Drug Design on the Cell BroadBand Engine
2007 (English)In: Parallel Architecture and Compilation Techniques: Conference Proceedings, PACT, IEEE Computer Society, 2007, 425-425 p.Conference paper (Refereed)
We evaluate a well known protein docking application in the bioinformatic field, Fourier Transform Docking (FTDock) (Gabb et al., 1997), on a Blade with two 3.2GHz cell broadband engine (BE) processor (Kahle et al., 2005). FTDock is a geometry complementary approximation of the protein docking problem, and uses 3D FFTs to reduce the complexity of the algorithm. FTDock achieves a significant speedup when most time consuming functions are offloaded to SPEs, and vectorized. We show the performance impact evolution of of-loading and vectorizing two functions of FTDock (CM and SC) on 1 SPU. We show total execution time of FTDock when CM and SC run in the PPU (bar 1), CM is off loaded (bar 2), CM is also vectorized (bar 3), SC is offloaded (bar 4) and SC is also vectorized (bar 5). Parallelizing functions that are not offloaded, using OpenMP for instance, on the dual-thread PPE helps to increase the PPEpipeline use and system throughput, and the scalability of the application.
Place, publisher, year, edition, pages
IEEE Computer Society, 2007. 425-425 p.
IdentifiersURN: urn:nbn:se:kth:diva-71998DOI: 10.1109/PACT.2007.40ISBN: 978-0-7695-2944-8OAI: oai:DiVA.org:kth-71998DiVA: diva2:487117
16th International Conference on Parallel Architecture and Compilation Techniques (PACT). Brasov. 15 September 2007 - 19 September 2007
QC 201201312012-01-312012-01-312012-01-31Bibliographically approved