NAMD2:: Greater scalability for parallel molecular dynamics
NAMD2:: Greater scalability for parallel molecular dynamics
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DOI：
10.1006/jcph.1999.6201
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发表时间：
1999-05-01
影响因子：
4.1
通讯作者：
Schulten, K
中科院分区：
文献类型：
--
作者：
Kalé, L;Skeel, R;Schulten, K
分子动力学程序模拟生物分子系统的行为，从而了解它们的功能。然而，这种模拟的计算复杂性是巨大的。并行机提供了满足这一计算挑战的潜力。为了利用这种潜力，有必要开发一个可扩展的程序。程序还必须易于应用程序员修改。本文提出的NAMD 2程序旨在提供这些理想的功能。它使用空间分解结合力分解来增强可伸缩性。它使用智能定期负载平衡，以便最大限度地利用可用的计算能力。它是模块化组织的，并使用Charm++（一种并行C++方言）实现，以增强其可修改性。它使用数值技术和算法的组合，以确保能量漂移最小化，确保长期运行计算的准确性。NAMD 2使用一个名为匡威的可移植运行时框架，该框架还支持多个并行范例之间的互操作性。因此，应用程序的不同组件可以用最合适的并行范例编写。NAMD 2在大多数并行机器上运行，包括工作站集群，并在220个处理器上产生了超过180的加速比。本文还介绍了一些基准应用程序的性能。(C)北京：科学出版社.
Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application-domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decomposition combined with force decomposition to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calculations. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications. (C) 1999 Academic Press.