HPC NEWS

German Cancer Research Center deploys Convey platforms

21 August 2013



The German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ) in Heidelberg, Germany, has installed two Convey hybrid-core (HC) computers. The Convey HC-2ex platforms are being used to accelerate the centre’s next-generation sequencing (NGS) pipeline, saving time and reducing energy consumption.

In 2012, DKFZ tested its first Convey HC computer using the server to accelerate a portion of its next-generation pipeline. Results were extremely positive; one of the initial jobs went from more than 18 hours on an 8 core system to 48 minutes on the Convey server. Based on that success, DKFZ purchased two Convey HC-2ex servers a few months later. These hybrid-core systems were integrated into an existing 1,600 compute core cluster. The Convey systems are now routinely used at DKFZ in the production analysis for all Burrows-Wheeler Aligner (BWA) algorithms.

Convey’s hybrid-core architecture pairs Intel x86 microprocessors with a coprocessor comprised of field-programmable gate arrays (FPGAs). Particular algorithms – BWA-based alignment, for example – are optimised and translated into code that’s loadable onto the coprocessor at runtime. This results in an order of magnitude performance increases with less power, space and cooling requirements.

‘We are extremely pleased with the Convey systems. Depending on the data, we are typically seeing between 10-20x acceleration, which is substantial,’ explained Dr Benedikt Brors, group leader Computational Oncology, Division Theoretical Bioinformatics at DKFZ. ‘And our entire workflow from one end to the other is reduced by a factor of two.’

Related internet links

Convey Computer
German Cancer Research Center