A survey of life sciences applications on the grid

The availability of powerful microprocessors and improvements in the performance of networks has enabled high performance computing on wide-area, distributed systems. Computational grids, by integrating diverse, geographically distributed and essentially heterogeneous resources provide the infrastructure for solving large-scale problems. However, heterogeneity, on the one hand allows for scalability, but on the other hand makes application development and deployment for such an environment extremely difficult. The field of life sciences has been an explosion in data over the past decade. The data acquired needs to be processed, interpreted and analyzed to be useful. The large resource needs of bioinformatics allied to the large number of data-parallel applications in this field and the availability of a powerful, high performance, computing grid environment lead naturally to opportunities for developing grid-enabled applications. This survey, done as part of the Life Sciences Research Group (a research group belonging to the Global Grid Forum) attempts to collate information regarding grid-enabled applications in this field. Arun Krishnan, Ph.D.: He did his undergraduate in Electrochemical Engineering in the Central Electrochemical Research Institute in India and went on to do his Ph.D. in Advanced Process Control from the University of South Carolina. He then worked in the control and high performance computing industries for about 3 years before moving to the Bioinformatics Institute in Singapore. He is currently a Young Investigator for the Distributed Computing in Biomedicine Group at BII. His research interests include parallel and distributed computing with special emphasis on grid computing and its application to the biomedical area. He is also interested in developing parallel algorithms for sequence analysis and protein structure prediction.     

MOLECULAR DOCKING: An example of grid enabled applications

The molecular docking web interface was developed to execute Autodock3.05 molecular docking program in the Grid environment. The nature of the application which allows the whole docking jobs to be broken up into multiple small independent tasks, has the potential of utilizing the availability of the Grid computing. Using the web interface, the whole docking procedures can be automated from the start to the end. Automation includes the preparation of the target receptor, creation of parameter files (gpf and dpf), calculation of grid energy, and docking of molecules. Once the job is split into small tasks, the tasks are submitted to Globus GRAM that submits the tasks to the resources available in the Grid environment. The execution of the grid-enabled AutoDock 3.05 is tested and the results showed that the process of molecular docking are faster compared if the execution is run on sequential computing resources.     

基于网格技术的密码学计算平台的设计

结合现有的网格技术、思想和密码计算的特点,分析了利用网格技术实现密码学计算的可行性,并结合J2EE开发方式的优势实现系统支持,最后提出了一种有效的、可行的密码计算网格平台构架。     

中国国家网格作业管理设计与实现

基于中国国家网格（CNGrid）及其系统软件CNGrid GOS,提出并实现了一种VegaBatch网格作业管理系统。VegaBatch通过基于队列长度预测的元调度策略解决了网格作业调度问题;利用双重同步机制维护全局网格作业信息视图;借助用户身份切换机制保障作业数据安全;增加作业重执行功能提供数据后处理能力。对比了国际上较为成熟的网格作业管理软件,讨论了VegaBatch解决的问题。该软件目前已部署在CNGrid环境,提供了功能丰富、安全可靠的网格作业管理功能,降低了CNGrid的使用管理成本,提升了用户体验。     

Effective time step restrictions for explicit MPM simulation

Time steps for explicit MPM simulation in computer graphics are often selected by trial and error due to the challenges in automatically selecting stable time step sizes. Our time integration scheme uses time step restrictions that take into account forces, collisions, and even grid-to-particle transfers calculated near the end of the time step. We propose a novel set of time step restrictions that allow a time step to be selected that is stable, efficient to compute, and not too far from optimal. We derive the general solution for the sound speed in nonlinear isotropic hyperelastic materials, which we use to enforce the classical CFL time step restriction. We identify a single-particle instability in explicit MPM integration and propose a corresponding time step restriction in the fluid case. We also propose a reflection-based boundary condition for domain walls that supports separation and accurate Coulomb friction while preventing particles from penetrating the domain walls.     

网格计算安全模型的研究

网格计算是一种新型的计算模式,具有数据处理能力强和运行成本低的特点。近年来,有关网格计算系统的安全性设计越发受到关注,但现有的网络安全技术在处理复杂的、动态的网格计算系统时,在访问控制、权限授予等环节的效果并不理想。首先分析了网格计算系统的安全性需求,其次研究并借鉴了现有颇具代表性的网络安全架构,最后我们从网格安全设计和实现的角度,对网格计算系统提出一种新的安全体系结构模型,并深入讨论了网格计算系统中各实体间交互时所采取的相应安全策略。     

一个小型网格原型系统的设计与实现

这个小型网格原型系统是基于OGSA(开放网格服务架构)体系结构和Web 服务架构而构建的网格服务的基础平台,按照OGSI网格服务规范标准,用GT3(Globus Toolkit 3.0)网格开发工具包开发实现。程序设计符合通常的分布式计算编程模型,它包括服务器端编程和客户端编程两个部分,它们之间的联系是通过WSDL服务描述文件来完成的。最后通过实验展示了其实用性。     

基于OGSA-DAI的数据集成模型研究

随着网格技术应用研究的发展,网格计算环境下数据库访问和集成现成为研究热点。以OGSA-DAI和异构数据库集成技术为基础,概述了数据集成的关键技术,提出了基于OGSA-DAI的数据集成模型,重点讨论了模型的体系结构、数据集成的步骤和实现方法,并以开发的基于此模型的虚拟数据库作为应用实例,验证了所提出模型的有效性。     

网格计算的安全性研究与技术实现

网格计算环境必须以现有的Internet为通信支撑平台,由于Internet本身的开放性和异构性,决定了网格计算面临着各种各样的安全威胁,因此网格安全已成为网格计算环境中的一个核心问题。该文简述了网格安全需求,分析了网格安全技术,并给出了基于Globus项目中网格安全的主要技术手段。     

一种网格计算中的资源定位策略

简述了网格计算的概念及其背景,然后引出资源定位问题,在资源定位问题上对如Napster采用的对等网格环境下的资源定位策略进行探讨,最后给出了策略的一种实现方法.     

网格体系结构、关键技术及其应用

网格是信息社会的网络基础设施,是下一代Web技术。通过介绍网格概念、特点,阐述了网格的组成与体系结构,诠释了网格系统的关键技术,分析了几个网格系统,最后讨论了网格的应用领域。     

Cognitive simulation as a tool for cognitive task analysis

Cognitive simulations are runnable computer programs that represent models of human cognitive activities. We show how one cognitive simulation built as a model of some of the cognitive processes involved in dynamic fault management can be used in conjunction with small-scale empirical data on human performance to uncover the cognitive demands of a task, to identify where intention errors are likely to occur, and to point to improvements in the person-machine system. The simulation, called Cognitive Environment Simulation or CES, has been exercised on several nuclear power plant accident scenarios. Here we report one case to illustrate how a cognitive simulation tool such as CES can be used to clarify the cognitive demands of a problem-solving situation as part of a cognitive task analysis.     

ODE: a tool for distributing object-oriented applications

Object-oriented applications are increasingly being deployed in distributed computing environments. Technologies, such as Java RMI, and architectures, such as CORBA, DCOM, and Enterprise Java Beans, are facilitating and enhancing this trend. The performance and eventual success of these applications is dependent on distribution decisions made by the application designer. This decision is a complex one, involving a large number of alternatives and multiple conflicting criteria. Rigorous approaches for effective distribution of object-oriented applications are still lacking. This paper describes the implementation of a practical and effective approach for distributing object-oriented applications. A prototype decision support system—object distribution environment (ODE)—that implements the approach in the form of a user-friendly tool for the design of distributed object-oriented applications is described. ODE has been successfully used in the distribution of a real world distributed object-oriented system.     

Under-approximation Heuristics for Grid-based Bounded Model Checking

In this paper, we consider the effect of BDD-based under-approximation on a hybrid approach using BDDs and SAT-BMC for error detection on a computing grid. We experimentally study effect of under-approximation approaches on a non-traditional parallelization of BMC based on state space partitioning. This parallelization is accomplished by executing multiple instances of BMC independently from different seed states, that are selected from the reachable states in different partitions. Such states are spread out across the state space and can potentially be deep. Since all processors work independently of each other, this scheme is suitable for bug hunting using a grid-like network. Our experimental results demonstrate improvement over existing approaches, and we show that the method can effectively utilize a large grid network.     

Simplifying autonomic enterprise Java Bean applications via model-driven engineering and simulation

The goal of autonomic computing is to reduce the configuration, operational, and maintenance costs of distributed applications by enabling them to self-manage, self-heal, and self-optimize. This paper provides two contributions to the Model-Driven Engineering (MDE) of autonomic computing systems using Enterprise Java Beans (EJBs). First, we describe the structure and functionality of an MDE tool that visually captures the design of EJB applications, their quality of service (QoS) requirements, and the adaptations applied to their EJBs. Second, the paper describes how MDE tools can be used to generate code to simulate adaptive systems for verification and plug EJBs into a Java component framework that provides runtime adaptation capabilities.     

FIRST: a flexible and interactive resampling tool for CFD simulation data

We introduce a flexible, variable resolution tool for interactive resampling of computational fluid dynamics (CFD) simulation data on versatile grids. The tool and coupled algorithm afford users precise control of glyph placement during vector field visualization via six interactive degrees of freedom. Other important characteristics of this method include: (1) an algorithm that resamples any unstructured grid onto any structured grid, (2) handles changes to underlying topology and geometry, (3) handles unstructured grids with holes and discontinuities, (4) does not rely on any pre-processing of the data, and (5) processes large numbers of unstructured grid cells efficiently. We believe this tool to be a valuable asset in the engineer's pursuit of understanding and visualizing the underlying flow field in CFD simulation results.     

网格技术及其在校园网安全中的应用

在信息化高速发展的今天,作为学校发展的重要基础设施-校园网也应逐渐完善,但是由于高校各部门、学院信息系统的异构和信息系统的漏洞,使得校园信息化进程缓慢.本文针对校园网资源分散和安全问题,提出了将网格技术应用于校园网,网格技术作为一种新兴的技术极大地解决了这一系列问题,从而实现了资源的高度共享,并通过网格认证和授权,在一定程度上较好地解决了校园网安全问题.     

MVSMg:一个基于网格的计算燃烧学可视化共享模型

提出了一种基于网格的计算燃烧学可视化共享模型MVSMg（Multilevel Visualization and Storage Model based on grid）,并给出了形式化定义。模型将共享分为静态共享和动态共享。网格环境下计算燃烧学的数据可视化分为多级,帮助领域专家进行不同深度的研究。对好的应用模块进行注册,并与处理所得数据一起分层存储．以利于其他用户共享。还提出了一个动态共享和注册管理算法。最终实现了数据和应用模块的共享,避免了重复开发和计算。