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.

Here are the installation steps as of December 2024, which is 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 and if you agree say “yes” to the license conditions
• The software will be installed in a `miniforge3` folder in your home directory. Change this if you prefer a different location.
• You can opt for automatic initialization of conda, 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:

conda config --set auto_activate_base false

• 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:

conda init --reverse bash