Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations
Scaling molecular dynamics beyond 100,000 processor cores for large-scale biophysical simulations
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DOI：
10.1002/jcc.25840
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发表时间：
2019-08-05
影响因子：
3
通讯作者：
Sanbonmatsu, Karissa Y.
中科院分区：
文献类型：
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作者：
Jung, Jaewoon;Nishima, Wataru;Sanbonmatsu, Karissa Y.
对生物相互作用复杂性的兴趣日益增长，这不断推动了在生物物理模拟中增加系统尺寸的需求，不仅需要强大和先进的硬件，而且需要适应性强的软件，可以容纳大量通过复杂力场相互作用的原子。为了解决这个问题，我们开发和实施的GENESIS分子动力学包设计的大量处理器的策略。通过最小化通信中涉及的过程的数量，远程静电相互作用被并行化。为了提高单指令多数据（SIMD）系统的性能，减少超大型系统的内存使用，提出了一种新的非绑定交互算法。在实空间非键合相互作用中，邻居搜索的内存使用量减少了约80%，从而显著加快了速度。使用描述物理3D染色质相互作用的实验数据，我们构建了第一个完整基因位点（GATA 4）的原子模型。总的来说，这些发展使完整生物分子复合物的第一个十亿原子模拟成为可能，实现了以1 ns/天的性能扩展到65，000个进程（130，000个处理器内核）。发布于2019年。本文是美国政府的作品，在美国属于公有领域。
The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accommodate a large number of atoms interacting through complex forcefields. To address this, we developed and implemented strategies in the GENESIS molecular dynamics package designed for large numbers of processors. Long-range electrostatic interactions were parallelized by minimizing the number of processes involved in communication. A novel algorithm was implemented for nonbonded interactions to increase single instruction multiple data (SIMD) performance, reducing memory usage for ultra large systems. Memory usage for neighbor searches in real-space nonbonded interactions was reduced by approximately 80%, leading to significant speedup. Using experimental data describing physical 3D chromatin interactions, we constructed the first atomistic model of an entire gene locus (GATA4). Taken together, these developments enabled the first billion-atom simulation of an intact biomolecular complex, achieving scaling to 65,000 processes (130,000 processor cores) with 1 ns/day performance. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.