The HPC is changing

We will soon be switching to a new High Performance Cluster, called Double Helix. This will mean that some of the commands you use to connect to the HPC and call modules will change. We will inform you by email when you are switching over, allowing you to make the necessary changes to your scripts. Please check our HPC changeover notes for more details on what will change.

Using software on the HPC

Software on the Genomics England HPC is managed through the module system framework.

Module system commands

You can list the software available with:

module avail

To load software, run:

module load lang/R/3.5.1-foss-2018b

Always specify the version of the software that you want to load, to avoid errors and unexpected results.

For instance, Running module load lang/R will load version 3.6.2 instead of my desired version of 3.5.1.

To unload software, run:

module unload lang/R/3.5.1-foss-2018b

Or you can switch to a different version of the same software (required software to be loaded first):

module switch lang/R/3.6.2-foss-2019b

Python package and environment management

You can use conda in the RE to access pre-made Python environments as well as creating your own. To install packages to your environments, you will need to use proxy paths.

Container support

The HPC supports Singularity for containerised workflows. If your workflow is written in Docker, Singularity is able to read Dockerfiles and convert them into Singularity images. Note that the usage of Singularity/Docker is optional. Softwares and tools can be loaded using module as before.