The Esrum HPC cluster at CBMR

Welcome to the Esrum high-performance computing (HPC) cluster at The Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR). The Esrum cluster is managed by the Data Analytics Platform (formerly the Phenomics Platform) and is available to employees at CBMR as well as collaborators visiting CBMR.

You are always welcome to contact us if you have questions or problems relating to the cluster, cohorts, other services or resources provided by the platform.

We kindly ask that you acknowledge the use of services or resources provided by the Data Analytics Platform. See Guidelines and policies for more information.

Note

This documentation assumes some familiarity with using Linux and bash (the default command-line). Users who lack this familiarity may benefit from taking the Mastering the terminal with Bash and Unix course offered by the Center for Health Data Science (HeaDS) at SUND. If you intend to make use of R or the RStudio servers, then you may also benefit from the From Excel to R offered by HeaDS.

Getting started

We hold an intro-workshop for the Esrum cluster a few times a year, based on interest, so please let us know if you'd like to attend a workshop. Future workshops will be announced to all employees at CBMR, while slides from past workshops are made available on the presentations page.

However, this documentation is explicitly written to help you get started with using Esrum, so you do not need to wait for the intro workshop to be announced:

  • Before you continue, please read our Guidelines and policies. You are expected our guidelines while using the Esrum cluster.

  • To get access to Esrum, you must first apply for access as described in Applying for access. Once you have access, you can connect to the cluster as described in connecting to the cluster page.

  • Connecting to Esrum gives you access to your personal home folder and to project and data set folders as described in Data storage on Esrum.

  • Users of Esrum have access to a large library of scientific and other software. This software is available via environment modules as described in Software on Esrum.

  • To run this or other software on Esrum, you must make use of the Slurm queuing system as described in Running jobs using Slurm.

  • Finally, Transferring data describes how to transfer your data to and from Esrum, to and from services like SIF and Computerome.

In addition, this documentation contains an overview of the cluster architecture and features, describes the various other services accessible as part of the HPC cluster, such as Rstudio servers, Shiny servers, and persistent podman containers.