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Run Jupyter on Orchestra 2

Project description

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Jupyter-O2 is a command-line tool that remotely runs Jupyter on Orchestra 2 (O2), an HPC cluster managed by the HMS Research Computing group.

Installation

First, follow the O2 wiki’s procedure to set up Jupyter for your account on O2. (If you have already installed Jupyter on O2, you can skip this step.)

Next, on your local machine:

Install Jupyter-O2.

pip install jupyter-o2

Then, generate the config file.

jupyter-o2 --generate-config

Follow the printed path to jupyter-o2.cfg and edit according to its instructions, particularly the DEFAULT_USER and INIT_JUPYTER_COMMANDS fields. You may copy this file to any of the locations listed by jupyter-o2 --paths if you wish.

Make sure you have X11 forwarding active (e.g. install XQuartz if on a Mac).

For more info on setting up Jupyter and troubleshooting Jupyter-O2, see the jupyter-o2 tips.

Usage

Jupyter-O2 should be run locally using the following command format:

jupyter-o2 [subcommand]

Examples: jupyter-o2 notebook or jupyter-o2 lab (try JupyterLab!)

This will automate the “Opening a Notebook” procedure on the O2 wiki.

Note that if Jupyter is installed on your machine, Jupyter-O2 can also be run as a Jupyter subcommand:

jupyter o2 lab

For info on the Jupyter-O2 command-line options, use jupyter-o2 --help.

Two-factor authentication

If you see a two-factor authentication prompt when SSH’ing into O2, you will need to tell Jupyter-O2 to request Duo pushes using the arguments --2fa --2fa-code 1.

Requirements and compatibility

  • python 2.7 or 3.6+
  • pexpect 4.5+
  • POSIX: Jupyter-O2 has not been tested on Windows, but it may work with Cygwin.
  • pinentry (suggested)

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