High performance 3D convolution for protein docking on IBM blue gene

Authors:
Akira Nukada;Yuichiro Hourai;Akira Nishida;Yutaka Akiyama
Affiliations:
Japan Science and Technology Agency, Saitama, Japan and The University of Tokyo, Tokyo, Japan;Computational Biology Research Center, AIST, Tokyo, Japan;Chuo University, Tokyo, Japan and Japan Science and Technology Agency, Saitama, Japan;Computational Biology Research Center, AIST, Tokyo, Japan
Venue:
ISPA'07 Proceedings of the 5th international conference on Parallel and Distributed Processing and Applications
Year:
2007

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Abstract

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).