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Basics

The basics of the eRN

The eRN software stack is a collection of software for use on the UFS HPC and other UFS computational infrastructures. The stack is designed:

  • For use by novice and experienced users.
  • To provide a consistent user experience.
  • To allow software from diverse scientific fields to be run.
  • To allow for reproducible research by retaining all previous software installs.
  • To prevent interference by environment settings and other software when using software.

Kindly acknowledge the eResearch and HPC unit in publications, that made use of the eRN software stack or the unit's infrastructure, by for example adding:

The author would like to acknowledge the eResearch & HPC unit of the University of the Free State for the computational resources provided.

Greeting

The greeting message can be turned off by running ern greeting off. Run ern greeting help for more information.

Disclaimer

Kindly familiarise yourself with the disclaimer you acknowledged. The disclaimer can be viewed by running ern disclaimer view. For more information regarding disclaimer related commands, run the command ern disclaimer help.

Data security compliance

The eResearch and High-Performance Computing (HPC) unit safeguards data on behalf of the University of the Free State (UFS) researchers. All data is stored in compliance with regulatory requirements, such as POPIA and, to a large extent, GDPR (as a non-EU member). For a more expansive discussion of the data protection measures see Data Security Compliance a signed letter can be requested from eRN support staff.

Using available software

Many utilities are bundled with the stack for internal use and to provide an improved and consistent user experience. Utilities are included to process data files such as JSON, CSV, and TSV. Run the command `ern docs utilities' for a discussion of the included utilities.

All software, except for the bundled mentioned utilities, must be loaded before being available for use. The command ern docs can be used to access documentation on installed software. Attempting to use software that have not been loaded yet, yields an error message that lists modules that provide the software. For more information of the module command run ern docs modules. A catalog of example commands are in development, run the ern docs snippets command for usage information.

Using projects

Using projects allows for automatically loading modules, setting environment variables, and running a script when cd to a project's directory. To configure a project, run the command ern project help.

Submitting jobs

Do not assume that because the eRN runs on a system, that the system has enough compute, memory and other resources to run all the available software. Newer installs warns of the available and suggested minimum resources required by software when software are run. This warning can be ignored but users should instead consider submitting jobs to a cluster.

Follow the instructions from ern cluster help to create a cluster configuration. Before submitting jobs load the module as instructed. Follow the instructions, outlined in ern jobs help, to submit a job.