NAMD & HELIUM Enabling Work on the PRACE IBM Prototypes

Xu Guo, EPCC, University of Edinburgh, EH9 3JZ, UK; Joachim Hein, EPCC, University of Edinburgh, UK; Martin Polak, ICA, Johannes Kepler University Linz, Austria; Paschalis Korosoglou, AUTH, Greece; Andrew Sunderland, STFC Daresbury Laboratory

The Partnership for Advanced Computing in Europe (PRACE) aims to provide a persistent pan-European HPC service, consisting of several tier-0 centres. The PRACE Preparatory Phase Project created the prerequisites for the target HPC service and now the project is ready for the Implementation Phase. The completed preparatory work looked into all aspects of the pan-European service, including the contractual and organisational issues, the system management, application enabling and future computer technologies.

The Work Package 6 (WP6) of PRACE Preparatory Phase was responsible for the application enabling on future petascale systems. A set of representative applications from a wide variety of application areas were selected into the PRACE Application Benchmark Suite (PABS). The PABS applications were ported to a number of PRACE prototype systems and their requirements for petascale architectures were captured. The applications scalability and optimisation strategies for petascaling were also investigated in the PRACE WP6 activities.

This talk will discuss the work done on the application codes NAMD (from University of Illinois at Urbana Champaign, US) and HELIUM (from Queen's University Belfast, UK), which are part of the PABS. We will focus on the work carried out on the PRACE prototype Huygens, which is an IBM Power6 system at SARA in Netherlands, and JUGENE, which is an IBM Blue Gene/P system at FZJ-JSC in Germany. A performance comparison with non- IBM systems available to PRACE will also be included in this talk.

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