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Life Science Grid

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Today's Life Scientists need to have advanced High Performance Computing (HPC) facilities at their disposal. For that reason, and commissioned by NBIC and e-Infra (the former BiGGrid), SURFsara has placed powerful computer clusters at the local sites of interested universities since 2007. The clusters are interconnected by a high speed SURFNET network and form a computational Grid. By using the Grid middleware gLite which runs at every node the compute power of these clusters can be used simultaneously by a single user. SURFsara and the user community take care of support. The Life Science Grid is open to all Life Scientists based in The Netherlands.

For some scientific disciplines, such as high energy physics and quantum chemistry, High Performance Computing (HPC) is part of the standard toolkit. For other scientific disciplines, for example the Life Sciences, this is not yet the case. Yet, HPC can be of big interest here as well.

To outsiders, HPC and especially Grid technology may seem daunting. With the Life Science Grid project, SARA aims to close the gap between the life sciences and HPC facilities. Accordingly, computer clusters have been placed at various locations throughout the Netherlands, e.g. AMC, LUMC, NKI, RU, WUR. SURFsara maintains these clusters from a distance, allowing users to fully focus on their research.

Currently, the Life Science Grid is able to run about 12000 jobs concurrently. Locally, every cluster can be utilized as a traditional computer cluster, thus leveraging significant computational power and data storage. The true force of the Life Science Grid, though, is that the clusters together form a Computing and Storage Grid, a virtual supercluster. Applications running locally on the cluster can also be executed in a distributed fashion on the entire Grid.

Clusters on site

By placing the computer clusters on site, SURFsara facilitates tight integration with local ICT infrastructure and present measuring equipment. Participants may share their data, but can also protect their data from others and keep it within the premises. Participating universities only need to provide 1m2 of floor space, 2 kW of electrical power and a fast network connection.

On their local cluster, participants have extra permissions. E.g., one can log in on the local cluster, which in some cases greatly simplifies debugging of (self-built) applications.

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"Overview of the Life Science Grid"

Currently, nine clusters are in place at the following sites:

  • LUMC – Leiden
  • TU Delft
  • WUR – Wageningen
  • BCBR – Utrecht
  • AMC – Amsterdam
  • Radboud Universiteit – Nijmegen
  • ErasmusMC – Rotterdam
  • RUG – Groningen
  • VU – Amsterdam

Each of these clusters has 128 processor cores and 18 Tb of nett storage with the exception of the ones at TU Delft, RUG Groningen, KeyGene and Erasmus MC Rotterdam, which have 32 cores.

Use of and Access to the Life Science Grid

For user information please consult the pages at the SURFsara Grid wiki, or mail to SURFsara helpdesk.

For more information you may contact SURFsara, phone number +31(0)20-800140. The following persons are involved with the Life Science Grid project: