This are my notes from Winter 2022 before the Richardson Lab ELOG was setup. TODO: Need to write a proper "HowTo" ELOG for jupyterhub + web server setup based on this.

JupyterHub on Chimay

[Early Jan 2022]

Cannot install using TLJH since it's only available for Ubuntu. So instead, installing step-by-step using guide available here - https://github.com/jupyterhub/jupyterhub-the-hard-way/blob/master/docs/installation-guide-hard.md

• Nginx webserver is used for HTTPS reverse-proxy for the jupyterhub. I installed nginx via apt-get, config at - /etc/nginx/sites-available/default

• I used cerbot to generate SSL certificates.

To start the webserver sudo systemctl start nginx.service

Goal: Setup JupyterHub as a systemd service and make it available over HTTPS.

To start the services needed for the hub sudo systemctl start jupyterhub.service

Note: Reload the daemon if you edited a service before you restart it, otherwise it will complain.

sudo systemctl daemon-reload

Logs

[Jan 26, 2020]

Ended up using the JupyterHub guide available here - https://github.com/jupyterhub/jupyterhub-the-hard-way/blob/master/docs/installation-guide-hard.md and SudoSpawner guide available here - https://jupyterhub.readthedocs.io/en/stable/reference/config-sudo.html

I was struggling with this quite a bit but eventually I figured out that I was running into trouble because I was trying to run jupyterhub command as a password-less sudo user as I thought that's what sudospawner needed. That seems not to be the case.

1. The systemd service jupyter.service has to be run as User=root and the ExecStart=/opt/jupyterhub/bin/jupyterhub -f /opt/jupyterhub/etc/jupyterhub/jupyterhub_config.py and ensure that /usr/sbin is in PATH. (This necessary as we need to spawn single-user jupyter servers for our users on-demand, so the User that runs the ExecStart needs to have permissions to run single-user server init commands.)
2. In jupyterhub_config.py, the spawner is configed as sudospawner - c.JupyterHub.spawner_class=sudospawner.SudoSpawner. I installed sudospawner in our jupytherhub environment via pip.
3. In jupyterhub_config.py, the authenticator used is PAM which allows linux users on chimay to login with there username and password and opens their shell in their home directories.

[Jan 27, 2020]

[10:30]

Attempted MATLAB integration following this guide - https://github.com/mathworks/jupyter-matlab-proxy

It annoyingly broke nodejs which broke jupyterhub as the proxy failed without it. I have now restored nodejs and the jupyterhub is back up.

[12:00]

User controls now has admin access on the hub. To add more admins - edit /opt/jupyterhub/etc/jupyterhub/jupyterhub_config.py by adding the username in c.Authenticator.admin_users

[15:15]

Argh! User's cannot access user-created conda environments in notebooks besides the default one i.e. the one for which kernelspec is available in /usr/local/share/jupyter/kernels. Non-sudo users also can't access this path to put a kernelspec in it! Sudo users who can do this end up having their custom environments visible to everyone. Argh! !FIX NEEDED!

[15:54]

After reading this (https://github.com/Anaconda-Platform/nb_conda_kernels/issues/185) I am putting

"CondaKernelSpecManager": { "kernelspec_path": "--user" }

in /opt/miniconda3/etc/jupyter/jupyter_config.json

WebServer down, fix yet to be tested.

[16:04]

Fix does not seem to be working.

[Tue Feb 1 17:02:46 2022]

ISSUE: User unable to use their custom conda environments in notebooks

STATUS: Fixed, refer to elog 'ligo-ds' no. 1

All future logs will be on the ELOG.