Parallel implementation of molecular dynamics simulation for short-ranged interaction

A parallel molecular dynamics simulation method, designed for large-scale problems, employing dynamic spatial domain decomposition for short-ranged molecular interactions is proposed. In this parallel cellular molecular dynamics (PCMD) simulation method, the link-cell data structure is used to reduce the searching time required for forming the cut-off neighbor list as well as for domain decomposition, which utilizes the multi-level graph-partitioning technique. A simple threshold scheme (STS), in which workload imbalance is monitored and compared with some threshold value during the runtime, is proposed to decide the proper time for repartitioning the domain. The simulation code is implemented and tested on the memory-distributed parallel machine, e.g., PC-cluster system. Parallel performance is studied using approximately one million L-J atoms in the condensed, vaporized and supercritical states. Results show that fairly good parallel efficiency at 49 processors can be obtained for the condensed and supercritical states (∼60%), while it is comparably lower for the vaporized state (∼40%).     

A novel computer virus propagation model and its dynamics

By taking into account the fact that, in general, a computer immediately possesses infectivity as soon as it is infected, a novel computer virus propagation model, known as the SLBS model, is established. It is proved that the dynamic behaviour of the model is determined by a threshold R ₀. Specifically, the virus-free equilibrium is globally asymptotically stable if R ₀≤1, whereas the virulent equilibrium is globally asymptotically stable if 1<R ₀≤4. It is conjectured that the virulent equilibrium is also globally asymptotically stable if R ₀>4. These results suggest some effective strategies for eradicating computer viruses distributed in the Internet.     

量子–经典混合神经网络及其故障诊断应用

量子神经网络由于结合了量子计算和神经网络的优点, 近年来受到了广泛的关注. 然而由于目前量子计算 资源受限(如量子比特数、量子逻辑门的保真度等)以及贫瘠高原现象(量子神经网络优化过程中解空间变得平坦时 出现的训练困难)的存在, 量子神经网络当前还难以大规模训练. 针对上述问题, 本文面向量子–经典混合神经网络 模型提出了一种基于无监督学习的特征提取方法. 所采用的无监督学习方法结合了量子自编码器和K-medoids聚类 方法, 可用于多层次结构的特征学习. 该方法创新地利用了K-mediods方法对训练得到的量子自编码器进行聚类, 以 最大化量子自编码器性质的差异. 进一步, 本文在轴承异常检测问题上, 通过实验验证了所提出的无监督特征提取 方法的有效性和实用性, 测试集准确率在二分类、四分类和十分类分别达到100%, 89.6%和81.6%.     

Processing of the molecular dynamics model by the parallel computer pax

Molecular dynamics model is processed by a parallel array type computer PAX, that has an architecture of nearest neighbor meash connection of processors. Two parallel schemes, named Lagrangian and Eulerian, are implemented, execution time and efficiency are analyzed and expressed in terms of the basic parameters such as problem size and array size. The Lagrangian scheme realizes high efficiency close to 1, which assures the linear speedup proportional to the size of the processor array. Parallel programming technique is also presented.     

A molecular dynamics implementation of the 3D Mercedes-Benz water model

The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution.Program summaryProgram title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water)Catalogue identifier: AEKM_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 20 501No. of bytes in distributed program, including test data, etc.: 551 044Distribution format: tar.gzProgramming language: Fortran 90Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer.Operating system: Linux, Unix, OS XHas the code been vectorized or parallelized?: The code has been parallelized using MPI.RAM: Depends on size of system, about 5 MB for 1500 molecules.Classification: 7.7External routines: A random number generator, Mersenne Twister (http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution.Nature of problem: Molecular dynamics simulation of a new geometric water model.Solution method: New force-field for water molecules, velocity–Verlet integration, representation of molecules as rigid particles with rotations described using quaternion algebra.Restrictions: Memory and cpu time limit the size of simulations.Additional comments: Software web site: https://gitorious.org/cashew/.Running time: Depends on the size of system. The sample tests provided only take a few seconds.     

Petascale molecular dynamics simulation using the fast multipole method on K computer

In this paper, we report all-atom simulations of molecular crowding — a result from the full node simulation on the “K computer”, which is a 10-PFLOPS supercomputer in Japan. The capability of this machine enables us to perform simulation of crowded cellular environments, which are more realistic compared to conventional MD simulations where proteins are simulated in isolation. Living cells are “crowded” because macromolecules comprise ∼30% of their molecular weight. Recently, the effects of crowded cellular environments on protein stability have been revealed through in-cell NMR spectroscopy. To measure the performance of the “K computer”, we performed all-atom classical molecular dynamics simulations of two systems: target proteins in a solvent, and target proteins in an environment of molecular crowders that mimic the conditions of a living cell. Using the full system, we achieved 4.4 PFLOPS during a 520 million-atom simulation with cutoff of 28 Å. Furthermore, we discuss the performance and scaling of fast multipole methods for molecular dynamics simulations on the “K computer”, as well as comparisons with Ewald summation methods.     

Vectorization of molecular dynamics Fortran programs using the cyber 205 vector processing computer

A concept of vectorization of molecular dynamics Fortran programs for the use of the Cyber 205 machine is presented. It is shown that for calculations with larger particle systems the program runs faster on the 205 than on the Cray-1 by about a factor of two. Against conventional computers like the Cyber 175 an acceleration by a factor 10–15 is expected. A bit control vector is used instead of a neighbour list, which in principal provides calculations up to 6912 particles for the memory capacity of the Cyber 205. However, because the application of the bit vector requires computation times which grow proportional to N², the CPU time for particle numbers of more than 2048 becomes prohibitively large.     

Efficient parallel implementation of Ewald summation in molecular dynamics simulations on multi-core platforms

We present a multi-step computation method to implement the Ewald summation for long-range electrostatic interactions in molecular dynamic simulations on a multi-core machine. Our methodology is based on the OpenMP programming model. It partitions computations of real-space summation among threads so that the global force of a single particle cannot be modified by more than one thread simultaneously. It requires neither a private copy of the force array for each thread nor an inspector at runtime. Compared with some other methods that can parallelise reduction operations on a force-array, our method achieves relatively higher speedups and lower L2 cache miss and bus utilisation ratios.     

自主可控计算机设计与实现

在基于国产高性能龙芯3A CPU芯片进行主板研制并成功实现的技术基础上,通过全面总结自主可控主板的软硬件及整机的实现过程,对自我研制主板的各主要功能电路及关键技术进行了详细阐述,对基于国产固件、操作系统进行整机系统的实现以及针对整机进行的性能测试进行了介绍说明,为国产自主可控计算机的发展提供技术借鉴。     

Chemical ideograms and molecular computer graphics

Molecular computer graphics (MCG) has become the indispensable complement of experimental chemical and biological tools and, in a way, will shape the evolution of these fields. This accelerated and popularized evolution takes root in the visual, even scenic, grasping of fundamental chemical concepts, perceived as veritable ideograms, which condense a vast amount of information with a few two- or threedimensional graphic symbols. With MCG one can carry out real computerized syntheses of chemical images. MCG is also an ideal tool through which to visualize the changes of a system as a function of time. This review article describes the potentials and advantages of structural MCG for visualizing the basic steps of important modelization concepts, particularly for handling on-line structures in information networks and in computer-assisted drug design (CADD) applications.     

三值光学计算机模拟器的设计与实现

三值光学计算机(ternary optical computer, TOC)作为一种新体系结构的计算机,具有处理器位数众多且易扩展、位功能可重构、位可分组使用等特点,在海量或复杂数据的快速处理方面有很大潜力,但它的应用开发探索尚处于初期。为了扩展其应用范围,提出了一种基于三值光学计算机体系架构的模拟器TOCSim设计方案。该方案通过软件形式模拟TOC的运行过程,并在普通PC机上实现其雏形。TOCSim主要模拟TOC处理器的重构策略、处理器位的分配策略、中间结果解码以及运算效果模拟等过程。通过本模拟器的模拟效果图与TOC原型机上的运行结果光图进行对比,表明该模拟器的设计方案是正确的、可行的。     

An efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations

This paper focuses on the implementation and the performance analysis of a smooth particle mesh Ewald method on several parallel computers. We present the details of the algorithms and our implementation that are used to optimize parallel efficiency on such parallel computers.     

A computer implementation of the partition of the unity procedure and its application to arthropod population dynamics. A case study on the European grape berry moth

This paper presents a new procedure to construct families of spatial approximation-prediction functions which depend on several parameters. The method is based on partitions of the unity. In order to find optimal functions in these families we introduce a Vietoris simplicial set associated to an influence radius. We consider error estimators induced by these Vietoris simplicial sets. A computational implementation of these mathematical models has been developed to be applied to any kind of finite discrete data. Our methods provide a useful tool for the analysis of the spatial distribution of species, which is imperative for developing accurate and efficient management of endangered and invasive species, biological conservation programs, etc. We demonstrate the application of our method to the analysis of the spatial distribution of the grape moth Lobesia botrana (Lepidoptera: Tortricidae) in the vineyards of La Rioja obtaining useful results for the management of this pest.     

Efficient computer implementation of coupled hydro-thermo-mechanical analysis

Hydro-thermo-mechanical analysis of reactor vessels based on the finite element method is a very demanding task due to its complexity as well as the large number of unknowns. This contribution deals with efficient computer implementation of the coupled analysis and attention is also devoted to domain decomposition methods which enable utilisation of parallel computers. The parallel processing leads to very good speedup and it also enables to solve significantly large problems in acceptable time. The proposed strategy is demonstrated on a coupled analysis of an existing reactor vessel.     

基于Linux的计算机集群系统的设计与实现

利用现成计算机构建由四台个人计算机组成的廉价、实用且性能优良的计算机集群。本研究设计是在有四台个人计算机组成的以太局域网内,建立一个基于Redhat9-Linux和MPI的集群计算环境,并在此基础上进行并行计算实验和性能测试。     

双冗余飞行控制计算机系统设计与实现

采用冗余技术是提高系统可靠性的重要手段。结合工程实践,详细介绍了一种双冗余飞行控制计算机系统的设计思路与方法。首先,描述系统设计结构和工作原理,然后,重点讲述如何在嵌入式实时操作系统VxW orks环境下进行多任务算法设计的要点。该冗余系统能有效地提高安全可靠性和任务可靠性,并具有良好的实时性和实用性的特点。     

超级计算机电源设计及实现

为了满足某千万亿次超级计算机高效率、低成本、高可靠的供电要求,采用了12 V直流分布式供电系统.详细介绍了机柜级、板级和处理器的电源设计框图和工作原理,采用SIMPLIS仿真软件对电压调节模块和其他DCDC变换器进行了仿真和验证.在此基础上,对系统稳定性进行了分析,提出了解决稳定性问题的若干措施.最后实测了系统运行时的部分电源电压波形.测量和运行结果表明,电源设计完全满足该超级计算机的供电要求.     

笔记本电脑嵌入式控制器的设计与实现

为了解决各类便携式计算机中电源管理与功耗控制问题,延长电池续航时间,提出了一种适用于笔记本电脑嵌入式控制器(embedded controller,EC)的设计方法.分析了EC的功能特性,在此基础上从硬件设计与软件实现两个方面给出设计思路.介绍了软件的实现,结合模块化思想提出了主要模块的解决方法,从而提高数据读取及功能控制等多项关键性功能的效果与效率.功能测试验证了该设计的可行性与有效性.