Python

Last modified:February 06, 2024

Anaconda Python is available in /usr/local.

modules

I recommend using pip to install additional python modules in your home directory. In the examples below, replace <module> with your module name:

pip:

pip install --user <module>

The package will be installed in $HOME/.local.

setup.py:

python setup.py install --prefix=$HOME/.local

Jupyter Notebook

performance

You can improve performance of jupyter notebook by accessing it directly from your Mac’s web browser (e.g. safari). Below are instructions:

1. Start a X2Go remote desktop session. Note the server name that you logged into.

2. In your X2Go session, open a terminal window, and run ‘jupyter notebook’ with the ‘–no-browser’ option:

   jupyter notebook --no-browser

   You will see output similar to the following:

   Copy/paste this URL into your browser when you connect for the first time,

   to login with a token:

   http://localhost:8780/?token=76e3a90efd4159sdfllfaa73e6f8sdf2b6dsdf3cddbc742f

   
   

   The number after the string ‘localhost:’ is called the port number. You will need this port number in the next step.

3. On your Mac, open a terminal window, and run the ‘ssh’ command to create a tunnel from your Mac to your X2Go session. The syntax is:

   ssh -L <port>:localhost:<port> <username>@<servername>neuro.berkeley.edu

   For example, user ‘joe’ logged into nx66.neuro.berkeley.edu via X2Go. His jupyter notebook started on port number 8780, so he ran the following in his Mac terminal:

   ssh -L 8780:localhost:8780 joe@nx66.neuro.berkeley.edu

   The ssh command will prompt you for a password and for your 2-step verification code or ssh key passphase (if you configured a SSH key).

4. Copy and paste the URL displayed above (in step #2) into the web browser on your Mac.