Using Conda#

Conda is an open source environment and package manager. Miniconda is a free installer for Conda, Python, and comes with a few other packages. Anaconda is also a package manager that has a much larger number of packages pre-installed.

A question that frequently comes up is “Should I use Anaconda or Miniconda?”

Note

It is not recommended to build your Miniconda and Conda virtual environments inside your /home directory due to its limited space quota (see Storage Accessible on Discovery). Use the /work file system instead. If your group needs access to /work, the group PI can request it using: New Storage Space request.

Creating an Environment#

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 different research projects or for testing purposes. This procedure uses the Anaconda module already available on Discovery.

If you are on a login node, move to a compute node by typing:

Requesting 1 node with 1 cpu core and load anaconda.#

srun --partition=short --nodes=1 --cpus-per-task=1 --pty /bin/bash
module load anaconda3/2022.05

To create a new Conda environment where <environment-name> is the path and name. You can see a list of your existing environments with conda env list.

conda create --prefix=/<path>/<environment-name> python=3.11 anaconda

Follow the prompts to complete the Conda install, then activate the environment.

source activate /<path>/<environment-name>

Your command line prompt will then include the path and name of environment.

(/<path>/<environment-name>) [username@c2001 dirname]$

Tip

conda config --set env_prompt '({name}) ' modifies your .condarc to only show the environments name as such:

(<environment-name>) [username@c2000 dirname]$

With your Conda environment activated you can install a specific package with

conda install [packagename]

To deactivate the current active Conda environment

conda deactivate

To delete a Conda environment and all of its related packages, run:

conda remove -n yourenvironmentname --all

Using Miniconda#

This procedure assumes that you have not installed Miniconda. If you need to update Miniconda, do not follow the installation procedure. Use conda update. This procedure uses the Miniconda3 version with Python version 3.8 in step 2, although there are other versions you can install (e.g., 3.9 or 3.11).

Installing Miniconda#

Attention

Make sure to log on to a compute node.

srun --partition=short --nodes=1 --cpus-per-task=1 --pty /bin/bash

Download Miniconda, check the hash key, and install as follows:

wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sha256sum Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p <dir>

Where <dir> is the full path to your desired installation directory (e.g., /work/mygroup/mydirectory/miniconda3).

Activate the base Miniconda environment

source <dir>/bin/activate

You can now create a new environment with this command where we’re using python version 3.8:

conda create --name my-py38env python=3.8

Type y if asked to proceed with the installation.

Now you can activate your new environment

conda activate my-py38env

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

Using Conda

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