Run Jupyter on Orchestra 2
Project description
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-o2Then, find the jupyter-o2.cfg file in etc/jupyter-o2. Run jupyter-o2 --paths to see possible and current locations.
jupyter-o2.cfg should be installed upon setup. If not, you may also copy jupyter_o2/jupyter-o2.cfg into any location in jupyter-o2 --paths.
Edit jupyter-o2.cfg according to its instructions, particularly the DEFAULT_USER, MODULE_LOAD_CALL, and SOURCE_JUPYTER_CALL fields.
Update: If upgrading from version 0.1 to 0.2, add DEFAULT_USER = <user> to jupyter-o2.cfg under [Defaults], substituting your O2 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
If Jupyter is installed on your machine, Jupyter-O2 can also be run as a Jupyter subcommand, e.g. 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 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 should require Cygwin and Cygwin’s version of Python.
Optional installs
pinentry (a command line tool)
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