Parallelization of AMBER molecular dynamics program for the AP1000 highly parallel computer

H. Sato, Y. Tanaka, H. Iwama, S. Kawakika, M. Saito, K. Morikami, T. Yao, S. Tsutsumi
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引用次数: 11

Abstract

The authors have parallelized the AMBER molecular dynamics program for the AP1000 highly parallel computer. To obtain a high degree of parallelism and an even load balance between processors for model problems of protein and water molecules, protein amino acid residues and water molecules are distributed to processors randomly. Global interprocessor communication required by this data mapping is efficiently done using the AP1000 broadcast network, to broadcast atom coordinate data for other processors' reference and its torus network; also for point-to-point communication to accumulate forces for atoms assigned to other processors. Experiments showed that a problem with 41095 atoms is processed 226 times faster with a 512 processor AP1000 than by a single processor.<>
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AP1000高并行计算机上AMBER分子动力学程序的并行化
作者在AP1000高并行计算机上并行化了AMBER分子动力学程序。为了使蛋白质和水分子模型问题的处理机之间具有高度的并行性和均匀的负载平衡,将蛋白质氨基酸残基和水分子随机分布到处理机中。该数据映射所需的全局处理器间通信利用AP1000广播网络高效完成,广播原子坐标数据供其他处理器及其环面网络参考;也用于点对点通信,为分配给其他处理器的原子积累力。实验表明,用512处理器AP1000处理41095个原子的问题比用单个处理器快226倍。
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