Creating an environment using Mamba on LANTA-HPC

Owned by Yutthana Wongnongwa
Last updated: Mar 29, 2024
5 min read

This article will guide you to create the environment using Miniconda on a LANTA HPC system. An overview of the content can be found in the table of contents below for immediate visualization of the interesting parts.

Using Mamba on LANTA HPC

Load Mamba module

  1. Use the ml av Mamba command to see which version of Mamba is available on the LANTA HPC system.

  2. Use the ml Mamba/xx.xx.x command to load the Mamba version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Mamba/23.11.0-0.

username@lanta:~> ml av Mamba ---------------------- /lustrefs/disk/modules/easybuild/modules/all ----------------------- Mamba/23.11.0-0 (D) Use "module spider" to find all possible modules and extensions. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys". username@lanta:~> ml Mamba/23.11.0-0

Unload Mamba module

Use the module unload Mamba command to unload the Mamba.

username@lanta:~> module unload Mamba

Use the module purge command to unload all currently loaded modules.

username@lanta:~> module purge

Before you use the module unload Mamba or module purge command, you must deactivate your environment with the conda deactivate command.

Activate your environment

  1. Use the conda env list command to view a list of your environments.

  2. If you want to activate your environment such as TensorFlow-2.6.0, you can use the conda activate tensorflow-2.12.1 command.

Deactivate your environment

Use the conda deactivate command to deactivate your environments.

Creating the environment in the user’s home

Create the environment

Use the conda create -n myenv commands to create the environment with myenv name.

Create the environment with a specific version of the packages

Use the conda create -n myenv python=3.9 commands to create the myenv environment with a specific version of python.

Use the conda create -n myenv python=3.9 numpy=1.23.5 commands to create the myenv environment with a specific version of python and numpy.

Creating the environment in the project’s home

Specify a location for the environment

Use the conda create --prefix /your project directory/envs commands to create the environment on the specific location.

Specify a location for the environment with a specific version of a package

Use the conda create --prefix /your project directory/envs python=3.9 commands to create the environment with a specific version of a package on a specific location.

Activate your environment in the project’s home

If you want to activate your environment in the project’s home, you can use the conda activate /your project directory/envs command.

Creating the environment from an requirements.yml file

A simple requirements.yml file

In the requirements.yml file, you need to specify the environment name and packages that you want to use.

Create the environment from the requirements.yml file in the user’s home

Use the conda env create -f requirements.yml commands to create the environment from the requirements.yml file in the user’s home.

Create the environment from the requirements.yml file in the project’s home

Use the conda env create -f requirements.yml --prefix /your project directory/envs commands to create the environment from the requirements.yml file on the specific location.

Removing the environment

Remove the environment in the user’s home

If you want to remove the myenv environment, you can use the conda remove --name myenv --all command.

Remove the environment in the project’s home

If you want to remove the environment in /your project directory/envs, you can use the rm -rf /your project directory/envs command.

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