Working with Conda/Miniconda/Anaconda

Conda is an open source environment and package manager. Miniconda is a free installer for Conda, Python, and a few other useful packages. Anaconda is also a package manager that has a much larger number of packages that you can install. A question that frequently comes up is “Should I use Anaconda or Miniconda?” The Conda documentation site has a topic that can help you to decide which package manager to use: https://docs.conda.io/projects/conda/en/latest/user-guide/install/download.html#anaconda-or-miniconda.

Creating a Conda virtual environment with Anaconda

Using a locally installed Conda virtual environment is highly recommended so that you can install the specific packages that you need. You can also have more than one environment with different packages for testing purposes. This procedure uses the Anaconda module already loaded on Discovery.

  1. To check what version of Python you have installed, type which python.
  2. To load anaconda, type module load anaconda3/3.7.
  3. To create your environment, type conda create -n <yourenvironmentname> python=3.7 anaconda, where <yourenvironmentname> is the name you want to give your environment. Tip: to see a list of all of your conda environments, type conda info -e.
  4. Follow the prompts to complete the Conda install.
  5. To activate your Conda environment, type source activate <yourenvironmentname>. Note that conda activate will not work on Discovery with this version.
  6. To install a specific package, type conda install -n <yourenvironmentname> [package].
  7. To deactivate the current, active Conda environment, type conda deactivate.
  8. To delete a Conda environment and all of its related packages, type conda remove -n <yourenvironmentname> --all.

Working with a Miniconda environment

This procedure assumes that you have not installed Miniconda previously. If you need to update Miniconda, don’t use the installation procedure. Use the conda update command. This procedure uses the Miniconda3 version with Python version 3.8 in step 2, although there are other versions you can install, such as Miniconda3 with Python 3.7.

To install Miniconda:

  1. If you are on a login node, move to a compute node by typing srun --partition=short --nodes=1 --cpus-per-task=1 --pty /bin/bash.
  2. Type wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh to get the latest version of Miniconda.
  3. Type sha256sum Miniconda3-latest-Linux-x86_64.sh to check the hash key of the package.
  4. Type bash Miniconda3-latest-Linux-x86_64.sh to start the installation.
  5. Press Enter to review the license agreement.
  6. Type yes to agree to the license agreement.
  7. Press Enter to accept the default installation location (your /home directory, e.g. /home/<yourusername>/miniconda3).
  8. Type yes if asked to initialize Miniconda using conda init.
  9. Type source miniconda3/bin/activate to activate the miniconda environment.

After installing and activating Miniconda, you can create a Conda environment. In the example below, the Conda envinronment is named “my-python38environment” and installs Python version 3.8.

  1. After completing steps 1 through 9 in the previous procedure, type conda create --name my-python38environment python=3.8.
  2. Type y if asked to proceed with the installation.
  3. Type conda activate my-python38environment to activate the environment.

To deactivate the environment, type conda deactivate. You can type this command again to deactivate the Miniconda environment.