Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application.
Tios: The Internet of Simulations. Turning Molecular Dynamics into a Data Streaming Web Application.
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Tios：模拟互联网。
DOI：
10.1021/acs.jcim.9b00351
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发表时间：
2019
影响因子：
5.6
通讯作者：
Meletiou A
中科院分区：
文献类型：
--
作者：
Meletiou A
当前大多数学术高性能计算 (HPC) 资源的配置往往会强制执行并不总是最佳的分子动力学 (MD) 模拟工作和思考方式。例如，当模拟的目的是产生玻尔兹曼加权系综的代表性样本时，理想的情况是能够做到这一点，即进入无限长度的运行模拟，从中实时收集数据，并且只有在样本质量得到保证后才终止模拟。当前的方法基于规定最大长度的批处理作业和数据分析的后处理风格，抑制了这种情况。本着物联网的精神，我们开发了 Tios，这是一个 Python 应用程序，它将 MD 模拟转变为可远程发现和访问的流式 Web 应用程序，研究人员可以根据需要连接和下载数据。 Tios 可免费使用，可与标准 MD 代码配合使用，并且无需对其进行修改。在本文中，我们概述了 Tios 的工作原理，并提供了一些展示其功能的测试用例。
The configuration of most current academic high-performance computing (HPC) resources tends to enforce ways of working with, and thinking about, molecular dynamics (MD) simulations that are not always optimal. For example, when the aim of the simulation(s) is to produce a representative sample of a Boltzmann weighted ensemble, the ideal scenario would be to be able to do just that—i.e. to tap into a running simulation of indefinite length, collect data from it in real time, and only terminate the simulation once the quality of a sample was assured. Current approaches, based on batch jobs of proscribed maximum length, and a postprocessing style of data analysis, inhibit this. In the spirit of the Internet of Things, we have developed Tios, a Python application that turns MD simulations into remotely discoverable and accessible streaming web applications to which researchers can connect and download data as they please. Tios is freely available, works with standard MD codes, and requires no modifications to them. In this paper we outline how Tios works and present a number of test cases that demonstrate its capabilities.