As part of the $5M grant awarded to the LibreTexts project last year, our team had two goals: to integrate Jupyter into the LibreTexts website and to create a computing cluster running JupyterHub to serve LibreTexts and UC Davis users. This quarter, we focused on researching how to create the cluster through building test servers.
Virtual Machine Environment
The first step in our journey to building a cluster was to familiarize ourselves with how to setup a single server. It was crucial for us to really understand all the details on how to setup a single server, as we would need the knowledge to setup each and every single node in the cluster. We decided to use VirtualBox as our starting playground so we had an easily disposable environments to learn from.
RAID1 and LVM
We started adding more features to the installations that we would eventually use in our cluster configuration. We started by adding a software RAID1 to our installations to familiarize ourselves with the process, and then we moved on to adding LVM too.
Redundant Array of Independent Disks, also known as RAID, provides multiple ways of orchestrating and synchronizing multiple hard drives in a computer network to establish reliable data storage within the network. We decided to use RAID1, which consists of an exact copy of a set of data on two or more disks. We chose RAID1 because it allows us to switch a drive while the server is live, in case a drive fails.
Logical Volume Manager, also known as LVM, is a device mapper target that provides logical volume management for the Linux kernel. The benefits of using LVM is the ability to use and manage "dynamic partitions". When using LVM "partitions", known just as logical volumes, we can manage them very easily through the command line if we wanted to either create additional partitions, or resize/delete any existing partitions.
While installing Ubuntu Live Server 18.04 with RAID1, we ran into an issue where the server failed to start. According to the Ubuntu 18.04.02 Release Notes:
The next generation Subiquity server installer, brings the comfortable live session and speedy install of Ubuntu Desktop to server users at last.
N.B., If you require multipath, full-disk encryption, or the ability to re-using existing partitions, you will want to continue to use the alternate installer which can be downloaded from http://cdimage.ubuntu.com/releases/18.04/release/
As of 18.04.1, the Subiquity server installer now supports LVM, RAID, vlans, and bonds.
After some researching, we learned however that a bug from the Ubuntu Live Server image caused the installer to fail to mount the boot partition, preventing the installation of Ubuntu on RAID1. We instead used this alternate installer (non-live server image file) to successfully install Ubuntu Server 18.04 with RAID1 on the virtual machines.
When installing Ubuntu Server with RAID1 and LVM on our virtual machines, we did not allot enough space on our hard disks for the operating system and JupyterHub combined. We determined that in total, the operating system and JupyterHub required about 15 GB of storage. To be safe, we now recommend to create two 20 GB virtual hard disks for setting up JupyterHub.
Our individual setups varied between each test server. In one successful setup, each hard disk contained two partitions. One partition contained 2.0 GB and was mounted on /boot as the boot partition. The other partition contained 19.5 GB, serving as primary storage.
We plan to have a stack of Ubuntu 18, RAID1, and LVM as our standard setup for each node in the cluster.
Our next step was trying to setup a bare-metal verion of JupyterHub in our virtual machines. We followed the instructions provided in the repository, jupyterhub-deploy-teaching, to install JupyterHub on our virtual machines and connect to it through the browser. The repository is a "light fork" from the JupyterHub's original jupyterhub-deploy-teaching repository, intended for UC Davis usage.
We ran into a few issues during the installation process. The Ansible script in the repository was missing some required installations. The package python3-distutils is required by JupyterHub but was not installed. The package was a part of Ubuntu 16.04, so the Ansible script did not need to specify installing python3-disutils previously. This was fixed in the Ansible Playbook via this commit.
We also encountered Conda errors while installing JupyterHub. We suspect that this is due to the submodules from the ansible-conda repository, which are fixed by running their updates in our automatic configuration and deploying script, setup.sh.
After succeeding in setting up JupyterHub on our virtual machines, we incorporated the changes into the configuration files and completed setup.sh to automate the installation process, testing it to make sure that it worked. The script setup.sh automates the following configuration tasks:
- Adds submodules from the ansible-conda repository.
- Adds the current user to as an admin and user.
- Generates a proxy_auth_token and inputs it into the configuration file.
- Generates a self-signed SSL certificate and cookie secret.
- Names the hosts and jupyter_hosts files properly from hosts.example and jupyter_hosts.example respectively.
- Runs Ansible Playbook.
Users can now save time by running the script to configure and deploy JupyterHub, rather than complete the above tasks manually. Using the script should be less error-prone compared to the manual setup.