Software Modules Basics

Estimated time: 30 minutes

Overview

Questions

• Why can’t I just use any software on Sagehen HPC?
• What is the module system?
• How do I find, load, and unload software modules?
• What if I need software that’s not installed?

Objectives

• Understand why HPC clusters use module systems
• Search for available software with module avail
• Load and unload modules for your work
• Manage module dependencies and version conflicts
• Know how to request new software installations

Why Modules? The Problem They Solve

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On a personal computer, you install software globally. On a shared cluster with hundreds of researchers, this creates conflicts:

• Alice needs Python 3.8; Bob needs Python 3.11; Charlie needs Python 2.7
• Package A needs Library X version 2.0; Package B needs version 3.0
• Some code compiles best with GCC 9; other code needs GCC 11

A module system allows users to load and unload software dynamically, so multiple versions coexist without conflict.

Lmod: Sagehen HPC’s Module Manager

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Sagehen uses Lmod with 90+ pre-installed modules covering programming languages, compilers, scientific libraries, bioinformatics tools, and more.

Viewing Available Modules

BASH

# List all available modules
module avail

# Search for a specific module
module avail miniconda3

# Show module details without loading
module show miniconda3/py313_26.3.2-2

The real module avail listing on Sagehen HPC — miniconda3’s versions are in the middle column, with (D) marking the default.

Loading and Unloading Modules

BASH

# Load default Python
module load miniconda3

# Load a specific version
module load miniconda3/py313_26.3.2-2

# Load multiple modules at once (check `module avail` for the exact
# names and versions installed on Sagehen)
module load miniconda3/py313_26.3.2-2

# Check what's loaded
module list

# Unload a specific module
module unload miniconda3

# Unload all modules
module purge

What Happens When You Load a Module

Loading a module modifies environment variables (PATH, LD_LIBRARY_PATH, etc.) so the system finds the right software executables and libraries:

BASH

# Before loading python
echo $PATH
# /usr/local/bin:/usr/bin:/bin:...

module load miniconda3/py313_26.3.2-2

# After loading python
echo $PATH
# /opt/linux/rocky/8/software/miniconda3/py313_26.3.2-2/bin:...

{alt=‘A terminal transcript comparing echo PATH before and after module load. After loading miniconda3/py313_26.3.2-2, PATH begins with that module’s bin and condabin directories under /opt/linux/rocky/8/software.’}

Module Families and Conflicts

Some modules belong to the same family. Loading one auto-unloads the other:

BASH

# Loading a second version of the same package auto-swaps it
module load cuda/11.8.0
module load cuda/12.2.1
# Lmod reports the swap: cuda/11.8.0 => cuda/12.2.1

The same applies to Python versions – only one can be active at a time.

Callout

Good Practice: Start Fresh

Always start your job scripts with no modules loaded:

BASH

#!/bin/bash
#SBATCH ...

# Always start fresh
module purge
module load miniconda3/py313_26.3.2-2

python my_analysis.py

This ensures reproducible results regardless of what was loaded interactively.

Requesting New Software

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If you need software that’s not installed:

1. Email its-hpc@pomona.edu with software name, version, use case, and documentation link
2. Include your username and how many people would use it
3. Expected response: within a few business days

Self-Install Alternative

You can install software in your home directory if needed:

BASH

mkdir -p ~/software
cd ~/software
# Download, configure, build with --prefix=~/software/
export PATH=~/software/bin:$PATH

Challenge

Challenge 1: Loading and Switching Modules

Practice loading, switching, and purging modules.

Steps:

1. Load default Python: module load miniconda3

2. Check the version: python --version

3. Switch to a different version:

   BASH

   module unload miniconda3
   module load miniconda3/py312_24.9.2-0
   python --version

4. List loaded modules: module list

5. Purge and reload:

   BASH

   module purge
   module load miniconda3/py313_26.3.2-2
   python --version
   module list

Questions:

• Which version loaded by default?
• What happens after module purge?
• Can you have two Python versions loaded at once?

Show me the solution

• The default module load miniconda3 loads the most recent stable version
• module purge removes all loaded modules; module list shows nothing
• No, loading a second Python version auto-unloads the first (same module family)

This demonstrates Lmod’s ability to manage multiple versions cleanly.

{alt=‘Terminal transcript of an Lmod session. module list shows miniconda3/py313_26.3.2-2 as the only loaded module; after module purge, module list reports no modules loaded; the user then loads miniconda3/py312_24.9.2-0 and echo PATH shows that version’s bin directory first.’}

Key Points

• The module system solves software version conflicts on shared HPC clusters
• Sagehen uses Lmod with 90+ pre-installed packages
• Use module avail to search, module load to activate, module purge to reset
• Only one version of each module family can be loaded at a time
• Always use module purge at the start of job scripts for reproducibility
• Request new software at its-hpc@pomona.edu