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.

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 for easier access.

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

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

Requirements and compatibility

python 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 using WSL2

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

Jupyter-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-code interact to 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-O2

1.1.4 - 2022-06-13

Fixed

Increased login timeout from 10 seconds to 60 seconds to reduce timeout errors

1.1.3 - 2022-03-06

Added

Option to use SSH public key authentication #14
Better warning messages for X11 DISPLAY error #15

1.1.2 - 2021-11-26

Added

Check for available updates #13

1.1.1 - 2021-11-24

Added

Fix segmentation fault on import Quartz
Fix try_quit_xquartz() in recent versions of macOS (Use the config option KEEP_XQUARTZ if quitting XQuartz is not desired.)
Remove check for root prompt at login()

1.1.0 - 2021-10-25

Jupyter-O2 detects and responds to Duo two-factor authentication prompts automatically, requesting a Duo push by default. This means that the arguments --2fa --2fa-code 1 are no longer required to use two-factor authentication; --2fa now has no effect.

Added

Automatic detection and handling of 2FA prompts #10
More error messages in case of job submission errors #11
Interactive mode for responding to 2FA prompt #2

1.0.6 - 2021-06-17

Added

Better error message if two-factor authentication fails
Warning if two-factor authentication is set incorrectly for the computer’s network location

1.0.5 - 2021-06-06

Removed

This version removes compatibility with Python 2.7, which has not been supported since version 1.0.2.

Added

Warning message for a common error if two-factor authentication is not used

Fixed

Fixed moving to a new jupyter port if the original port was occupied

Updated

Packaging system now supports PEP 517
Raised minimum dnspython version to 2.0

1.0.4 - 2021-02-02

Added

Option to change SLURM partition

Fixed

#3 Improved handling of hostname decode error

1.0.2 - 2020-08-24

Added

#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 their release notes.

Release files for jupyter-o2 1.1.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for jupyter-o2 1.1.4
File	Size	Uploaded
jupyter-o2-1.1.4.tar.gz	30.3 kB	Jun 13, 2022	Details

Built distribution (wheel)

Table of built distributions (wheels) for jupyter-o2 1.1.4
File	Interpreter	ABI	Platform	Reset
jupyter_o2-1.1.4-py2.py3-none-any.whl 22.9 kB Jun 13, 2022	Python 3, Python 2	none	any	Details

Total release size: 53.2 kB

Release files / jupyter-o2-1.1.4.tar.gz

Download URL	jupyter-o2-1.1.4.tar.gz
Size	30.3 kB
Tags	Source
SHA-256 checksum How to use checksums	`d01ee2f347851888f0c800c52d88ca338ea573fd80cd0e7cfb3021fff0942098`
BLAKE2b-256 checksum How to use checksums	`21f767367980642d7729ff53ee553eacd8c67913d88db40c59a9929dec6f48d6`
Upload date	Jun 13, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.13`

Release files / jupyter_o2-1.1.4-py2.py3-none-any.whl

Download URL	jupyter_o2-1.1.4-py2.py3-none-any.whl
Size	22.9 kB
Tags	Python 2 Python 3
SHA-256 checksum How to use checksums	`4399d2340c5f17de4270eb3a3fdd5b4648bb620f9d62b1cb098f5a91aef32bd6`
BLAKE2b-256 checksum How to use checksums	`341ec818096bf2d753f4916715b65227a2d669522bb01883fae9377115767804`
Upload date	Jun 13, 2022
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.3 CPython/3.9.13`