Modules

Lmod is a Lua based module software management system that helps manage the user environment (PATH, LD_LIBRARY_PATH) through module files. LMOD is used on the HPC systems Gaea, Hera, and Jet.

View Active Modules

Use module list to see what modules are loaded in your environment.

$ module list

Find Modules

Lmod provides several commands to help you find modules including module avail, and module spider.

To view a list of available modules in MODULEPATH use module avail <module>. The command will show only modules that can be loaded in the current environment.

$module avail

The command module spider <module> will show all modules and versions with the name. This includes modules that cannot be loaded in the current environment.

$ module spider cray-netcdf/4.9.0.1
----------------------------------
cray-netcdf: cray-netcdf/4.9.0.1
----------------------------------

You will need to load all module(s) on any one of the lines below
before the "cray-netcdf/4.9.0.1" module is available to load.

aocc/3.2.0  cray-hdf5/1.12.2.1
aocc/3.2.0  cray-hdf5/1.12.2.3
aocc/3.2.0  cray-hdf5/1.12.2.7
gcc/10.3.0  cray-hdf5/1.12.2.1
gcc/10.3.0  cray-hdf5/1.12.2.3

NOTE: module spider command reports all modules along with all module trees in the hierarchical system while module avail does not. To see all possible modules and their versions, use module spider

Load Modules

User module load to load a module into the current environment of a session or job.

$ module load <module>

Use module unload to remove a loaded module

$ module unload <module>

LMOD employs a hierarchical system that, when used properly, considers dependencies and prerequisites for a given software package.

For example, the cray-netcdf module depends on the cray-hdf5 module and cannot be seen by the standard module avail commands nor be loaded until the cray-hdf5 module is loaded.

The LMOD hierarchical system will automatically deactivate or swap an upstream module dependency.

When that happens, any downstream module will still be loaded but inactivated.

$ module load cray-hdf5

$ module load cray-netcdf

$ module unload cray-hdf5

Inactive Modules:
cray-netcdf

In this example, the cray-netcdf module depends on the cray-hdf5 module. When the cray-hdf5 module is unloaded, the cray-netcdf module becomes inactive.

Reloading the cray-hdf5 module will reactivate the cray-netcdf module.

Adding Additional Module Paths

Do not manually set the MODULESPATH environment variable. Manually setting the MODULESPATH environment variable will produce unknown behavior.

Use module use <path> or module use -a <path> to add more module paths.

Modules with sh, bash, and ksh scripts

How can I get the shell functions created by modules in bash shell scripts such as job submission scripts?

Make sure that shell functions and alias works correctly in bash interactive sub-shells.

Once that works then change the first line of the shell script to be:

#!/bin/bash -l

Note: That is not a minus one.

This will cause the startup scripts to be sourced before the first executable statement in the script.

Why doesn’t the module command work in shell scripts?

First it is recommended that the script be a bash script and not a shell script, so start the script with #!/bin/bash.

The environment variable BASH_ENV must point to a file which defines the module command. MODULEHOME should point to the file that defines the module command.

You can also do the following in your script before using the module command

$ source $MODULESHOME/init/sh

Command Summary

Command	Description
module list	List active modules in the user environment
module avail [module]	List available modules in MODULEPATH
module spider [module]	Query all modules in MODULEPATH and any module hierarchy
module load [module]	Load a module file in the users environment
module unload [module]	Remove a loaded module from the user environment
module swap [module1] [module2]	Replace module1 with module2
module use [-a] [path]	Prepend or Append path to MODULEPATH
module unuse [path]	Remove path from MODULEPATH
module show [module]	Show content of commands performed by loading module file

Warning

Do not use the command module purge on Gaea. This will remove all modules currently loaded by default in your environment and may lead to errors, and can make your session unusable. If you do run the command to purge your module environment, log out and back in to Gaea to restore the default environment with the default modules loaded.