The Esrum cluster at CBMR

Welcome to the Esrum 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.

• For an overview of the cluster architecture and features, see the Overview page.

• To get access to the cluster and to run simple jobs, see the Using the cluster pages.

• For services such as Rstudio, Shiny, and persistent containers, see the Other services pages.

• For ways to make working on the cluster easier, see the Tips and tricks page.

• For presentations about esrum, emails, and other communications, see the Communications pages.

You are always welcome to contact us if you have questions or problems relating to the cluster. See the Contact page for information about how and where to contact us.

This documentation is licensed under the Creative Commons CC-BY 4.0 license; you are free to use it as you see fit provided that you give appropriate credit.

Contents:

• 1. Contact
• 2. Overview
• 3. Guidelines
• 4. Using the cluster
  • 4.1. Accessing the cluster
  • 4.2. Projects, data, and home folders
  • 4.3. Running jobs using Slurm
  • 4.4. Environment modules
  • 4.5. Transferring data
• 5. Other services
  • 5.1. R
  • 5.2. RStudio
  • 5.3. Jupyter notebook
  • 5.4. Running containerized software
  • 5.5. Public and private Shiny servers
• 6. Tips and tricks
  • 6.1. Creating environment modules
  • 6.2. Persistent sessions with tmux
  • 6.3. Batching commands outside Slurm
  • 6.4. Writing robust bash scripts
• 7. Troubleshooting
• 8. Communications
  • 8.1. Welcome to CBMRs Compute Cluster Esrum!
  • 8.2. Workshops and other presentations