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.

In general Mamba and conda environments cannot be used together with any of our preinstalled software modules that depend on Python.

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

• In case you want to use the base environment, you can reactivate it using:

mamba activate base

In case you did not let Mamba change your login scripts during the installation, manual activation of the initial mamba/conda environment can be achieved using the following commands:

. ~/miniforge3/etc/profile.d/conda.sh
. ~/miniforge3/etc/profile.d/mamba.sh

Note that you have to run these every time you want to use Mamba.

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 the previous step, to have mamba available on login, using:

 
~/miniforge3/bin/mamba init