Finding and Loading Modules

Estimated time: 25 minutes

Overview

Questions

• How do I find specific software on Sagehen HPC?
• How do I load and unload modules?
• How do I learn what a module does before loading it?
• What if I need software that isn’t available?

Objectives

• Use module avail with search patterns to find software
• Load and unload modules with module load and module unload
• Use module help and module show to inspect modules
• Know what to do if software isn’t available

Searching for Software

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On a cluster with hundreds of modules, finding specific software efficiently is essential.

Built-in filtering

Lmod can filter the listing itself – pass a search string to module avail:

BASH

$ module avail r

The match is a substring match against the whole module name and version, so a single letter matches far too much – on Sagehen this returns not just r/4.5.1 but also ansys/2023r1, apptainer, fmriprep, rstudio-server, rust, trimmomatic, and dozens more, all because they contain an “r” somewhere. Use a longer, more specific string:

BASH

$ module avail rstudio
$ module avail conda
$ module avail gaussian

module avail conda is a good example of why searching matters: it finds both anaconda3 and miniconda3. There is no standalone python module on Sagehen – searching for python finds nothing, because Python is provided inside the conda distributions. When a direct name search comes up empty, think about what the software might ship inside.

Deeper searches: spider and keyword

BASH

$ module spider gaussian     # every version of a module, plus how to load it
$ module keyword chemistry   # searches module descriptions, not just names

module spider knows about every module and version on the system, and module keyword searches the descriptive text – useful when you don’t know the package’s exact name.

Check for a module before you reach for conda, and ask before you compile.

Callout

Why not just pipe to grep?

You’ll see module avail -t | grep name suggested online, but on Sagehen it returns nothing: Lmod prints the listing to standard error rather than standard output, and this Lmod version treats a trailing -t as a search pattern rather than a flag (hence the confusing No module(s) or extension(s) found!). If you want a grep pipeline, the options must come before the subcommand and stderr must be redirected:

BASH

$ module -t avail 2>&1 | grep -i conda

The built-in filters above are simpler and always work – prefer them.

Loading and Unloading Modules

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Your first module load

BASH

$ module load miniconda3

Now check what modules you have loaded:

BASH

$ module list
Currently Loaded Modules:
  1) miniconda3/py313_26.3.2-2

To see what this module actually changed:

BASH

$ which python
/opt/.../miniconda3/py313_26.3.2-2/bin/python

Unloading modules

When you’re done with software, unload it:

BASH

$ module unload miniconda3
$ which python
/usr/bin/python

python now refers to the system Python (if it exists) or isn’t available.

Callout

Key Commands Summary

Command	Purpose
module avail	List all available modules
module load <name>	Load a module
module list	Show currently loaded modules
module unload <name>	Unload a module
which <program>	Show the full path to a program

Learning What a Module Does

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Callout

Check Before You Load

Always use module help before loading an unfamiliar module. This prevents surprises and shows you what dependencies will be automatically loaded.

Using module help

BASH

$ module help r

This prints whatever help text the module’s packager provided – typically a short description of the software, the version, and any usage notes. The amount of detail varies from module to module.

Understanding module dependencies

Some modules automatically load other modules they depend on (for example, an MPI library or a maths library). When that happens, module list after a single module load will show more than one loaded module. That is normal – unloading the module you asked for also removes what it pulled in.

Using module show

To see exactly what a module does to your environment:

BASH

$ module show r/4.5.1

Output (simplified):

prepend_path("PATH","/opt/.../r/4.5.1/bin")
setenv("R_HOME","/opt/.../r/4.5.1")

The prepend_path line is the heart of it: loading the module puts that version’s bin directory at the front of your PATH.

When Software Isn’t Available

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If you can’t find the software you need:

1. Double-check your search with module avail name and module spider name
2. Check the Sagehen documentation for software inventory
3. Request installation by emailing its-hpc@pomona.edu with:
   • Software name and version
   • Research purpose
   • License information (open-source, commercial, etc.)
   • Links to documentation

Challenge

Challenge 1: Load, Check, and Unload

1. Load the go module (the default version)
2. Use module list to confirm it’s loaded
3. Use which go to find its location
4. Unload it
5. Try which go again; notice the difference

BASH

$ module load go
$ module list
$ which go
$ module unload go
$ which go

Show me the solution

BASH

$ module load go
$ module list
Currently Loaded Modules:
  1) go/1.23.1

$ which go
/opt/.../go/1.23.1/bin/go

$ module unload go
$ which go
/usr/bin/which: no go in (...)

The key insight: after unloading, the command is gone from your PATH – you fall back to a system-wide copy if one exists, or to nothing at all.

Challenge

Challenge 2: Understand Module Dependencies

1. Check which modules are currently loaded
2. Load the R module
3. Check again: what was automatically loaded?
4. Unload only R (not its dependencies)

BASH

$ module list
$ module load r
$ module list
$ module unload r
$ module list

Show me the solution

After module load r:

Currently Loaded Modules:
  1) r/4.5.1

After module unload r:

No modules loaded

If a module pulls in dependencies when it loads, those dependencies can remain loaded after you unload it – Lmod treats them cautiously because other loaded modules might also rely on them. If module list still shows leftovers you don’t need, unload them explicitly, or use module purge to clear everything.

Key Points

• Use module avail with search terms or grep to find software
• module load activates software; module unload deactivates it
• Use module help to understand what a module does before loading
• Use module show to see exact environment modifications
• Modules can automatically load prerequisites
• If software isn’t available, contact its-hpc@pomona.edu to request it