Modules

GNU Modules

Many large institutions use the concept of Modules to load software into user environments. They provide a way to add and remove environmental variables that provide access to UMIACS' large set of software that we offer on our Red Hat Enterprise Linux (RHEL) and Ubuntu platforms. They work by customizing your shell environment which is done automatically for the two major shell families (bash/sh (default shell) and tcsh/csh). If you use an alternate shell, please look to source the appropriate script for your shell in /usr/share/Modules/init.

Initially your module environment is empty, though included in your module path are local operating system specific modules, locally built software modules, and binary software modules (Matlab, Intel Compiler, etc.).

Available Software

To see if a piece of software is available, use the module avail command. This can be given a trailing prefix on the command line to search a subset of the available software.

[username@nexusstaff00 ~]$ module avail cuda
--------------------------- /opt/common/.modulefiles ---------------------------
cuda/3.2.16  cuda/6.5.14     cuda/9.0.176   cuda/11.0.3  cuda/11.8.0
cuda/4.2.9   cuda/7.0.28     cuda/9.1.85    cuda/11.1.1  cuda/12.0.1
cuda/5.0.35  cuda/7.5.18     cuda/9.2.148   cuda/11.2.2  cuda/12.1.1
cuda/5.5.11  cuda/8.0.27rc2  cuda/10.0.130  cuda/11.3.1
cuda/5.5.22  cuda/8.0.44     cuda/10.1.243  cuda/11.4.4
cuda/6.0.37  cuda/8.0.61     cuda/10.2.89   cuda/11.7.0

[username@nexusstaff00 ~]$ module avail Python3
------------------------- /opt/local/stow/.modulefiles -------------------------
Python3/3.5.2   Python3/3.8.2   Python3/3.8.15  Python3/3.9.16
Python3/3.6.15  Python3/3.8.10  Python3/3.9.5   Python3/3.10.4
Python3/3.7.13  Python3/3.8.12  Python3/3.9.6   Python3/3.10.10
Python3/3.7.16  Python3/3.8.13  Python3/3.9.12  Python3/3.11.2

Some pieces of software may have default versions that are loaded if no version is explicitly specified, indicated by (default) coming after their name/version in the output of module avail. If a piece of software does not have any default version and you load it without specifying a version, you will load the most recent version of it.

Adding Modules into your Environment

You can simply add a module into your environment by using the module add <module> command.

[username@nexusstaff00 ~]$ module add cuda

You can also specify a specific version of the software when we have multiple ones available.

[username@nexusstaff00 ~]$ module add Python3/3.10.10

Listing Modules

You can list the currently loaded modules in your environment by using the list command.

[username@nexusstaff00 ~]$ module list
Currently Loaded Modulefiles:
 1) Python3/3.10.10   2) cuda/12.1.1

Showing a Module

You can show what the module is going to add to your environment (and the dependencies that will be added) with the show command.

[username@nexusstaff00 ~]$ module show cuda
-------------------------------------------------------------------
/opt/common/.modulefiles/cuda/12.1.1:

conflict        cuda/12.0.1 cuda/11.8.0 cuda/11.7.0 cuda/11.4.4 cuda/11.2.2 cuda/11.1.1 cuda/11.0.3 cuda/10.2.89 cuda/10.1.243 cuda/10.0.130 cuda/9.2.148 cuda/9.1.85 cuda/9.0.176 cuda/8.0.61 cuda/8.0.44 cuda/8.0.27rc2 cuda/7.5.18 cuda/7.0.28 cuda/6.5.14 cuda/6.0.37 cuda/5.5.22 cuda/5.5.11 cuda/5.0.35 cuda/4.2.9 cuda/3.2.16
prepend-path    PATH /opt/common/cuda/cuda-12.1.1/bin
prepend-path    LD_LIBRARY_PATH /opt/common/cuda/cuda-12.1.1/lib64
prepend-path    LD_RUN_PATH /usr/lib64/nvidia:/usr/lib/nvidia:/opt/common/cuda/cuda-12.1.1/lib64:/opt/common/cuda/cuda-12.1.1/lib
prepend-path    LIBRARY_PATH /usr/lib64/nvidia:/usr/lib/nvidia:/opt/common/cuda/cuda-12.1.1/lib64:/opt/common/cuda/cuda-12.1.1/lib
prepend-path    CPATH /opt/common/cuda/cuda-12.1.1/include
prepend-path    PKG_CONFIG_PATH /opt/common/cuda/cuda-12.1.1/pkgconfig
setenv          CUDA_HOME /opt/common/cuda/cuda-12.1.1
-------------------------------------------------------------------

Removing Modules in your Environment

If you want to remove a module because it conflicts or you want to clean up your environment you can by using the module rm <module> command.

Using Modules in Scripts

To use modules within a shell script or interpreted language you will need to load a file from /usr/share/Modules/init into your program.

Bash

. /usr/share/Modules/init/bash
module add gcc

Tcsh

source /usr/share/Modules/init/tcsh
module add gcc

Modules in Non-Interactive Shell Sessions

In non-interactive shell sessions (non-login shells), the Modules configuration environment will not automatically load. This will also occur if the OS version of the compute node you are scheduled on is different from the OS version of the submission node you are submitting the job from.

If you will need the use of Modules in non-interactive SLURM jobs, cross-OS jobs, or other similar sessions, you will need to include the following in your shell init scripts. For SLURM specifically, please ensure you include these statements after any #SBATCH directives in your submission batch scripts, otherwise these directives will not work.

Bash

. /usr/share/Modules/init/bash
. /etc/profile.d/ummodules.sh

Tcsh

source /usr/share/Modules/init/tcsh
source /etc/profile.d/ummodules.csh

Modules on RHEL9 Desktop Sessions

Because of changes made in GNOME between RHEL8 and RHEL9, the module command will not work on desktop sessions out of the box. In order to use modules in a shell opened from a desktop session, you must source the modules init script. See #Modules in Non-Interactive Shell Sessions for the required commands. For convenience, we recommend adding this to the top of your shell init file (e.g ~/.bashrc, ~/.tcshrc), this way it gets sourced automatically with each new shell.

Note that this issue does not affect RHEL9 SSH sessions, only sessions using the desktop GUI.

Additional Help

You can type module with no arguments for a full list of commands or man module for further information.

Online Resources

• Project Page (SourceForge)
• Introduction to Modules
• Modules FAQ
• user-setup