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蛍光X線ホログラムからの3次元原子像再生のXcalableMPによる並列化

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(1)情報処理学会論文誌. プログラミング. Vol.10 No.1 30 (Jan. 2017). 発表概要. 蛍光 X 線ホログラムからの 3 次元原子像再生の XcalableMP による並列化 窪田 昌史1,a). 松下 智裕2. 八方 直久1. 2016年6月9日発表. 蛍光 X 線ホログラフィーは,特定元素周辺の数 nm にわたり 3 次元原子配列を再生できる 3 次元中距離 局所構造解析技術である.3 次元原子像再生には離散フーリエ変換(DFT)を適用しているが,この DFT の処理に長時間を要しているのが現状である.本研究では,この DFT に対して並列処理プログラミング 言語 XcalableMP を用いて並列化処理を行った.入力 X 線波長が 21 種類のエネルギー,179 × 360 点の ホログラムデータから 3 次元の各軸 201 点の直交座標の原子像データを求める処理を,8 ノード 96 コアの. Xeon X5660 2.8 GHz の PC クラスタ上で実行したところ,逐次実行に対し 94 倍の高速化が達成された.. Parallelization of Three-dimensional Atomic Image Reconstruction from X-ray Fluorescence Holograms with XcalableMP Atsushi Kubota1,a). Tomohiro Matsushita2. Naohisa Happo1. Presented: June 9, 2016. X-ray fluorescence holography is a three-dimensional middle range local structure structural analysis method, which can provide three-dimensional atomic images around specific elements within a radius of a few nanometers. Three-dimensional atomic images are reconstructed by applying discrete Fourier transform (DFT) to hologram data. Presently, it takes long time to process this DFT. In this study, the DFT program is parallelized by using a parallel programming language XcalableMP. The DFT process, whose input is 21 holograms data of 179 × 360 points and output is a three-dimensional atomic image of 2013 points, is executed on PC cluster which consists of 8 nodes of Intel Xeon X5660 processors and 96 cores in total and we confirmed that the parallelized DFT execution is 94 times faster than the sequential execution.. 1 2. a). 広島市立大学 Hiroshima City University, Hiroshima 731–3194, Japan (公財)高輝度光科学研究センター Japan Synchrotron Radiation Research Institute, Hyogo 679–5198, Japan [email protected]. c 2017 Information Processing Society of Japan . 30.

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