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Anaconda

Description

Anaconda provides Python and a long list of packages as well as Jupyter and environment and package manager conda and pip.

Anaconda brings a long list of Python packages. You can list them using

conda list

Availability

On our systems we provide Anaconda3, which gets update regularly.

Usage

module load Anaconda3

Additional Packages

to install additional packages please see Additional Packages

Jupyter

For Jupyter information please see JupyterLab

Managing Virtual Environments, Versions with Anaconda

Anaconda is a high performance distribution of Python that includes the most popular packages for data science (numpy, scipy,…). It also features conda, a package, dependency and environment manager. With Anaconda you can run multiple versions of Python in isolated environments.

conda

when using conda the system may complain about:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
    $ conda init <SHELL_NAME>
Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.

Please do not run conda init. This would add hard coded environment changes in your $HOME/.bashrc. Instead initialise the conda environment using:

module load Anaconda3
eval "$(conda shell.bash hook)"
This should also be used in your batch submission scripts when working with conda environments.

conda environments

By default conda environments are located into the $HOME/.conda directory. This can be changed using $CONDA_ENVS_PATH. This variable is set in the Workspace module. Which enables you to share conda environments.

Move / Migration of conda environments

If conda environments need to be transfered on the system, e.g. from $HOME to $WORKSPACE you can use the conda pack (see official conda pack documentation).

If your environment is already moved file system locations, you can recreate a new environment with the specification of the old environment. Therefore, we specify the location of the old environment, load the Anaconda module, initialize conda, and get the specification of the old environment. Then importantly unset the CONDA_ENVS_PATH to install the new conda environment in the default location and create it.

export CONDA_ENVS_PATH=${HOME}/anaconda3/envs ## or where you had your old envs
module load Anaconda3
eval "$(conda shell.bash hook)"
conda info --envs
conda activate oldEnvName     ## choose your old environment name
conda list --explicit > spec-list.txt
unset CONDA_ENVS_PATH
conda create --name myEnvName --file spec-list.txt  # select a name