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Setting up a mamba environment

Prerequisite

  • you are on a login node (not gateway, use ssh htc-login)
  • System Environment set up (see initialise)

Setup new environment

You don't need to follow this instructions for setting up the MNE environment. For this you can see Setting up MNE Python.

You have to use a compute node to setup new environments or install new packages in an existing environment. ALWAYS !.

 srun --mem=16G --time="04:00:00" --pty bash

In the next step, we actually create the environment and install some packages:

# if you used setup_sysenv.sh you can use NOG_ENV_DIR
# if not you must specify it first (the directory where your environments go)
module load Mamba/23.11.0-0
mamba create -p "${NOG_ENV_DIR}/env_name" python=3.12 -y # choose whatever name / python version. The -y tells the command to skip asking for confirmation
source activate "${NOG_ENV_DIR}/env_name" # DO NOT USE mamba activate or conda activate !!!


mamba install -c conda-forge matplotlib numpy pandas # you name it
conda deactivate

Often times conda is not 100% up to date with packages. So if installing packages via mamba fails, consider using pip. Or use pip for everything Python and mamba for non-Python things (e.g. ffmpeg).

We can check that everything works by activating the environment. Check that the Python version is correct and also attempt loading a package you've installed:

source activate "${NOG_ENV_DIR}/env_name"
python

and in the python shell:

import numpy as np
# exit()

If none of the above throw an error and the Python version is correct you're good to go. Also don't forget to conda deactivate.