Jupyter Hub on SciNet

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Disclaimer: the following describes is an experimental setup at SciNet running on good, but out-of-warrantee hardware.*

  • Four jupyterhub servers, each with 128 GB of memory and 16 or 20 cores.
  • Access using an ssh tunnel via login.scinet.utoronto.ca:
$ ssh USER@login.scinet.utoronto.ca -L8888:jupyterhub:8000 -N -f
  • This will select (round-robin) one of the four jupyterhub servers.
  • Point your browser to 'localhost:8888' and log in with your SciNet account.
  • The browser should now show the files in your $HOME on SciNet. (If not, try reloading the page, it may have timed out).
  • You can open or create Python 2, Python 3, and R notebooks.
  • Large number of python packages preinstalled.

Jupyterscreen3.png

Tips to get started

  • Jupyter can also browse your (SciNet) files and edit them.
  • Use the 'new' button to create a new python notebook.
  • Give your notebooks reasonable names.
  • To execute a python input line, press `Shift-Enter`.
  • Save your work periodically (even though there is autosave).
  • To work similarly to `ipython --pylab`, do:
In [1]: from pylab import *
        %matplotlib notebook

Advantages and Disadvantages of a Notebook Environment

Drawbacks:

  • Notebook files (.ipynb) are not scripts.
  • Does not (always) work well with version control.
  • Designed to run in browser.
  • Back-end runs on shared resources.
  • Graphics is inline, which is great for quick exploration but make tweaking a plot harder (IPython+X works better for this).
  • You can jump around in the notebook, and execute different parts: hard to keep track of what you did.

Advantages:

  • You can jump around in the notebook, and execute different parts: Easier exploration, experimentation and debugging.
  • Auto-save
  • You can rerun parts of your code (while, e.g., keeping large data in memory)
  • You can add text portions, making your notebook more like an article.
  • Which in turn can be useful for sharing, demos, teaching, ...
  • You can still export as a script.
  • Also has a terminal.
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