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).
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Nukada, A., Hourai, Y., Nishida, A., Akiyama, Y. (2007). High Performance 3D Convolution for Protein Docking on IBM Blue Gene. In: Stojmenovic, I., Thulasiram, R.K., Yang, L.T., Jia, W., Guo, M., de Mello, R.F. (eds) Parallel and Distributed Processing and Applications. ISPA 2007. Lecture Notes in Computer Science, vol 4742. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74742-0_84
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DOI: https://doi.org/10.1007/978-3-540-74742-0_84
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