Implementation of a Non-bonded Interaction Calculation Algorithm for the Cell Architecture

Authors:
Eduard Fomin;Nikolay Alemasov
Affiliations:
Institute of Cytology and Genetics, Siberian Branch of the Rusian Academy of Science, Novosibirsk, Russia 630090;Institute of Cytology and Genetics, Siberian Branch of the Rusian Academy of Science, Novosibirsk, Russia 630090
Venue:
PaCT '09 Proceedings of the 10th International Conference on Parallel Computing Technologies
Year:
2009

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Abstract

Calculation of non-bonded interactions takes up to 80% of the total execution time of a molecular dynamics program. It can be accelerated by porting the algorithm to the Cell architecture. A simple method of such porting has been applied to the MOLKERN program, which simulates the structure and dynamics of biomolecular models. A 32-fold speedup was achieved for calculation of short-range non-bonded interactions, and threefold, for long-range Coulomb interactions. The overall program speedup proved to be more than 4.