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Erschienen in:
2007 | OriginalPaper | Buchkapitel
High Performance 3D Convolution for Protein Docking on IBM Blue Gene
verfasst von : Akira Nukada, Yuichiro Hourai, Akira Nishida, Yutaka Akiyama
Erschienen in: Parallel and Distributed Processing and Applications
Verlag: Springer Berlin Heidelberg
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We have developed a high performance 3D convolution library for Protein Docking on IBM Blue Gene. The algorithm is designed to exploit slight locality of memory access in 3D-FFT by making full use of a cache memory structure. The 1D-FFT used in the 3D convolution is optimized for PowerPC 440 FP2 processors. The number of SIMOMD instructions is minimized by simultaneous computation of two 1D-FFTs. The high performance 3D convolution library achieves up to 2.16 Gflops (38.6% of peak) per node. The total performance of a shape complementarity search is estimated at 7 Tflops with the 4-rack Blue Gene system (4096 nodes).