Pixi

Pixi is a package management tool for managing software environments and dependencies, similar to tools like Conda. We will use it to set up and manage the software environment needed for this workshop.

1 Installation

To install Pixi on the Arrhenius cluster for you as a user, run the following command from any directory:

curl -fsSL https://pixi.sh/install.sh | sh

This installs Pixi in the .pixi directory in your home directory.

Add the following lines to your ~/.bashrc file to make Pixi available from any new shell session:

export PATH="$HOME/.pixi/bin:$PATH"

Start a new shell, or run source ~/.bashrc, and then verify the installation:

pixi --version

2 Usage

The workshop environment has already been created, so you do not need to build it yourself.

2.1 Interactive usage

To activate the workshop environment in an interactive session, run this command from any directory:

pixi shell --manifest-path /nobackup/proj/disk/naiss2026-4-1504/apps/pixi.toml

This starts a new shell with access to the tools needed for the workshop. Run exit when you are finished to leave the Pixi shell.

2.2 SLURM script usage

To activate the Pixi environment in a SLURM script, add the following lines before any analysis commands:

export PATH="$HOME/.pixi/bin:$PATH"
export PIXI_CACHE_DIR="${TMPDIR:-/tmp}/pixi-cache-$USER"
eval "$(pixi shell-hook --manifest-path /nobackup/proj/disk/naiss2026-4-1504/apps/pixi.toml)"