Software Modules¶

What are Software Modules?¶

High-Performance Computing (HPC) environments host a diverse array of software applications, libraries, and compilers. Managing these efficiently can be challenging due to varying versions, configurations, and dependencies, which can lead to conflicts if not handled properly. For instance, one user might require Python 3.6 for their workflow, while another needs Python 3.12. If both versions were installed in a standard system location (e.g., /usr/bin or /usr/local/bin), they could interfere with each other, causing instability and compatibility issues.

To address this, HPC systems employ a module system. Software packages are installed in non-standard locations, avoiding conflicts with system-wide paths. Instead of modifying global settings, users dynamically manage their software environments using modules. With simple commands, users can load, unload, and switch between different software packages and versions, ensuring a clean and consistent environment tailored to their needs.

How Software Modules Work¶

Software modules are managed using the module command. When you load a module, it sources a lightweight configuration file that dynamically adjusts environment variables, paths, and dependencies, making the correct software version available. Unloading a module reverts these changes, restoring your environment to its previous state.

This approach gives you fine-grained control over your software environment, enabling adjustments without impacting other users or system-wide configurations

Module Availability¶

Software modules are only available on compute nodes and are not accessible on the login nodes.

It’s also important to be aware of differences between the clusters:

Ocelote and El Gato both run CentOS 7 and share the same system libraries and modules. These clusters can generally be used interchangeably.
Puma, however, runs Rocky Linux 9, which has different system libraries and modules than Ocelote and El Gato. As a result, workflows that work on Ocelote or El Gato may not be transferable to Puma without modifications.

Module Commands¶

Default Versions

If multiple versions of software are available on the system, the newest is made the default. This means loading a module without specifying the version will select the most recent. We strongly recommend including version information in your module statements. This ensures that you maintain a consistent environment for your analyses in the event of a software upgrade.

Command	Description
`module avail`	Display all the software and versions installed on the system.
`module avail <search_term>`	Display all installed modules matching `<search_term>`. For example `module avail python`.
`module list`	Display the software you have loaded in your environment.
`module whatis <module_name>`	Displays some descriptive information about a specific module.
`module show <module_name>`	Displays system variables that are set/modified when loading module `<module_name>`. This can be helpful for locating the executables that are provided by the module.
`module load <module_name>`	Load a software module in your environment
`module unload <module_name>`	Unload a specific software package from your environment
`module swap <module_name>/<version1> <module_name>/<version2>`	Switch versions of a software module.
`module purge`	Unload all software modules from your environment
`module help`	Display a help menu for the module command

Examples¶

Loading Modules¶

Loading Python 3.9

[netid@cpu39 ~]$ module avail python

------------------- /opt/ohpc/pub/modulefiles --------------------
   python/3.6/3.6.5     python/3.9/3.9.10
   python/3.8/3.8.2     python/3.11/3.11.4 (D)
   python/3.8/3.8.12
[netid@cpu39 ~]$ module load python/3.9
[netid@cpu39 ~]$ python3 --version
Python 3.9.10
[netid@cpu39 ~]$ module swap python/3.9 python/3.11

The following have been reloaded with a version change:
  1) python/3.9/3.9.10 => python/3.11/3.11.4

[netid@cpu39 ~]$ python3 --version
Python 3.11.4

Finding Executables and Libraries¶

If you're looking for the specific variables that will be modified when loading a module, you can use the command module show. For example:

Environment variables modified by Gromacs module

[netid@cpu38 ~]$ module show gromacs
---------------------------------------------------------
   /opt/ohpc/pub/moduledeps/gnu8-openmpi3/gromacs/2021.5:
---------------------------------------------------------
whatis("Name: gromacs ")
whatis("Version: 2021.5 ")
whatis("Molecular dynamics for biophysical chemistry ")
setenv("GROMACS_BASE","/opt/ohpc/pub/apps/gromacs/2021.5")
prepend_path("PATH","/opt/ohpc/pub/apps/gromacs/2021.5/bin")
prepend_path{"CPPFLAGS","-I/opt/ohpc/pub/apps/gromacs/2021.5/include",delim=" "}
prepend_path("MANPATH","/opt/ohpc/pub/apps/gromacs/2021.5/share/man")
prepend_path("PKG_CONFIG_PATH","/opt/ohpc/pub/apps/gromacs/2021.5/lib64/pkgconfig")
prepend_path{"LDFLAGS","-L/opt/ohpc/pub/apps/gromacs/2021.5/lib64",delim=" "}
prepend_path("LD_LIBRARY_PATH","/opt/ohpc/pub/apps/gromacs/2021.5/lib64")
unload("gnu8")
load("gnu8")
help([[ Adds gromacs to your environment
]])

These paths can help you to determine the locations of the executables, libraries, header files, etc. available to you after loading the software. For example, the environment variable PATH is what allows the system to find executables, so, in the case above, we would look at the line: prepend_path("PATH","/opt/ohpc/pub/apps/gromacs/2021.5/bin") to determine where Gromacs' executables live. We can then search this path to see what they are:

Executables provided by Gromacs

[netid@cpu38 ~]$ ls /opt/ohpc/pub/apps/gromacs/2021.5/bin
gmx_mpi     GMXRC      gmx-completion.bash  gmx-completion-gmx_mpi.bash
GMXRC.bash  GMXRC.csh  demux.pl             xplor2gmx.pl
GMXRC.zsh

Compilers¶

Puma¶

Compiler	Version	Module Command
gcc	12.2.0	`module load gnu12/12.2.0`
gcc	13.2.0	`module load gnu13/13.2.0 # Recommended. Loaded by default.`
intel	2023.2.1	`module load intel/2023.2.1`
intel	2024.0.0	`module load intel/2024.0.0 # Default`
intel	2024.1.2	`module load intel/2024.1.2`

Ocelote and El Gato¶

Compiler	Version	Module Command
gcc	5.4.0	`module load gnu/5.4.0`
gcc	7.3.0	`module load gnu7/7.3.0`
gcc	8.3.0	`module load gnu8/8.3.0 # Recommended. Loaded by default`
Intel	2020.1	`module load intel/2020.1`
Intel	2020.4	`module load intel/2020.4`

Software Install Requests¶

If you need to use a software package and it is not installed on the system, we can install it for you, provided it meets the criteria outlined in our software policies. Software can be requested by using our HPC software install request Form. There is no expected time frame for how long it takes to install software, as there are many variables that determine this. If you haven't heard back within a week, it may be appropriate to follow up.

For software that doesn't meet the criteria outlined in our policies and doesn't fall into the unsupported software category, it may be possible for you to install it locally. We have instructions documented in our user installations section.