Setting up Python and JupyterLab

Setting up JupyterLab

Overview

Teaching: 0 min
Exercises: 0 min
Questions

  • What is JupyterLab?

  • How do I setup JupyterLab on COLA computers?

Objectives

  • Explain what JupyterLab is and why we are using it

  • Explain how to setup JupyterLab on COLA servers

  • Explain what you can do with JupyterLab

Why do we need to setup another program?

We have been using the Unix command line to type and execute our Python commands. This is not a nice interface for working, especially as our codes get larger. We will use a browser-based interface called JupyterLab or Jupyter notebook. Jupyter notebooks are also ideal for scientific research because they make it easy to document our work, include equations in our documentation, show our analysis results, and link to other resources like journal articles. Let’s set it up and see what it can do!

Setup JupyterLab on COLA Computers

1. Login to a COLA computer (X refers to the computer number)

$ ssh -Y -l YOURUSERNAME colaX.gmu.edu

2. Load the anaconda module

$ module load anaconda/3

3. Setup a password for Jupyter. This will be different from your COLA or Mason passwords.

$ jupyter notebook --generate-config
$ jupyter notebook password

4. Start the Jupyter server with the following command

$ jupyter lab --no-browser --ip=`hostname` --port=8878

5. In a separate XQuartz or MobusXterm window, log into cola6 again with the following command

$ ssh -N -L 8878:colaX.gmu.edu:8878 YOURUSERNAME@colaX.gmu.edu

Nothing will happen after you type your password

6. Open a web browser and go to http://localhost:8878. It will ask you to enter the password you created in step 1.

Jupyter will appear in your local browser

What can go wrong here?

There are various errors that can happen that will not allow the Jupyter to launch properly:

Traceback (most recent call last): File “/homes/sknapp4/.conda/envs/aoes/lib/python3.6/site-packages/traitlets/traitlets.py”, line 528, in get value = obj._trait_values[self.name] KeyError: ‘allow_remote_access’

Solution: Try launching Jupyter with the following command

$ jupyter lab –no-browser –ip=’0.0.0.0’ –port=8878

If you get an Invalid Credentials error, check the messages on the screen where you launched jupyter lab Sometimes port 8878 is in use and it will find a different port. The error messages will tell you which port you should use.

These errors messages look like:

jupyter lab –no-browser –ip=`hostname` –port=8878 [I 14:12:20.887 LabApp] The port 8878 is already in use, trying another port.

Solution: Repeat step 6 using the reccomended port.

8. In the upper right corner, you will see your current environemnt is Python (aoes).

If it only says Python, click on Python and a menu will appear. Select Python (aoes).

What do I do now that JupyterLab is setup?

Now that you have completed the setup process, you need to execute steps 5,6,and 7 when you want to run JupyterLab.

Test that you can login and launch JupyterLab

Logout of COLA computers. Login again and launch JupyterLab

Key Points

  • JupyterLab is an interactive Python interface that is ideal for scientific work

  • Launching JupyterLab is a multi-step process

  • Launch the server on a COLA computer jupyter lab --no-browser --ip=hostname --port=8878

  • Login to COLA computer with special login line: ssh -N -L 8878:colaX.gmu.edu:8878 YOURUSERNAME@colaX.gmu.edu

  • Open JupyterLab in your web browser: http://localhost:8878