Setup and running Jupyter notebooks

Disclaimer: These notes started few years ago from the official SWC lesson but then evolved quite a bit to include other topics.

Starting Python in a Jupyter notebook

There are many ways to run Python commands:

• from a Unix shell you can start a Python shell and type commands there,
• you launch Python scripts saved in plain text *.py files,
• you can execute Python cells inside Jupyter notebooks; the code is stored inside JSON files, displayed as HTML

Today we will be using a Jupyter notebook. You have two main options:

1. Main option: use JupyterHub on our second training cluster: point your browser to https://uu.c3.ca, log in with yesterday’s username and today’s password, then launch a Jupyter Hub server with time = 6 hours, memory = 2000 MB, GPU configuration = None, user interface = JupyterLab
2. Second option: use syzygy.ca with one of the following accounts:
   • if you have a university computer ID  →  go to https://syzygy.ca, under Launch select your institution, then log in with your university credentials
   • if you have a Google account  →  go to https://syzygy.ca, under Launch select either Cybera or PIMS, then log in with your Google account
   • if you have a GitHub account  →  go to https://westgrid.syzygy.ca, sign in with your GitHub account

In either case start a new Python 3 notebook.

Finally, the 3rd option for more advanced users, if you have Python + Jupyter installed locally on your computer, and you know what you are doing, you can start a Jupyter notebook locally from your shell by typing jupyter notebook. If running locally, for this workshop you will need the following Python packages installed on your computer: numpy, matplotlib, pandas, scikit-image, xarray, nc-time-axis, cartopy, netcdf4.

Jupyter interface at uu.c3.ca

• File | Save As to rename your notebook
• File | New Launcher to open a new launcher dashboard, e.g. to start a terminal
• File | Logout to terminate your job (everything is running inside a Slurm job!)

Navigating notebook cells

Explain: tab completion, annotating code, displaying figures inside the notebook.

• Esc - leave the cell (border becomes blue) to the control mode
• “A” - insert a cell above the current cell
• “B” - insert a cell below the current cell
• “X” - delete the current cell
• “M” - turn the current cell into the markdown cell
• “H” - to display help
• Enter - re-enter the cell (border becomes green) from the control mode
• can enter Latex equations in a markdown cell, e.g. $int_0^\infty f(x)dx$

print(1/2)   # to run all commands in the cell, either use the Run button, or press shift+return