Scalable Molecular Dynamics with NAMD on Blue Gene / L-猫眼课题宝

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2012

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Sameer Kumar;Chao-Da Huang;G. Zheng;Eric J. Bohm;A. Bhatele;James C. Phillips;Hao Yu;L. Kalé

NAMD（NANoscale Molecular Dynamics）是一个生产分子动力学（MD）应用程序，用于生物分子模拟，包括蛋白质，细胞膜和水分子的组装。在生物分子模拟中，问题的大小是固定的，需要执行大量的迭代来理解有趣的生物现象。因此，我们需要MD应用程序扩展到数千个处理器，即使一个处理器上的单个时间步长非常小。NAMD已经在几种并行计算机架构上证明了其性能。在本文中，我们提出了各种编译器优化技术，使用单指令多数据（SIMD）指令，以获得良好的顺序性能与NAMD嵌入式440核心。我们还提出了几种技术来扩展NAMD到20，480个节点的Blue Gene/L。这些包括用于本地化通信的拓扑特定优化、针对Blue Gene/L torus优化的新消息传递协议（因为它们不需要消息排序）、拓扑感知负载平衡以及计算和通信的重叠。我们还介绍了各种分子系统的性能结果，其尺寸范围从5570到327，506个原子。

NAMD (NAnoscale Molecular Dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes and water molecules. In a biomolecular simulation, the problem-size is fixed and a large number of iterations need to be executed to understand interesting biological phenomenon. Hence we need MD applications to scale to thousands of processors, even though the individual time step on one processor is quite small. NAMD has demonstrated its performance on several parallel computer architectures. In this paper, we present various compiler optimization techniques that use Single Instruction Multiple Data (SIMD) instructions to get good sequential performance with NAMD on the embedded 440 core. We also present several techniques to scale NAMD to 20,480 nodes of Blue Gene/L. These include topology specific optimizations to localize communication, new messaging protocols that are optimized for the Blue Gene/L torus (as they do not require message ordering), topology aware load balancing, and overlap of computation and communication. We also present performance results of various molecular systems with sizes ranging from 5570 to 327,506 atoms.

Scalable Molecular Dynamics with NAMD on Blue Gene / L

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