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Jupyter

There are multiple IDEs on the UPPMAX clusters, among other Jupyter. Here we describe how to run Jupyter.

Jupyter is an IDE specialized for the Python programming language.

Info

  • You can run Python in a Jupyter-notebook, i.e. in a web interface with possibility of inline figures and debugging.
  • Jupyter-lab is installed in the python>=3.10.8 module

Warning

Always start Jupyter in a ThinLinc session and preferably in an interactive session.

Want to see a video?

If you want to see a video how to start Jupyter on Rackham, go here

Introduction

Jupyter is web application that allows literature programming for Python. That is, Jupyter allows to create documents where Python code is shown and run and its results shown, surrounded by written text (e.g. English).

Additionally, Jupyter allows to share files and hence includes a file manager.

Jupyter is:

  • started and running on a server, for example, an interactive node
  • displayed in a web browser, such as firefox.

Jupyter can be slow when using remote desktop webpage (e.g. https://rackham-gui.uppmax.uu.se).

  • For UPPMAX, one can use a locally installed ThinLinc client to speed up Jupyter. See the UPPMAX documentation on ThinLinc <https://www.uppmax.uu.se/support/user-guides/thinlinc-graphical-connection-guide>_ on how to install the ThinLinc client locally.

  • It is also possible to run Jupyter with a local browser to speed up the graphics but still use the benefits of many CPU:s and much RAM.

  • The Jupyter project <https://jupyter.org/>_ contains a lot of information and inspiration
  • The Jupyter Notebook documentation <https://jupyter-notebook.readthedocs.io/en/stable/>_

Start

Step 1: login to a remote desktop

Login to a remote desktop:

  • Login to the remote desktop website at rackham-gui.uppmax.uu.se
  • Login to your local ThinLinc client

Step 2: start an interactive session

Start a terminal. Within that terminal, start an interactive session from the login node (change to the correct NAISS project ID).

For Rackham

interactive -A <naiss-project-id>  -t 4:00:00

For Snowy

interactive -M snowy -A <naiss-project-id>  -t 4:00:00

Step 3: start Jupyter in the interactive session

Within your terminal with the interactive session, load a modern Python module:

module load python/3.11.8

Then, start jupyter-notebook (or jupyter-lab):

jupyter-notebook --ip 0.0.0.0 --no-browser

Leave this terminal open. Start a notebook like this:

module load python/<version>
jupyter-notebook --ip 0.0.0.0 --no-browser

or jupyter lab:

jupyter-lab --ip 0.0.0.0 --no-browser

  • copy-paste one of the URL addresses from the jupyter output in the terminal into the address files in the open firefox session.

  • Make Jupyter work in background, start Firefox with the copied URL address.

  • <ctrl-z>
  • bg
  • firefox <URL> &
    • Example firefox http://127.0.0.1:8889/tree?token=7c305e62f7dacf65d74a4b966e2851987479ad0a258de33f &

Jupyter in a virtual environment (venv)

You could also use jupyter- (lab or notebook) in a venv virtual environment.

If you decide to use the --system-site-packages configuration you will get jupyter from the python modules you created you virtual environment with. However, you won't find your locally installed packages from that jupyter session. To solve this, reinstall jupyter within the virtual environment by force (option -I):

pip install -I jupyter

and run it as above.

Be sure to start the kernel with the virtual environment name, like "project A", and not "Python 3 (ipykernel)".

Run Jupyter in your local browser