/bc_example_jupyter

Batch Connect - Example Jupyter Notebook Server

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Batch Connect - Example Jupyter Notebook Server

GitHub Release GitHub License

An example Batch Connect app that launches a Jupyter Notebook server within a batch job.

⚠️ I've used this repository as a test to make sure that I can get a simple OnDemand app up, running, and available within the Parallel Cluster environment in development at work. I was able to get it running, but this isn't yet ready for use as a template app for future Jupyter apps in our environment. Here are the outstanding issues as I see them:

  • The form.yml includes configuration options that don't have a use for our users, like setting the account and queue, as well as getting an email on launch. The initial form should be simplified and tested.
  • I haven't landed on a strategy for managing dependencies. Ideally spack can load them, but I haven't looked in to what's available and what's possible to do as a custom setup. I think that should be doable, it's just not the priority as I write this.
  • Enhancement: Hopefully I can eventually figure out what needs to happen for the set_host in submit.yml to be configured globally at the cluster level. That would make me feel better, since currently my plan is to just set it for every single app, since they'll all need it. See notes in submit.yml.erb for details.

Prerequisites

This Batch Connect app requires the following software be installed on the compute nodes that the batch job is intended to run on (NOT the OnDemand node):

  • Jupyter Notebook 4.2.3+ (earlier versions are untested but may work for you)
  • OpenSSL 1.0.1+ (used to hash the Jupyter Notebook server password)

Optional software:

  • Lmod 6.0.1+ or any other module purge and module load <modules> based CLI used to load appropriate environments within the batch job before launching the Jupyter Notebook server.

Install

These are command line only installation directions.

We start by downloading a zipped package of this code. This allows us to start with a fresh directory that has no git history as we will be building off of this.

# Download the zip from the GitHub page
wget https://github.com/OSC/bc_example_jupyter/archive/master.tar.gz

# Create a catchy directory
mkdir my_jupyter_app

# Unzip the downloaded file into this directory
tar xzvf master.tar.gz -C my_jupyter_app --strip-components=1

# Change the working directory to this new directory
cd my_jupyter_app

From here you will make any modifications to the code that you would like and version your changes in your own repository:

# Version our app by making a new Git repository
git init

#
# Make all your code changes while testing them in the OnDemand Dashboard
#
# ...
#

# Add the files to the Git repository
git add --all

# Commit the staged files to the Git repository
git commit -m "my first commit"

Contributing

  1. Fork it ( https://github.com/OSC/bc_example_jupyter/fork )
  2. Create your feature branch (git checkout -b my-new-feature)
  3. Commit your changes (git commit -am 'Add some feature')
  4. Push to the branch (git push origin my-new-feature)
  5. Create a new Pull Request