Documentation for Paul's Dotfiles

If you are using @pgierz's dotfiles, this guide provides some useful features.

Using the analysis_toolbox

The HPC and Data Processing Group periodically provides a pre-configured module with various scientific Python and R packages and libraries pre-installed. The advantages of this are:

• You, as a user, don't need to install and maintain your own conda environment
• Conda environments typically contain many files which is not good for the performance of distributed storage systems, such as the one from Albedo. By offering a global environment to the users that covers most of the packages used we hope to reduce the number of private conda environments existing in our system.

Basic Usage

You can access this package using the standard module load command:

$ module avail analysis_toolbox
$ module load analysis_toolbox/01.2024

You can inspect which packages are available via:

$ mamba list -p /albedo/soft/sw/conda-sw/analysis-toolbox/01.2024  # Alternatively `conda list`

Branching Off

It might be that our pre-configured toolbox does not contain all of the tools you might need. To that end, it is possible to build on top and add your own packages:. There are two possibilities.

1. Cloning the environment: Using this method, you create your own local copy of the toolbox and use it as a starting point. Here is how it can be done:

   $ mamba create --name <MY_ENV> --clone /albedo/soft/sw/conda-sw/analysis-toolbox/01.2024
   

2. Stacking Environments: In this case you still build on top of the original environment, but only install new binaries. You can keep the $PATH of the initial environment. Examples are provided in greater detail here, but effectively you need:

   $ conda activate --stack <MY_ENV>