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Welcome to the user documentation of the BIH high-performance computing (HPC) cluster, also called HPC 4 Research. The BIH HPC cluster is managed by CUBI (Core Unit Bioinformatics). This documentation is maintained by BIH CUBI and the user community. It is a living document that you can update and add to. See How-To: Contribute to this Document for details.

⮅ The global table of contents is on the left, the one of the current page is on the right. ➡

Additional resources

Getting Started

Read the following set of pages (in order) to learn how to get access and connect to the cluster.

  1. Getting Access
  2. Connecting
  3. Storage
  4. Slurm
  5. Getting Help (Writing Good Tickets; if no answer found, contact the HPC Helpdesk).
  6. HPC Tutorial

Acknowledging BIH HPC Usage

Acknowledge usage of the cluster in your manuscript as "Computation has been performed on the HPC for Research/Clinic cluster of the Berlin Institute of Health". Please add your publications using the cluster to this list.

News & Maintenance Announcements

  • 🎃 October 22nd 2024: Kernel & Slurm upgrades on (almost) all nodes.
  • 🐏 July 16th: New high-memory node hpc-mem-5 with 4 TB of RAM.
  • 🚂 Until autumn 2024: Operation Exodus – Migration of all data from GPFS to CephFS storage.
  • 🍁 September 30th 2024: Unmounting of /fast on all non-transfer nodes.
  • ðŸŠĶ October 31st 2024: Retirement of GPFS/DDN storage.

See Maintenance for a detailed list of current, planned, and previous maintenance and update work.

Technical Details

If you are interested in how this HPC cluster is set up on a technical level, we got you covered. There is an entire section on this.

Documentation Structure

The documentation is structured as follows:

  • Administrative information about administrative processes such as how to get access, register users, work groups, and projects.
  • Connecting technical help for connecting to the cluster.
  • Storage describes how and where files are stored.
  • HPC tutorial a first demo project for getting you started quickly.
  • Cluster Scheduler technical help for using the Slurm scheduler.
  • OnDemand Portal introduces web HPC access.
  • Best Practice guidelines on recommended usage of certain aspects of the system.
  • Static Data (Cubit) documentation about the static data (files) collection on the cluster.
  • How-To short(ish) solutions for specific technical problems.
  • Getting Help explains how you can obtain help in using the BIH HPC.
  • Miscellaneous contains a growing list of pages that don't fit anywhere else.