jupyter-o2 0.2.0

Run Jupyter on Orchestra 2

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

Installation

First, follow the O2 wiki’s procedure to set up Jupyter for your account on O2.

Next, install Jupyter-O2.

$ pip install jupyter-o2

Then, find the jupyter-o2.cfg file in etc/jupyter-o2, where etc is located either in the environment root or the system-wide /etc directory. Edit this file according to its instructions, particularly DEFAULT_USER, MODULE_LOAD_CALL, and SOURCE_JUPYTER_CALL.

Note: jupyter-o2.cfg should be installed upon setup. If not, you may also copy jupyter_o2/jupyter-o2.cfg into your home folder as .jupyter-o2.cfg.

Update: If upgrading from version 0.1 to 0.2, add DEFAULT_USER = <user> to jupyter-o2.cfg under [Defaults], substituting your O2 login username for <user>.

For more info on setting up Jupyter and troubleshooting Jupyter-O2, see jupyter_o2_tips.rst.

Usage

$ jupyter-o2 <subcommand>

Example: jupyter-o2 notebook

This will launch an X11-enabled ssh, start an interactive node running jupyter notebook, ssh into that interactive node to allow requests to be forwarded, and finally open the notebook in your browser.

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

Requirements and compatibility

• python 2.7 or 3.6 (tested)

• pexpect.pxssh

• POSIX: Jupyter-O2 has been tested on MacOS. It may work on Linux, and on Windows it requires Cygwin and Cygwin’s version of Python.

Optional installs

• pinentry (a command line tool)

TODO

• use logging to allow different levels of verbosity