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Batch Connect - Example Jupyter Notebook Server Palmetto

GitHub Release GitHub License

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

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