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Conda on Phoebe and Koios

On Phoebe, conda comes from the Miniforge3 module in the system stack, on the login node and on all compute nodes. Use this module rather than installing your own Miniforge or Anaconda. Koios has no Miniforge3 module: install Miniforge3 into your home directory instead (see on Koios). Neither cluster has a system-wide conda installation (/etc/profile.d/conda.sh does not exist).

On Phoebe

Load the Miniforge3 module and initialise conda for the current shell:

module load Miniforge3
source ${EBROOTMINIFORGE3}/etc/profile.d/conda.sh

This does not modify your ~/.bashrc, so conda is only active in this shell. Use the same two lines at the start of batch job scripts.

Three versions are installed: Miniforge3/24.7.1-2, 25.3.1-0 and 26.3.2-3. Without a version, module load Miniforge3 picks the newest. Name a version in job scripts, for example module load Miniforge3/26.3.2-3, so that a new default doesn't change your environment.

On Koios

Download the Miniforge3 installer and install it into your home directory, without changing ~/.bashrc:

wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
bash Miniforge3-Linux-x86_64.sh -b -p $HOME/miniforge3

Activate it in each shell and at the start of batch job scripts:

source $HOME/miniforge3/etc/profile.d/conda.sh

The rest of this page works the same, with this line in place of the two Phoebe lines.

Create and use an environment

conda create --name myenv python=3.12
conda activate myenv

With the Phoebe module, the defaults work without a ~/.condarc:

  • Environments go to ~/.conda/envs, so they are available on all compute nodes.
  • Downloaded packages are cached in ~/.conda/pkgs.
  • The module's own base environment is on CVMFS and read only: create your own environment instead of installing packages into base.

On Koios, environments and the package cache are in ~/miniforge3/envs and ~/miniforge3/pkgs.

A small Python environment takes about 250 MB, and the package cache grows with every environment you create. Home directories have no quota, but the storage is shared (see storage), so remove environments you no longer use and clean the cache from time to time:

conda env remove --name myenv
conda clean --all

To share one environment with your project group, create it in the project directory with --prefix and activate it by path:

conda create --prefix /mnt/proj/pNNN_name/envs/myenv python=3.12
conda activate /mnt/proj/pNNN_name/envs/myenv

In a batch job

On Phoebe:

#!/bin/bash
#SBATCH --job-name=conda-example
#SBATCH --partition=cpu
#SBATCH --ntasks=1

module load Miniforge3
source ${EBROOTMINIFORGE3}/etc/profile.d/conda.sh
conda activate myenv

python my_script.py

On Koios, replace the module load and first source line with source $HOME/miniforge3/etc/profile.d/conda.sh.

Guides that use conda