Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
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DOI：
10.1147/rd.521.0177
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发表时间：
2008-01-01
影响因子：
1.3
通讯作者：
Kale, L. V.
中科院分区：
文献类型：
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作者：
Kumar, S.;Huang, C.;Kale, L. V.
NAMD（nanoscale molecular dynamics，纳米级分子动力学）是一种生产分子动力学（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，必须执行大量的迭代才能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IBM PowerPC（（R））440处理器内核。我们还提出了几种技术来扩展NAMD应用程序的IBM蓝色基因/L（TM）（BG/L）系统的20,480个节点。这些技术包括局部化通信的拓扑特定优化、针对BG/L环面优化的新消息传递协议、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5，570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 must be executed in order to understand interesting biological phenomena. Hence, we need MD applications to scale to thousands of processors, even though the individual timestep 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 obtain good sequential performance with NAMD on the embedded IBM PowerPC((R)) 440 processor core. We also present several techniques to scale the NAMD application to 20,480 nodes of the IBM Blue Gene/L (TM) (BG/L) system. These techniques include topology-specific optimizations to localize communication, new messaging protocols that are optimized for the BG/L torus, topology-aware load balancing, and overlap of computation and communication. We also present performance results of various molecular systems with sizes ranging from 5,570 to 327,506 atoms.