All HPC facilities, worldwide, provide software in a very different way to personal and corporate computing platforms. JCU HPC uses environment modules to deliver multiple versions of software to researchers using our multi-user HPC cluster. This approach is widely used for the following reasons:
- Most operating systems weren't written to deal with having multiple versions of the same software available. Even in cases where multiple versions are installed, e.g., java, it is left to a system administrator to set the version which everyone will use.
- Using environment modules, Individual users or groups can determine which version of software they wish to use.
- Loading of modules with version information maximizes your chance of being able reproduce your results upon demand.
- In the corporate world, system administrators have to configure a default version of piece of software (e.g., java) that everyone will use.
- Using environment modules also improves performance by reducing the length of your search path (executable of interest found sooner). It also reduces the chance of you having to deal with application name conflicts.
In 2021, HPC staff commenced a major project to replace all existing software (including conda environments) with containerized versions of the same software and/or environments. The container delivery platform being using is Apptainer (singularity) which mirrors the approach that all other HPC facilities are using or moving toward using. The move to containerized HPC is being driven by a requirement for all research to be done in a reproducible way.
Environment Modules Cheat Sheet.
Information Requests
You will need to replace any occurrence of <software-name>
and/or <version> below with an appropriate name/value.
module avail
module avail <software-name> # A partial match will be sufficient.
module help <software-name>
module show <software-name>/<version> # For apptainer based software, you will see aliases that have been created for ease of use.
module list
Modification of your environment (paths & aliases)
You will need to replace any occurrence of <software-name>
and/or <version> below with an appropriate name/value.
module load <software-name>/<version> # Omission of "/<version>" will result in the default version (changes over time) being loaded. # Note that the default version may be the "safest", rather than the latest, version.
module switch <software-name>/<version>
module unload <software-name> # The specification of a version shouldn't be required.
module purge
Information specific to JCU HPC configuration
Most module files, when loaded, will set an environment variable <SOFTWARE>_HOME
which holds the installation home for the software. For example, try
module load vcftools echo $VCFTOOLS_HOME ls -lR $VCFTOOLS_HOME
The most common environment variable modified by the loading of an environment variable is PATH
. This has been done for convenience.