Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
Multiple program/multiple data molecular dynamics method with multiple time step integrator for large biological systems
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DOI：
10.1002/jcc.24511
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发表时间：
2017-06-15
影响因子：
3
通讯作者：
Sugita, Yuji
中科院分区：
文献类型：
--
作者：
Jung, Jaewoon;Sugita, Yuji
分子动力学（MD）模拟的离散化对于研究大型生物系统（如核糖体、病毒和细胞环境中的多种蛋白质）的构象动力学是必不可少的。为了提高并行计算的效率，我们必须通过引入区域分解方案来减少处理器之间的数据传输量。此外，重要的是要优化计算平衡之间的真实空间的非键相互作用和倒易空间的远程静电相互作用。在这里，我们介绍了一种新的并行化方案的大规模MD模拟的大规模并行超级计算机组成的CPU。我们利用多程序/多数据（MPMD）的方法分离的实空间和倒数空间的计算在不同的处理器上。我们还利用了r-ARMA多时间步长积分器的MPMD方法的框架上，在一个有效的方式：当倒数空间的计算被跳过在r-ARMA，为他们分配的处理器被用于一半的实空间计算。新方案使我们能够使用两倍的处理器，可在传统的单程序的方法。在K计算机上对100万（STMV）、850万（8_STMV）和2880万（27_STMV）原子系统进行全原子分子动力学模拟的最佳性能分别为65、36和24 ns/天。MPMD方案可以分别从STMV、8_STMV和27_STMV系统的单程序方法的最大性能加速23.4、10.2和9.2 ns/天，这对应于57%、39%和60%的加速。这表明通过增加处理器的数量而不损失并行计算效率可以显著加速。(c)2016 Wiley Periodicals，Inc.
Parallelization of molecular dynamics (MD) simulation is essential for investigating conformational dynamics of large biological systems, such as ribosomes, viruses, and multiple proteins in cellular environments. To improve efficiency in the parallel computation, we have to reduce the amount of data transfer between processors by introducing domain decomposition schemes. Also, it is important to optimize the computational balance between real-space non-bonded interactions and reciprocal-space interactions for long-range electrostatic interactions. Here, we introduce a novel parallelization scheme for large-scale MD simulations on massively parallel supercomputers consisting of only CPUs. We make use of a multiple program/multiple data (MPMD) approach for separating the real-space and reciprocal-space computations on different processors. We also utilize the r-RESPA multiple time step integrator on the framework of the MPMD approach in an efficient way: when the reciprocal-space computations are skipped in r-RESPA, processors assigned for them are utilized for half of the real-space computations. The new scheme allows us to use twice as many as processors that are available in the conventional single program approach. The best performances of all-atom MD simulations for 1 million (STMV), 8.5 million (8_STMV), and 28.8 million (27_STMV) atom systems on K computer are 65, 36, and 24 ns/day, respectively. The MPMD scheme can accelerate 23.4, 10.2, and 9.2 ns/day from the maximum performance of single-program approach for STMV, 8_STMV, and 27_STMV systems, respectively, which correspond to 57%, 39%, and 60% speed up. This suggests significant speedups by increasing the number of processors without losing parallel computational efficiency. (c) 2016 Wiley Periodicals, Inc.