How to start an IPython Notebook session

We now have a number of compute nodes in the Shark cluster which also have a connection to the LUMC internal network (EAS384, helicos01, ...). This means we can start an IPython Notebook session on one of these nodes and connect to it from our desktop machine. We created special notebook.q queue for this.

Starting a session

To start a notebook, just type this from a terminal on Shark:

notebook

You can do this from the head node since a job will be started for you on one of the compute nodes in the notebook.q queue. (It might take a while before your job is scheduled.)

The notebook session will be started from the current directory. For example:

mvermaat1@shark:~/test44$ notebook 
2013-08-26 15:29:07.032 [NotebookApp] Using existing profile dir: u'/home/mvermaat1/.config/ipython/profile_default'
2013-08-26 15:29:07.269 [NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
2013-08-26 15:29:07.302 [NotebookApp] Serving notebooks from local directory: /home/mvermaat1/test44
2013-08-26 15:29:07.302 [NotebookApp] The IPython Notebook is running at: https://helicos01.lumcnet.prod.intern:8888/
2013-08-26 15:29:07.302 [NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

Open the link shown after The IPython Notebook is running at: (in this example https://helicos01.lumcnet.prod.intern:8888/) in your desktop browser and have fun. When you're done, press Ctrl-C to end the session.

Password protection

To prevent anyone on our network from connecting to your session and run arbitrary commands on Shark as your user, the session is protected with a password. The first time you start a notebook session you will be asked to type a password (twice). You can choose any password you like. To reset it, remove the ~/.notebook.password file.

Inline plots

You can use IPython's matplotlib integration to have inline plots in your notebook. Actually, you can only have them inline since there is no X server on Shark to open a plot window.

For now, it's necessary to define a matplotlib backend for this to work in your matplotlibrc file. For me, the Agg backend works:

username@shark:~$ cat ~/.config/matplotlib/matplotlibrc 
backend: Agg

To enable inline plots, run the following in your notebook:

%matplotlib inline

After that, you can plot away:

import matplotlib.pyplot as plt
plt.plot([2,5,2,8,9,5,3])