Using Python software on ARCHIE (Rocky 9.6 Linux, September 2025)

Anaconda

Following the November 2025 upgrade we are no longer using Anaconda to make python and associated environments available. This is due to recent changes in the Anaconda license.

Miniforge will now be used for this purpose in conjunction with the conda-forge channel.

It is possible that some python environments that have been created previously may continue to work, but it may be advisable to create new environments from scratch.

Miniforge

Miniforge ia a community maintained (conda-forge) minimalistic conda installer which we now use to deliver python based software. Loading the miniforge module provides access to python-3.12.10 along with a minimal set of packages (and their dependencies), including:

  JupyterLab 4.4.5
  keras 3.11.2
  matplotlib 3.10.8
  mpi4py 4.1.0
  numpy 2.3.2
  pandas 2.3.2
  scipy 1.16.1
  spyder 6.0.8
  Tensorflow(-gpu)  2.18.0
  torchvision 0.21.0
  PyTorch 2.6.0

All other additional python packages should be installed by the user in their own file space. It is recommended to create python environments for this purpose.

Loading the Minforge module

 module load miniforge/python-3.12.10/25.3.0

Mamba v Conda

Conda is an open source package manager used by Anaconda and other platforms. However, in recent years Mamba has been gaining in popularity as an alternative. Mamba is a C++ based drop-in replacement for the conda package manager and is reputedly faster, particularly when installing packages. The mamba command will be used in all examples below, however, if you encounter problems you can simply swap the conda command in place of mamba, with the same arguments.

Listing installed packages

You should be able to use mamba or conda to list installed packages.

 mamba list

Python environments

To install additional packages, it is advisable to do this using python environments. This allows the creation of separate environments, each containing their own files, packages, and package dependencies.

An environment can be created with a command like:

 mamba create --name mamba-test

Once created, it must be activated before packages can be installed and/or used:

 mamba activate mamba-test

To exit the environment and return to the default use

 mamba deactivate

Installing packages

To install packages from the default conda-forge channel e.g. mpi4py

 mamba install mpi4py

To install from a different channel e.g. bioconda

mamba install --channel bioconda mpi4py

Removing packages

 mamba remove mpi4py

Removing environments (and their contents)

mamba env remove --name mamba-test

This will not remove any of the packages installed as part of the base environment made available via the miniforge module.

Summary of commands

For a summary of conda (and by extension mamba) commands, see the conda cheat sheet. In most cases "conda" can simply be replaced by "mamba".

Troubleshooting

When installing packages, you may see the following warning:

warning  libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.    
warning  libmamba Please make sure you understand Anaconda Terms of Services.    
warning  libmamba See: https://legal.anaconda.com/policies/en/

This is due to the presence of the "defaults" channel entry in your .condarc file. To prevent this from happening, edit $HOME/.condarc and remove the defaults entry:

channels:
  - bioconda
  - conda-forge
  - defaults     <-- remove
  - r

so that it becomes:

channels:
  - bioconda
  - conda-forge
  - r