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:
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.
For security reasons, all software installed as part of the OS must be kept up to date.
Software installed using the traditional, compile from source, method comes with serious consequences to reproducible research.
Operating system and software providers release software with a defined lifecycle.
In many cases, the above points mostly relate to risk of work not being reproducible. Moving to containerized delivery of software provides a guarantee of reproducibility, assuming that the container platform continues to be available and supported. |
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 |
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 |
List all jobs in the queues |
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List jobs owned by a given userid |
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Environment module files for conda environments have been removed, since discovery of a few conda environments that couldn't be reinstalled. After you issue the command
module load conda3 |
you will be able to use the conda command to list environments available.
Conda environments will not be available on future HPC platforms.
There is increasing pressure to move HPC workloads into the public cloud. Reliance on in-house HPC infrastructure will decrease with time.
It's possible that HPC will be directed to implement a NOEXEC option on all user filesystems, which would mean software you have installed yourself will not be executable. I would hope that there is a documented security vetting process prior to such a directive being given to us. We have had a request for implementation of such an option in the past but chose not to take any action (there was no directive).