounted, it behaves just like a normal filesystem.

The hub server on its own only has about 28GB of disk space, so to supplement this, we have about 3TB of additional storage mounted at /var/lib/docker.

The original copies of all files are located at /var/lib/docker/export/home (the directory /var/lib/docker/export is the root of the NFS host filesystem). They are additionally mounted at /home on the hub server, and that is the location from which they should always be accessed.

There is a cron job that runs every hour to back up the files in /home using the script /srv/backup/backup.sh. The script runs duplicity once every hour, which is a backup service that performs a full backup every seven days and otherwise performs incremental backups. The files get encrypted and then backed up to a Rackspace Cloud Files container, from which they can also be restored, if necessary. In addition, another script (/srv/backup/cleanup.sh) gets run once a day, and will remove old backups. Only the most recent two full backups are kept.

Logs for the duplicity service are in /srv/backup/duplicity.log. Logs for NFS don't have their own log file; they can be found just in /var/log/syslog.

JupyterHub

The JupyterHub setup itself is actually pretty straightforward. JupyterHub runs in a docker container from the image compmodels/jupyterhub, which is built from jupyter/jupyterhub. The differences are that our version of JupyterHub uses a special blend of Google authentication with local system users and spawns user servers inside docker containers on the node servers using a spawner based on the system user docker spawner. What this basically means is:

Users are created on the hub server with a username that needs to be the same as their Google username.
In addition to their username, JupyterHub stores the pid of each user.
When they login, JupyterHub authenticates the users with Google.
Once authenticated, JupyterHub spawns a docker container on one of the node servers and mounts the user's home directory inside the container.
A user is created inside the docker container with the appropriate username and pid, so that they have access to the files in their home directory.

You should be able to see the JupyterHub docker container with docker ps. To get the JupyterHub logs, you can run docker logs --tail=10 jupyterhub.

Restuser

When a new user is added to JupyterHub, it ensures that the user exists on the system by communicating with a service called restuser. This is just a simple REST API that can create new users on the system. This is necessary, because JupyterHub is running in a docker container, and so can't actually create users on the system directly.

When users are created, their home directory is created on the NFS mount. The skeleton directory used to initialize their home directory can be found at /srv/skeldir. Logs for the restuser service can be found at /var/log/restuser.log.

Swarm

To spawn the user docker containers, we use a load-balancing clustering system called swarm. Essentially, swarm exposes an interface that looks just like the normal docker interface, and figures out in the background where to start new containers. For example, to get a list of the docker containers that are running through swarm (i.e., the user containers that are running on all node servers):

docker --tls -H 127.0.0.1:2376 ps

To get the logs for a container running through swarm, you can run docker --tls -H 127.0.0.1:2376 logs --tail=10 jupyter-username, where username is the username for the user that you want logs from.

Swarm itself also runs in a docker container, so you can get the logs with docker logs --tail=10 swarm.

Culling containers

Each docker container started through swarm is allocated 1GB of memory (currently there is no limit on CPU, but if a problem arises, we can institute one as well). Each node server has 32GB of memory, meaning that we can run about 31*7=217 containers at once. We actually have slightly more users than that, so we've set up a script that runs every hour and shuts down user containers if they haven't been accessed in 24 hours. The script runs in a docker container called cull, so logs can be accessed via docker logs cull.

Activity statistics

There is another service that runs and periodically checks which users have been active recently. It then saves that information into a sqlite database, which can subsequently be downloaded and analyzed. This script runs in a docker container called stats, so logs can be accessed via docker logs stats. The sqlite database is saved to /srv/stats/db/activity.sqlite.

Node servers

In general, the node servers probably don't need to be accessed directly because logs for all the user containers can be accessed through swarm on the hub server.

Each node server is a NFS client, with the NFS filesystem mounted at /home. Additionally, each node server is set up to run the singleuser IPython notebook servers in docker containers. The image is based on jupyter/systemuser, with the only differences being that nbgrader is installed so that students can validate and submit their assignments, and that terminado is installed so that users can have access to a terminal if they so desire.

Deploying

⚠️ Note: you'll need to install Ansible from source (devel branch) to get the current versions of the Docker modules.

To deploy this setup:

./script/deploy

Note that this will stop JupyterHub if it is currently running -- so don't run this when people might be using the hub!

If you need to run a particular subset of the deploy operations, you can pass a -t flag to specify a "tag". For example, to do all tasks relating to the statistics service, you would run ./script deploy -t stats. These tags are defined in the tasks themselves, for example if you look at roles/jupyterhub_host/tasks/stats.yml you'll see that the tasks all have a "stats" tag as well as a "rebuild-tag".

compmodels/jupyterhub-deploy

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