Asynchronous replica exchange for molecular simulations
Asynchronous replica exchange for molecular simulations
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DOI：
10.1002/jcc.20839
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发表时间：
2008-04-15
影响因子：
3
通讯作者：
Parashar, Manish
中科院分区：
文献类型：
--
作者：
Gallicchio, Emilio;Levy, Ronald M.;Parashar, Manish
提出了一种副本交换方法的异步实现，该方法解决了传统同步副本交换实现的一些局限性。在异步副本交换中，处理器对独立于其他处理器发起和执行温度副本交换，从而消除了对在常规同步实现中发现的处理器同步的需要。分子系统上的说明性计算表明，异步副本交换，相反的同步实现，是能够利用在接近最高效率的松散耦合池的处理器与异构的速度，如那些发现在计算网格和CPU清除环境。它还表明，采用非最近邻温度交换，这是简单的异步算法内实现，可以导致更快的温度平衡跨处理器。(c)2007 Wiley Periodicals，Inc.
An asynchronous implementation of the replica exchange method that addresses some of the limitations of conventional synchronous replica exchange implementations is presented. In asynchronous replica exchange pairs of processors initiate and perform temperature replica exchanges independently from the other processors, thereby removing the need for processor synchronization found in conventional synchronous implementations. Illustrative calculations on a molecular system are presented that show that asynchronous replica exchange, contrary to the synchronous implementation, is able to utilize at nearly top efficiency loosely coupled pools of processors with heterogeneous speeds, such as those found in computational grids and CPU scavenging environments. It is also shown that employing non-nearest-neighbor temperature exchanges, which are straightforward to implement within the asynchronous algorithm, can lead to faster temperature equilibration across processors. (c) 2007 Wiley Periodicals, Inc.