Environment Modules on H4H🔗

To prevent repeated installations of software commonly used across the cluster,

The Environment Modules system is used to provide a standard set of precompiled programming languages, software tools and libraries accessible to all users on H4H.
For many common tasks these modules will be sufficient to complete your analysis.

For cases where a software dependency is unavailable you have two courses of action:

Contact the cluster administrators and request they install it
Install the software locally in your H4H home directory (see Installing Packages)

Basic `module` Commands🔗

The user interface for the Modules package is accessible via the module command. In general, loading a module will modify environment variables such as your PATH or MANPATH to provide access to the requested software. To view an overview of available subcommands for module, run module -t. Note that module is generally only available during job execution and thus cannot be loaded from the Login or Data nodes.

To view a short list of available subcommands, simply type module into the terminal.

module avail

Opens a list of all available modules using the less command, allowing you to browse the pages with arrow keys
You can pass a pattern string to the command to only show modules matching the pattern
If you pass a specific module name (case sensitive), the utility will show you a list of available versions and a description of that module

module spider

Similar to avail, but specifically lists all available versions
Also supports passing module names or patterns

module whatis

Get the description text for a module using its name

module load

Load the module into your current environment
This works by modifying your PATH environment variable

module list

Lists all loaded modules
Accepts patterns, which can be useful if you have a lot of modules loaded

module unload

Removes a loaded module from your current environment

Try it yourself🔗

Allocate an interactive so you have access to the module command
Solution
```
salloc -c 2 --mem=4G -t 0:30:0
```
Use module avail or module spider to find the module for the most recent R version available on the cluster
Solution
```
module spider R  # Most recent version at time of writing is 4.2.1
```
Get a description of the most recent R module
Solution
```
module whatis R/4.2.1
```

Load the most recent R module, inspecting the $PATH variable before and after loading

Solution

echo $PATH
module load R/4.2.1
echo $PATH  # Note that loading a module changes your current PATH

Get the version of R and confirm it matches the module you loaded
Solution
```
R --version
```
Unload the R module
Solution
```
module unload R/4.2.1
```

Module Collections🔗

If your analysis requires many modules it can be tedious to load all of them in your scripts. To get around this, the module system provides a mechanism to save the state of your currently loaded modules into a collection. This collection can then be restored from the collection file in your job script or interative session.

Try it yourself:

Allocate an interative job on the cluster, if you don't already have one
Solution
```
salloc -c 2 --mem=4G -t 0:30:0
```
View the documentation for the module command and note the options for the save and restore sub-commands
Solution
```
module # could also do module help, module --help or man module
```

Use module spider to find the most recent versions of samtools and picard

Solution

module spider samtools  # Most recent at time of writing is 1.14
module spider picard  # Most recent at time of writing is 2.10.9

Load the samtools and picard modules from step 3.

Solution

module load samtools/1.14
module load picard/2.10.9

Save your currently loaded packages to a collection called test_collection

Solution

module save test_collection  # If you don't specify a collection name it saves to your default collection

Open the module help pages and find the command to view available collections
Solution
```
module
module savelist
```
Open the module help pages and find the command to unload all modules and then run it
Solution
```
module purge
```
List loaded modules to confirm the command worked
Solution
```
module list
```
Restore your module collection
Solution
```
module restore test_collection
```
List loaded modules again to confirm that your command worked
Solution
```
module list  # Should see samtools and picard
```
Use the module documentation to find the command to list the contents of a module collection then run it on test_collection
Solution
```
module -t
module savelist test_collection
```
Use the module documentation to find the command to delete a collection then remove test_collection and unload all packages
Solution
```
module -t
module saverm test_collection
module purge
```

Customizing Defaults🔗

There are many options available to customize the default behavior of modules. These can be by creating a .modulerc file in your $HOME directory.

Alternatively, there are a number of enviromental variables which can be set to modify how module commands and sub-commands behave. Please refer to the Environment Modules documentation for more details.

References🔗

Environment Modules

Environment Modules on H4H🔗

Basic module Commands🔗

Try it yourself🔗

Module Collections🔗

Customizing Defaults🔗

References🔗

Basic `module` Commands🔗