Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP
Parallelizing a Molecular Dynamics Algorithm on a Multiprocessor Workstation Using OpenMP
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DOI：
10.1021/ci050126l
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发表时间：
2005-10
影响因子：
5.6
通讯作者：
K. B. Tarmyshov;F. Müller-Plathe
中科院分区：
文献类型：
--
作者：
K. B. Tarmyshov;F. Müller-Plathe
原子分子动力学程序YASP已经被并行化，用于共享内存的计算机体系结构。并行化被限制在最耗费CPU时间的部分：邻居列表构造、非绑定、角度和二面体力的计算以及约束。大部分连续的FORTRAN代码被保留；并行构造被插入为使用OpenMP标准的编译器指令。只有在邻居列表的情况下，数据结构才必须改变。对于数千个原子及以上的系统，并行代码比顺序代码实现了有用的加速比。在IBM Regatta p690+上，吞吐量随着处理器数量的增加而增加，最多12-16个处理器，具体取决于模拟系统的特性。在双处理器至强系统上，加速比约为1.7。
The atomistic molecular dynamics program YASP has been parallelized for shared-memory computer architectures. Parallelization was restricted to the most CPU-time-consuming parts: neighbor-list construction, calculation of nonbonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbor list did the data structure have to be changed. The parallel code achieves a useful speedup over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on the characteristics of the simulated systems. On dual-processor Xeon systems, the speedup is about 1.7.