How to upgrade existing Python packages

To upgrade existing packages in the container, you will need to get an interactive session on a GPU node.

srun --time=01:00:00 --nodes=1 --cpus-per-task=4 --partition=gpu --gres=gpu:1 --pty /usr/bin/bash

Load the version of the ml-gpu module you want to use. For example:

module load ml-gpu/20220603

Next, create a directory to install the upgraded packages to. This should be within your group's /work directory, and specific to the version of the ml-gpu container that you're using.

ml-gpu python -m venv --system-site-packages /work/LAS/your-lab/mlgpuvenv-20220603

Now you can upgrade the packages with pip.

ml-gpu /work/LAS/your-lab/mlgpuvenv-20220603/bin/pip3 install --upgrade somepackage

To confirm the packages are upgraded:

ml-gpu /work/LAS/your-lab/mlgpuvenv-20220603/bin/pip3 freeze | grep somepackage

Your upgraded package is now installed.

To use these upgraded packages in your batch scripts, load the ml-gpu module, then invoke python like this:

ml-gpu /work/LAS/your-lab/mlgpuvenv-20220603/bin/python

Be sure to replace the path with the actual location you installed the packages.


PyTorch is already included in the container. If you decide to install a different version, it likely will not work with newer GPU cards unless you follow the instructions on the PyTorch website, and adapt them to install it to your virtual environment. Also be sure to use the CUDA version that's listed on the pre-installed software page. E.g.

torch installation options

To install this to your virtual environment, you would do the following:

ml-gpu /work/LAS/your-lab/mlgpuvenv-20220603/bin/pip3 install  --upgrade torch torchvision torchaudio --extra-index-url