Working with ipython notebooks

What does this mean?

There are many python distributions, many python versions (2.7.xx, 3.nn) and… many ways to use python:

interactively or by running a script (or running a script and then typing interactive commands)

using python in a Linux terminal, the Spyder GUI (Graphical User Interface) a Windows cmd terminal or powershell, a Mac terminal, or whatever GUI the distribution you have installed on Windows or Mac provides

using the default python interpreter or the ipython interpreter

> python
Python 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> "python interpreter in a terminal".upper()
'PYTHON INTERPRETER IN A TERMINAL'
>>>
> ipython
Python 3.6.7 | packaged by conda-forge | (default, Feb 28 2019, 09:07:38)
Type 'copyright', 'credits' or 'license' for more information
IPython 7.3.0 -- An enhanced Interactive Python. Type '?' for help.
In [1]: "ipython interpreter in a terminal".upper()
Out[1]: 'IPYTHON INTERPRETER IN A TERMINAL'
In [2]:
Do you really want to exit ([y]/n)? y

using ipython notebooks

Using an ipython notebook means that:

you will use an ipython interpreter

in a web browser (rather than a terminal)

a notebook is the content of the web page where you have interacted with python. You can save it (.ppynb file) and share it, and it will display both the commands you have used and the output/results of your command

How does it work?

Using an ipython notebooks implies the following steps:

determine if you will use python on your local computer or a remote computer and go to that computer

the selected computer mostly depends on the data you need to work with. The idea is to move the computation (i.e. python) near the data, and not move/replicate the data

choose/initialize the distribution and version of python you need to use on the selected computer

e.g. you can use the CDAT distribution on the LSCE servers

start the ipython notebook server with the appropriate parameters (on the selected computer, with the selected python)

this will start a temporary web server that you can connect to, in order to use the notebooks

the server will display the URL that you have to use. The URL has an authentication token and only you (or the person who has a copy of the full URL) can connect to your server

the basic way to start a server is to just type jupyter notebook, but only do this if you want to work locally on your desktop/laptop! See the next section for working on a remote computer

the jupyter notebook command will start the notebook server, and it will automatically start a web browser on the same computer. That's OK on your local computer, but on a remote server, the browser will probably seem to be slow (and out of date) and will use unnecessary resources of the server. This will be frustrating for you and the other users of the server

if you have to work on a remote computer, the idea is to start the ipython server on the remote computer and use a web browser on your local computer (thanks to an ssh tunnel)

in a web browser, open the temporary URL displayed by the ipython server and start using the ipython notebooks

when you are finished, do not forget to kill the ipython server by typing ^C^C (2x CTRL-C). Otherwise the server and the python processes started by the server will keep on using resources on the computer

Warning! Closing the browser, or using the Logout button in the browser will not stop the ipython server

Working correctly with the notebooks

Reminder

Make sure you read and understand the How does it work? section above

If you have a python installed on your own desktop/laptop, you can just start a local notebook server and browser with
jupyter notebook

On a remote and shared server, only start the notebook server and use a local browser to connect to the notebook server through an ssh tunnel

Prerequisites

Digging ssh tunnels

The ssh tunnels will allow you to connect a web browser running locally on your computer to a notebook server running on a remote server

From a local LSCE computer to obelix

plink -L 7225:localhost:7225 jypeter@obelix
plink -L 7225:localhost:7225 jypeter@obelix
ssh -X -t -L7100:localhost:7100 jypeter@ssh1.lsce.ipsl.fr ssh -L7100:localhost:7100 obelix
plink -X -t -L7100:localhost:7100 jypeter@ssh1.lsce.ipsl.fr ssh -L7100:localhost:7100 obelix
plink -ssh -X -t -L 7100:localhost:7100 jypeter@ssh1.lsce.ipsl.fr ssh -L7100:localhost:7100 obelix
plink -X -t -L 7100:localhost:7100 jypeter@ssh1.lsce.ipsl.fr ssh -L7100:localhost:7100 obelix
ssh -X -t -L 7100:localhost:7100 jypeter@ssh1.lsce.ipsl.fr ssh -L 7100:localhost:7100 obelix
(cdatm_py3) jypeter@obelix3 - ...jypeter - 44 >jupyter notebook --no-browser --port=7100
[I 23:37:26.017 NotebookApp] [nb_conda_kernels] enabled, 14 kernels found
[I 23:37:26.977 NotebookApp] [nb_conda] enabled
[I 23:37:26.978 NotebookApp] Serving notebooks from local directory: /home/users/jypeter
[I 23:37:26.978 NotebookApp] The Jupyter Notebook is running at:
[I 23:37:26.978 NotebookApp] http://localhost:7100/?token=256f8fa26c8478f136720e0c0c24c4995b6682d9febf6387
[I 23:37:26.978 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 23:37:26.992 NotebookApp]
To access the notebook, open this file in a browser:
file:///home/users/jypeter/.local/share/jupyter/runtime/nbserver-1442-open.html
Or copy and paste one of these URLs:
http://localhost:7100/?token=256f8fa26c8478f136720e0c0c24c4995b6682d9febf6387

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