On the performance of molecular dynamics applications on current high-end systems
On the performance of molecular dynamics applications on current high-end systems
复制标题
论分子动力学应用在当前高端系统上的性能
DOI：
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发表时间：
2005
期刊：
影响因子：
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通讯作者：
P. Sherwood
中科院分区：
文献类型：
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作者：
J. Hein;Fiona Reid;Lorna Smith;I. Bush;M. Guest;P. Sherwood
在分子模拟中有效利用当前的高性能计算（HPC）平台依赖于本代并行分子动力学代码有效利用这些平台及其组件（包括CPU和内存）的能力。在本文中，我们研究了一系列流行分子动力学代码在英国国家HPC资源、IBM p690+集群和SGI Altix 3700上的效率和扩展性。主要集中在琥珀色，Dl_Poly和Namd模拟代码，我们证明了主要的性能和可扩展性的优势，通过分布式，而不是复制的数据的方法。
The effective exploitation of current high performance computing (HPC) platforms in molecular simulation relies on the ability of the present generation of parallel molecular dynamics code to make effective utilisation of these platforms and their components, including CPUs and memory. In this paper, we investigate the efficiency and scaling of a series of popular molecular dynamics codes on the UK's national HPC resources, an IBM p690+ cluster and an SGI Altix 3700. Focusing primarily on the Amber, Dl_Poly and Namd simulation codes, we demonstrate the major performance and scalability advantages that arise through a distributed, rather than a replicated data approach.