2010 Best Practices Competition IT & Informatics HPC

Published Resources for the Life Sciences
250 First Avenue, Suite 300, Needham, MA 02494 | phone: 781‐972‐5400 | fax: 781‐972‐5425
UPPMAX’s users traditionally come from research areas such as physics, chemistry, and computer
science. Lately, however, the number of Life Sciences users has increased dramatically. This is
mainly due to the technical advances, affordability and increased deployment of next‐generation
sequencing (NGS) machines.
In 2008 it had become apparent, to Swedish researchers, that the tsunami of data from NGS
systems created a problem that individual research grants could not solve. In many cases, Life
Sciences research teams were trying to manage the problem themselves. However, due to the
sheer volume of data, they wasted a lot of time copying data between systems, waiting for others
to complete their computing before they could start their own ‐ and often writing custom code to
manage jobs that would typically max‐out system resources. In short, the teams often spent as
much time solving computing challenges as they did on scientific research!
It was for these reasons that, in 2008, a national consortium of life sciences researchers was formed
to address the challenges presented by this massive increase in bioinformatics data. These
researchers would normally compete for resources and research funding. However, it had become
apparent that a centralized facility was required. The computation and data storage requirements
of NGS data created a workload that, at peak processing times and for long‐term data archiving, had
to be handled by a larger facility.
The consortium therefore submitted an application to SNIC and the Knut and Alice Wallenberg
Foundation to fund a centralized life sciences compute and storage facility to be hosted at UPPMAX.
The united conviction of the consortium being that a sufficient compute and storage facility would
ultimately strengthen their attempts to combat disease.
The application was successful with the Knut and Alice Wallenberg Foundation noting that the
consortium’s collaborative effort was a major advantage.
And so, the “UPPmax NEXt generation sequence Cluster & Storage (UPPNEX)” project was formed.
Today, a 150 node (1200 core) compute cluster from HP with Infiniband as interconnect is in
production with half‐a‐petabyte (500TBs) of Panasas parallel storage. The solution passed a onemonth
acceptance period, at the first time of asking, and entered production in October 2009.
The objectives of the UPPNEX solution were to provide Life Sciences Researchers throughout
Sweden with:
1. Sufficient high‐performance computing resources to cover their regular and peak project
requirements