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This article will guide you to run a python script using Slurm script on a LANTA HPC system.

Using Miniconda via Easybuild

Load Miniconda module

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

  2. Use the ml Miniconda3/xx.xx.x command to load the Miniconda version that you want to use. If you don't specify a version, the default version (D) is loaded, which is Miniconda3/22.11.1-1.

username@lanta:~> ml av Miniconda
---------------------- /lustrefs/disk/modules/easybuild/modules/all -----------------------
   Miniconda3/22.11.1-1

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 Miniconda3/22.11.1-1

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-2.6.0 command.

username@lanta:~> conda env list
# conda environments:
#
base                     /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1
netcdf-py39              /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1/envs/netcdf-py39
pytorch-1.11.0           /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1/envs/pytorch-1.11.0
tensorflow-2.6.0         /lustrefs/disk/modules/easybuild/software/Miniconda3/22.11.1-1/envs/tensorflow-2.6.0
username@lanta:~> conda activate tensorflow-2.6.0
(tensorflow-2.6.0) username@lanta:~>

Creating an environment in the user’s home

Create an environment

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

username@lanta:~> conda create -n myenv
Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /your directory/envs/myenv

Proceed ([y]/n)? y
...
username@lanta:~>

Create an environment with a specific version of the packages

username@lanta:~> conda create -n myenv python=3.9
username@lanta:~> conda create -n myenv python=3.9 scipy=0.17.3

Creating an environment in the project’s home

Specify a location for an environment

username@lanta:~> conda create --prefix /your project directory/envs

Specify a location for an environment with a specific version of the packages

username@lanta:~> conda create --prefix /your project directory/envs python=3.9

Activate your environment in the project’s home

username@lanta:~> conda activate /your project directory/envs

Creating an environment from an environment.yml file

A simple environment.yml file

name: test
dependencies:
  - python=3.9
  - numpy=1.23.1
  - pandas

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

username@lanta:~> conda env create -f environment.yml

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

username@lanta:~> conda env create -f environment.yml --prefix /your project directory/envs

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