How to run a Jupyter notebook on deepthought

March 1, 2021

Series: An Introduction To Using DeepThought For Bioinformatics

Most of these instructions come from the official jupyter docs and you should use those as a guide. I have distilled this to the essence, to make it easier to complete on deepthought.

Set up

Before you run jupyter-notebook for the first time, we need to do some set up. If you have done this, you can skip to the next step.

Install jupyter

Before beginning you will need to install the jupyter commands. You need to make sure you have the python module loaded. You should have added this to your ~/.bashrc in a previous lesson. If you get command not found after this, talk to Rob.

pip3 install --user jupyter

Set up the notebook

We start by running the automatic configurator command:

jupyter notebook --generate-config

Make a self-signed certificate

We are going to make a certificate so that we can use encryption on our connection to stop people spying on us.

Use this command to create the certificate.

openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout ~/.jupyter/jupyter.key -out ~/.jupyter/jupyter.pem

It will ask you several questions. I answered like this … but you should put your name and email!

Country Name (2 letter code) [AU]:
State or Province Name (full name) [Some-State]:SA
Locality Name (eg, city) []:Adelaide
Organization Name (eg, company) [Internet Widgits Pty Ltd]:Flinders
Organizational Unit Name (eg, section) []:
Common Name (e.g. server FQDN or YOUR name) []:Rob Edwards
Email Address []:robert.edwards@flinders.edu.au

Edit the configuration file

We need to make some changes to the configuration file to let jupyter know where everything is. Use nano to edit the file:

nano ~/.jupyter/jupyter_notebook_config.py

We want to find the line that looks like #c.NotebookApp.certfile=''. For each of the lines, we are going to use the search command, Ctrl-w (for Where Is?). Press the Ctrl and w keys and the search box will appear at the bottom left of the screen. Type certfile and press return and nano will jump to that line.

You can leave that line as it is.

After that line paste these lines

c.NotebookApp.certfile = '$HOME/.jupyter/jupyter.pem'
c.NotebookApp.keyfile = '$HOME/.jupyter/jupyter.key'
c.NotebookApp.ip = '*'
c.NotebookApp.open_browser = False
c.NotebookApp.port = 8004

Press Ctrl-o to save the file (output) and then Ctrl-x to exit nano.