Utrecht Bioinformatics Center
Infrastructure

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High Performance Computing

The high performance compute (HPC) facility, as part of the Utrecht Bioinformatics Center (UBC) offers extensive computing possibilities for all researchers of the Utrecht Science Park. From a large UU starting grand, the HPC has grown with the support of the community to the largest cluster on the campus, allowing both small and very large groups to run their computing. There are over 50 PI groups and 750 users registrered and generally over 50 different users active each day. These groups vary between disciplines, from life sciences to linguistics.

Facts & Figures

  • The cluster consists of a collection of compute servers (>2000 CPUcores, 30 GPUs, 20 TB ram), 1.7 PB high performance storage and 1.1 PB archive storage running on CentOS Linux.
  • It is controlled by the SLURM batch-wise queueing system with a few head nodes and data transfer nodes.
  • Data storage is separated between PI groups.
  • We provide a central GUIX software management system, notebook services and containersupport.
  • Two full time staff members are available to maintain, innovate and support this essential research resource.

Costs

To ensure future sustainability, users can participate after a free trial by buying virtual shares to cover their compute demand (in 2020: €1200,-/50k CPUhrs; €1150/5k GPUhrs; €180/TB high-perf storage/yr; €45,-/TB archive storage/yr).

Trial usage:

The HPC is for and by the community, and for this reason we want to have an extremely low threshold to start using the HPC facility for researchers on the Utrecht Life Science Campus. Before people join the HPC community with paid accounts which helps ensure the sustainability of this service, there is an option to run in a trial configuration without costs to see if the HPC works for you. This trial account can be compared with ¼ share (so ~12.5 kCPUhrs, ~1.6 kGPUhrs, 250GB storage) and is valid for one year, but ad-hoc projects can always be discussed. Each PI can start a trial account only once. Just as for regular accounts, there are limits to the extend users can reserve resources for their jobs. All trial users share the limits of 1 regular account.

The HPC provides the neurogenetics group with a powerful tool to analyse large genomics datasets using a suite of compute heavy approaches most notably deep learning and various mixed linear models.
Jan H. Veldink
Jan H. VeldinkProfessor of Neurology and Neurogenetics,
Department of Neurology,
University Medical Center Utrecht Brain Center,
Utrecht University

More information: HPC facility wiki*
Contact: Ies Nijman

* Only available on managed networks of the collaborating institutes

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