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). Esrum is managed by the Data Analytics Platform (DAP), and is available to all employees at CBMR and their collaborators.

In addition to the Esrum HPC cluster, the platform also provides two RStudio servers, access to more than 80 human cohorts, a project registry for tracking your projects at CBMR, and open source tools and pipelines. We kindly ask that you acknowledge the use of services and resources that we provide. See the acknowledgements section on the Guidelines and policies page for more information.

You are also always welcome to contact us if you have questions or problems relating to the cluster, cohorts, other services or resources provided by the platform. Additionally, we will gladly assist with general bioinformatics issues.

Getting started

We hold intro-workshops for Esrum based on interest, so please let us know if you'd like to attend; upcoming workshops are announced to all employees at CBMR. Slides from past workshops are available via 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 next intro workshop to use Esrum:

  1. Please read the Guidelines and policies for using Esrum before you continue.

  2. To get access to Esrum and related resources, please see the Applying for access page

  3. Once your request has been approved, you can connect to the cluster as described in the connecting to the cluster page.

  4. On Esrum, you'll find your home folder, datasets, projects, and network drives laid out as described on the Data storage on Esrum page.

  5. Users of Esrum have access to a large library of software provided by DAP and UCPH-IT. The Software on Esrum page describes how to access this software, and how to request software that is not currently available.

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

  7. Finally, the Transferring data page describes how to transfer your data to and from Esrum, and to and from services like SIF or Computerome.

See the Table of Content for various other services, tips and trips for using Esrum, and more.

Tip

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 and R for Data Science courses.