Python Virtual Environments

Python has a built-in virtual environment, which contains a particular version of python with additional packages/modules that can be activated/deactivated at will. This guide will cover the basics on how to create an environment and install packages on it.

Create a New Virtual Environment

This should be done from an interactive session on a compute node.

To get an interactive session on a compute node, run the following:

srun --time=01:00:00 --nodes=1 --cpus-per-task=8 --partition=interactive --pty /usr/bin/bash

Set Up

To setup a python virtual environment, you will need to load your specific version of python. To find a list of available versions, you can run:

module spider python

Next, I would have to see if there are any prerequesite modules for python.

module spider <version-of-python-here>

For example:

module spider python/3.8.8-ucekvff

The output of this says that the python/3.8.8-ucekvff module requires gcc/10.2.0-zuvaafu . So we must load it first before we can load the python module. 

For example:

module load gcc/10.2.0-zuvaafu
module load python/3.8.8-ucekvff

Before proceeding, ensure that you are in your /work directory and not your /home directory. 

After running your module, create your virtual environment by typing in:

python -m venv <name-of-environment>

This will create a directory that contains the environment.

Activate the Environment

Activate the environment by running:

$ source <name-of-environment>/bin/activate

Your terminal will now look like this:

(<name-of-environment>) [user@bigram2 jones-lab]

Install packages

To search for certain packages, you can type in:

pip search <package-name>

If you wish to install a certain package, you can use:

pip install <package-name>

If you want a certain version of said package, you can give the package name followed by "==" with the version number:

pip install <package-name>==1.0.0

Deactivate the Environment

To get out of the environment simply type:

deactivate

(This will not disconnect you from pronto/the node you are currently on)

Use a Virtual Environment in a Batch Job

# Load the python module. This should be the same version that was used to create the environment
module load gcc/10.2.0-zuvaafu
module load python/3.8.8-ucekvff
# Activate the environment as before. Replace /work/LAS/jones-lab/<name-of-environment> with the actual path to the environment.
source /work/LAS/jones-lab/<name-of-environment>/bin/activate
# Run your script. It will have access to all of the modules you installed in the environment.
python my_script.py

More Information

If you plan on creating more environments, please ensure that you are creating them in /work instead of /home.

For more commands and further documentation, please visit: https://docs.python.org/3/tutorial/venv.html