Package: jupyter-o2
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.InstallationFirst, follow theO2 wiki’s procedureto 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.pipinstalljupyter-o2Then, generate the config file.jupyter-o2--generate-configFollow the printed path tojupyter-o2.cfgand edit according to its instructions, particularly theDEFAULT_USERandINIT_JUPYTER_COMMANDSfields.
You may copy this file to any of the locations listed byjupyter-o2--pathsfor easier access.Make sure you have X11 forwarding active (installXQuartzif on a Mac).For more info on setting up Jupyter and troubleshooting Jupyter-O2, see thejupyter-o2 tips.Requirements and compatibilitypython 3.6+pexpect 4.5+POSIX: Jupyter-O2 requires a POSIX environment such as macOS or Linux.
If you have a Windows machine, you can try usingWSL2UsageJupyter-O2 should be run locally using the following command format:jupyter-o2[subcommand]Examples:jupyter-o2notebookorjupyter-o2lab(tryJupyterLab!)This will automate the “Opening a Notebook” procedure
on theO2 wiki.Note that if Jupyter is installed on your machine, Jupyter-O2 can also be run as a Jupyter subcommand:jupytero2labFor info on the Jupyter-O2 command-line options, usejupyter-o2--help.Two-factor authenticationJupyter-O2 detects the Duo two-factor authentication prompt and
requests a Duo push by default (code 1).
To send a pre-generated code, use the argument--2fa-code<code>,
replacing<code>with your code.Experimental: use--2fa-codeinteractto interactively respond to the Duo prompt.
This allows you to request a phone or text push and enter the code you receive.Changelog for Jupyter-O21.1.4 - 2022-06-13FixedIncreased login timeout from 10 seconds to 60 seconds
to reduce timeout errors1.1.3 - 2022-03-06AddedOption to use SSH public key authentication #14Better warning messages for X11 DISPLAY error #151.1.2 - 2021-11-26AddedCheck for available updates #131.1.1 - 2021-11-24AddedFix segmentation fault onimport QuartzFixtry_quit_xquartz()in recent versions of macOS (Use the config optionKEEP_XQUARTZif quitting XQuartz is not desired.)Remove check for root prompt atlogin()1.1.0 - 2021-10-25Jupyter-O2 detects and responds to Duo two-factor authentication
prompts automatically, requesting a Duo push by default.
This means that the arguments--2fa--2fa-code1are no longer
required to use two-factor authentication;--2fanow has no effect.AddedAutomatic detection and handling of 2FA prompts #10More error messages in case of job submission errors #11Interactive mode for responding to 2FA prompt #21.0.6 - 2021-06-17AddedBetter error message if two-factor authentication failsWarning if two-factor authentication is set incorrectly
for the computer’s network location1.0.5 - 2021-06-06RemovedThis version removes compatibility with Python 2.7,
which has not been supported since version 1.0.2.AddedWarning message for a common error if two-factor
authentication is not usedFixedFixed moving to a new jupyter port if the original port was occupiedUpdatedPackaging system now supports PEP 517Raised minimum dnspython version to 2.01.0.4 - 2021-02-02AddedOption to change SLURM partitionFixed#3 Improved handling of hostname decode error1.0.2 - 2020-08-24Added#6 Jupyter-O2 now requires only a single ssh session.
The second ssh session is now disabled by default and can be
re-enabled in the config file.For information about older versions, see theirrelease notes.