Mamba installation

Mamba (https://mamba.readthedocs.io/en/latest/index.html) is an alternative to Anaconda, which is released under an open source license. In order to use it on Hábrók you can install it into your home directory. This can be done following the instructions on their website. There is an important caveat, however, which is that you should NOT let it start up the base environment on log in, as that would break any other Python software on the cluster.

Please also note, that you should only use mamba/conda repositories that have licenses that allow your intended usage.

Here are the installation steps (tested in December 2024), which are based on the instructions on the website, which suggest to use miniforge ( https://github.com/conda-forge/miniforge#install):

• Run the miniforge installer

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

• Check the license conditions, and if you agree say “yes” to these.
• The software will be installed in a miniforge3 folder in your home directory. Change this, if you prefer a different location. Note that the instructions will assume you've opted for a miniforge3 folder in your home directory.
• You can opt for automatic initialization of mamba, but you must disable the automatic activation of the base environment, as otherwise you will get conflicts with a lot of software that we provide on the cluster. Alternatively, you can run an initialization command every time you want to use mamba.
• After logging in again, disable the automatic activation of the base environment using:

mamba config --set auto_activate_base false

• Manual activation of the initial mamba/conda environment can be achieved using the following command, where bash is your actual command line shell:

eval "$( $HOME/miniforge3/bin/conda shell.bash hook)"

• You can activate the base environment using:

mamba activate base

• In order to undo the login profile modifications for mamba you can use the following command, where bash is your actual command line shell:

mamba init --reverse bash

You can reverse this using:

~/miniforge3/bin/mamba init