Unity software overview

Ways to install packages

apt package manager

The Ubuntu system package manager apt downloads its packages pre-compiled from the Ubuntu repository. These are in standard locations like /usr/bin so that they are always found in your $PATH. This requires administrator access. To avoid conflicts, most software is only available in one version. As a rule, we only install basic support packages this way, not research software.

Environment modules

There are a wide variety of modules available with the module command. Most software requests can be found this way. The admins usually compile and install software in /modules/apps/ or in /modules/spack/packages/.

Relevant documentation:

• Introduction to environment modules
• How to use environment modules

Conda environments

The conda package manager allows users to compile software easily and without administrator privileges. Conda creates environments for a set of compatible software, and you can activate the environments as needed.

Relevant Documentation:

• Conda environments

Virtual environments in Python

The venv module in Python creates a light virtual environment that allows users to isolate specific versions of the Python interpreter and software libraries for their projects. It comes with the standard library of Python and does not require a separate installation. Venv is ideal for project-based workflows.

Relevant documentation:

• Virtual environments in python

R package management

Generally you can use R’s native install.packages() and it should work as intended. However, if you have external dependencies, using them with our standard modules r-rocker-ml-verse/*-apptainer may run into issues. You can build a container for it, using a recipe like this:

Bootstrap: docker
From: rocker/ml-verse:{{ R_VERSION }}

%arguments
    R_VERSION=4.4.0

%post
    apt-get -y update
    apt-get -y install jags

    # Install R packages
    Rscript -e 'install.packages("pak")'
    Rscript -e 'pak::pak(c("rjags", "jagsUI", "coda", "EnvStats", "sads"))'

And then build the container giving a destination image name (.sif) and the preceding definition file:

apptainer build --ignore-fakeroot-command my-r.sif my-r.def

Relevant Documentation:

• R

Containers: Docker, Singularity, and Apptainer

While Docker is not supported in an HPC environment, Apptainer provides nearly equivalent capability. It’s possible to pull an existing Docker image into a local Apptainer image file like this:

apptainer pull docker://ollama/ollama

If you need to install your own set of software, you can create and build your own container as show preceding in R Package Management