Gesellschaft fr Informatik e.V.

Lecture Notes in Informatics

INFORMATIK 2009 - Im Focus das Leben P-154, 721-729 (2008).

Gesellschaft für Informatik, Bonn


Stefan Fischer, Erik Maehle, Rüdiger Reischuk (eds.)

Copyright © Gesellschaft für Informatik, Bonn


Implementation of an effective non-bonded interactions kernel for biomolecular simulations on the cell processor

Horacio Emilio Pérez Sánchez and Wolfgang Wenzel


In biomolecular simulations intensive computations are spent in nonbonded interactions kernels, i.e., electrostatic interactions. Therefore this part can be considered as a bottleneck, and its optimization permits biomolecular simulation methods to deal with more complex systems or to simulate longer time scales. Using novel computational architectures, i.e., the Cell processor, and programming it adequately in parallel, can considerably improve the performance of biomolecular simulation methods. Programming the Cell processor is difficult, but we show a strategy, using the metacompiler Cellsuperscalar. We obtain sustained speedups of around 150 times.

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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-241-3

Last changed 24.01.2012 22:06:20