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2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)最新文献

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Towards flexible automated support to improve the quality of computational science and engineering software 向灵活的自动化支持,以提高计算科学和工程软件的质量
D. Falessi, F. Shull
Continual evolution of the available hardware (e.g. in terms of increasing size, architecture, and computing power) and software (e.g. reusable libraries) is the norm rather than exception. Our goal is to enable CSE developers to spend more of their time finding scientific results by capitalizing on these evolutions instead of being stuck in fixing software engineering (SE) problems such as porting the application to new hardware, debugging, reusing (unreliable) code, and integrating open source libraries. In this paper we sketch a flexible automated solution supporting scientists and engineers in developing accurate and reliable CSE applications. This solution, by collecting and analyzing product and process metrics, enables the application of well-established software engineering best practices (e.g., separation of concerns, regression testing and inspections) and it is based upon the principles of automation, flexibility and iteration.
可用硬件(例如,在尺寸、架构和计算能力方面)和软件(例如,可重用库)的持续发展是常态,而不是例外。我们的目标是使CSE开发人员能够花更多的时间通过利用这些演进来寻找科学结果,而不是被困在修复软件工程(SE)问题上,比如将应用程序移植到新的硬件、调试、重用(不可靠的)代码,以及集成开源库。在本文中,我们概述了一个灵活的自动化解决方案,支持科学家和工程师开发准确可靠的CSE应用。这个解决方案,通过收集和分析产品和过程度量标准,使建立好的软件工程最佳实践(例如,关注点分离、回归测试和检查)的应用成为可能,并且它是基于自动化、灵活性和迭代的原则。
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引用次数: 2
Practical formal correctness checking of million-core problem solving environments for HPC 用于高性能计算的百万核问题解决环境的实用形式正确性检查
D. C. B. D. Oliveira, Zvonimir Rakamaric, G. Gopalakrishnan, A. Humphrey, Qingyu Meng, M. Berzins
While formal correctness checking methods have been deployed at scale in a number of important practical domains, we believe that such an experiment has yet to occur in the domain of high performance computing at the scale of a million CPU cores. This paper presents preliminary results from the Uintah Runtime Verification (URV) project that has been launched with this objective. Uintah is an asynchronous task-graph based problem-solving environment that has shown promising results on problems as diverse as fluid-structure interaction and turbulent combustion at well over 200K cores to date. Uintah has been tested on leading platforms such as Kraken, Keenland, and Titan consisting of multicore CPUs and GPUs, incorporates several innovative design features, and is following a roadmap for development well into the million core regime. The main results from the URV project to date are crystallized in two observations: (1) A diverse array of well-known ideas from lightweight formal methods and testing/observing HPC systems at scale have an excellent chance of succeeding. The real challenges are in finding out exactly which combinations of ideas to deploy, and where. (2) Large-scale problem solving environments for HPC must be designed such that they can be “crashed early” (at smaller scales of deployment) and “crashed often” (have effective ways of input generation and schedule perturbation that cause vulnerabilities to be attacked with higher probability). Furthermore, following each crash, one must “explain well” (given the extremely obscure ways in which an error finally manifests itself, we must develop ways to record information leading up to the crash in informative ways, to minimize offsite debugging burden). Our plans to achieve these goals and to measure our success are described. We also highlight some of the broadly applicable concepts and approaches.
虽然正式的正确性检查方法已经在许多重要的实际领域中大规模部署,但我们认为这样的实验还没有出现在100万CPU内核规模的高性能计算领域。本文介绍了基于此目标启动的Runtime Verification (URV)项目的初步结果。untah是一个基于异步任务图的问题解决环境,迄今为止已经在超过20万个核上显示出了令人鼓舞的结果,包括流体-结构相互作用和湍流燃烧等各种问题。untah已经在Kraken, Keenland和Titan等领先平台上进行了测试,包括多核cpu和gpu,结合了一些创新的设计功能,并且正在遵循开发路线图进入百万核制度。迄今为止,URV项目的主要成果主要体现在两个方面:(1)来自轻量级形式化方法和大规模测试/观察HPC系统的各种众所周知的想法有很好的成功机会。真正的挑战在于找出应该部署哪些想法组合,以及在哪里部署。(2) HPC的大规模问题解决环境必须被设计成能够“早崩溃”(在较小的部署规模下)和“经常崩溃”(具有有效的输入生成方式和时间表扰动,导致漏洞被攻击的概率更高)。此外,在每次崩溃之后,必须“很好地解释”(考虑到错误最终表现出来的极其模糊的方式,我们必须开发出以有信息的方式记录导致崩溃的信息的方法,以尽量减少场外调试负担)。描述了我们实现这些目标和衡量我们成功的计划。我们还重点介绍了一些广泛适用的概念和方法。
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引用次数: 4
Design and rationale of a quality assurance process for a scientific framework 科学框架的质量保证过程的设计和基本原理
H. Remmel, B. Paech, C. Engwer, P. Bastian
The testing of scientific frameworks is a challenging task. The special characteristics of scientific software e.g. missing test oracle, the need for high performance parallel computing, and high priority of non-functional requirements, need to be accounted for as well as the large variability in a framework. In our previous research, we have shown how software product line engineering can be applied to support the testing of scientific frameworks. We developed a process for handling the variability of a framework using software product line (SPL) variability modeling. From the variability models, we derive test applications and use them for system tests for the framework. In this paper we examine the overall quality assurance for a scientific framework. First, we propose a SPL test strategy for scientific frameworks called Variable test Application strategy for Frameworks (VAF). This test strategy tests both, commonality and variability, of the framework and supports the framework's users in testing their applications by creating reusable test artifacts. We operationalize VAF with test activities that are combined with other quality assurance activities to form the design of a quality assurance process for scientific frameworks. We introduce a list of special characteristics for scientific software that we use as rationale for the design of this process.
科学框架的检验是一项具有挑战性的任务。科学软件的特殊特性,例如缺少测试oracle,对高性能并行计算的需求,非功能需求的高优先级,以及框架中的巨大可变性都需要考虑在内。在我们之前的研究中,我们已经展示了如何应用软件产品线工程来支持科学框架的测试。我们开发了一个使用软件产品线(SPL)可变性建模来处理框架可变性的过程。从可变性模型中,我们派生出测试应用程序,并将它们用于框架的系统测试。在本文中,我们研究了一个科学框架的整体质量保证。首先,我们提出了一种科学框架的SPL测试策略,称为框架变量测试应用策略(VAF)。该测试策略测试框架的通用性和可变性,并通过创建可重用的测试工件来支持框架用户测试他们的应用程序。我们通过与其他质量保证活动相结合的测试活动来实施VAF,以形成科学框架的质量保证过程的设计。我们介绍了一系列科学软件的特殊特性,我们将这些特性作为设计该过程的基本原理。
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引用次数: 7
Implementing continuous integration software in an established computational chemistry software package 在已建立的计算化学软件包中实现持续集成软件
Robin M. Betz, R. Walker
Continuous integration is the software engineering principle of rapid and automated development and testing. We identify several key points of continuous integration and demonstrate how they relate to the needs of computational science projects by discussing the implementation and relevance of these principles to AMBER, a large and widely used molecular dynamics software package. The use of a continuous integration server has both improved collaboration and communication between AMBER developers, who are globally distributed, as well as making failure and benchmark information that would be time consuming for individual developers to obtain by themselves, available in real time. Continuous integration servers currently available are aimed at the software engineering community and can be difficult to adapt to the needs of computational science projects, however as demonstrated in this paper the effort payoff can be rapid since uncommon errors are found and contributions from geographically separated researchers are unified into one easily-accessible web-based interface.
持续集成是快速和自动化开发和测试的软件工程原则。我们确定了持续集成的几个关键点,并通过讨论这些原则与AMBER(一个大型且广泛使用的分子动力学软件包)的实现和相关性,展示了它们如何与计算科学项目的需求相关。持续集成服务器的使用既改善了全球分布的AMBER开发人员之间的协作和沟通,也使单个开发人员自己获取的耗时的故障和基准信息实时可用。目前可用的持续集成服务器是针对软件工程社区的,很难适应计算科学项目的需要,然而,正如本文所展示的那样,由于发现了罕见的错误,并且来自地理上分散的研究人员的贡献被统一到一个易于访问的基于web的界面中,因此努力的回报可以很快。
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引用次数: 7
Water Science Software Institute: An open source engagement process 水科学软件研究所:一个开源的参与过程
S. Ahalt, B. Minsker, M. Tiemann, L. Band, M. Palmer, R. Idaszak, C. Lenhardt, M. Whitton
We have conceptualized a public/private Water Science Software Institute (WSSI) whose mission is “to enable and accelerate transformative water science by concurrently transforming both the software culture and the research culture of the water science community”. To achieve our goals, we have applied an Open Community Engagement Process (OCEP), based in large part on the principles and practices of Agile and Open Source software development. This manuscript describes the WSSI and the OCEP model we have developed to operationalize the WSSI.
我们构想了一个公共/私人水科学软件研究所(WSSI),其使命是“通过同时改变水科学界的软件文化和研究文化来实现和加速水科学的变革”。为了实现我们的目标,我们应用了一个开放社区参与过程(OCEP),它在很大程度上基于敏捷和开源软件开发的原则和实践。本文描述了WSSI和OCEP模型,我们已经开发了WSSI的操作。
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引用次数: 8
Exploring issues in software systems used and developed by domain experts 探索领域专家使用和开发的软件系统中的问题
Jette Henderson, D. Perry
Software engineering researchers have paid a good deal of attention to fault cause, discovery, and repair in software systems developed by software professionals. Yet, not all software is developed by software professionals, and consequently, not as much research has been conducted that explores fault cause, discovery, and repair in software systems developed by domain experts. In this exploratory paper, we outline research plans for studying the types of faults that domain experts encounter when developing software for their own research. To attain this goal we propose a multiple case study that will allow us to explore questions about domain expert software use, needs, and development.
软件工程研究人员对软件专业人员开发的软件系统中的故障原因、发现和修复给予了大量关注。然而,并不是所有的软件都是由软件专业人员开发的,因此,在由领域专家开发的软件系统中,对故障原因、发现和修复进行探索的研究并不多。在这篇探索性的论文中,我们概述了研究领域专家在为自己的研究开发软件时遇到的故障类型的研究计划。为了达到这个目标,我们提出了一个多案例研究,这将允许我们探索有关领域专家软件使用、需求和开发的问题。
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引用次数: 1
Binary instrumentation support for measuring performance in OpenMP programs 二进制仪器支持测量OpenMP程序中的性能
Mustafa Elfituri, Jeanine E. Cook, Jonathan J. Cook
In parallel computations, evaluating the causes of poor speedup is an important development activity to reach the goal of creating the most efficient parallel computation possible. In our research on irregular parallel computations, especially graph algorithms, we had specific measurement needs for which a dearth of tools could be found. We created PGOMP, a small library-based profiling tool for the Gnu OpenMP implementation, and show its use here in discovering some of the causes of poor speedup in graph computations.
在并行计算中,为了达到创建最高效并行计算的目标,评估加速差的原因是一项重要的开发活动。在我们对不规则并行计算,特别是图算法的研究中,我们有特定的测量需求,而缺乏相应的工具。我们创建了PGOMP,这是一个用于Gnu OpenMP实现的小型基于库的分析工具,并在这里展示了它在发现图形计算加速差的一些原因中的用途。
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引用次数: 1
Implicit provenance gathering through configuration management 通过配置管理进行隐式的来源收集
Vitor C. Neves, V. Braganholo, Leonardo Gresta Paulino Murta
Scientific experiments based on computer simulations usually consume and produce huge amounts of data. Data provenance is used to help scientists answer queries related to how experiment data were generated or changed. However, during the experiment execution, data not explicitly referenced by the experiment specification may lead to an implicit data flow missed by the existing provenance gathering infrastructures. This paper introduces a novel approach to gather and store implicit data flow provenance through configuration management. Our approach opens some new opportunities in terms of provenance analysis, such as identifying implicit data flows, identifying data transformations along an experiment trial, comparing data evolution in different trials of the same experiment, and identifying side effects on data evolution caused by implicit data flows.
基于计算机模拟的科学实验通常会消耗和产生大量数据。数据来源是用来帮助科学家回答有关实验数据是如何产生或改变的问题。然而,在实验执行过程中,没有被实验规范明确引用的数据可能导致隐式数据流被现有的来源收集基础设施遗漏。本文介绍了一种通过配置管理来收集和存储隐式数据流来源的新方法。我们的方法在来源分析方面开辟了一些新的机会,例如识别隐式数据流,识别实验试验中的数据转换,比较同一实验的不同试验中的数据演变,以及识别隐式数据流对数据演变的副作用。
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引用次数: 5
A case study: Agile development in the community laser-induced incandescence modeling environment (CLiiME) 案例研究:社区激光诱导白炽建模环境(clime)中的敏捷开发
Aziz Nanthaamornphong, Karla Morris, D. Rouson, H. Michelsen
The multidisciplinary requirements of current computational modeling problems preclude the development of scientific software that is maintained and used by selected scientists. The multidisciplinary nature of these efforts requires the development of large scale software projects established with a wide developer and user base in mind. This article describes some of the software-engineering practices adopted in a scientific-software application for a laser-induced incandescence community model. The project uses an Agile and Test-Driven Development approach to implement the infrastructure for the development of a collaborative model that is to be extended, modified, and used by different researchers. We discuss some of the software-engineering practices that can be exploited through the life of a project, starting with its inception when only a hand full of developers are contributing to the project and the mechanism we have put in place in order to allow the natural expansion of the model.
当前计算建模问题的多学科要求阻碍了由选定的科学家维护和使用的科学软件的开发。这些工作的多学科性质要求开发具有广泛开发人员和用户基础的大型软件项目。本文描述了在激光诱导白炽社区模型的科学软件应用中采用的一些软件工程实践。该项目使用敏捷和测试驱动开发方法来实现协作模型开发的基础设施,该模型将被不同的研究人员扩展、修改和使用。我们讨论了在项目的整个生命周期中可以利用的一些软件工程实践,从它的初始阶段开始,当只有一堆开发人员为项目做出贡献时,以及我们为了允许模型的自然扩展而放置的机制。
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引用次数: 16
DSLs, DLA, DxT, and MDE in CSE
Bryan Marker, R. V. D. Geijn, D. Batory
We narrate insights from a collaboration between researchers in Software Engineering (SE) and in the domain of Dense Linear Algebra (DLA) libraries. We highlight our impressions of how software development for computational science has traditionally been different from the development of software in other domains. We observe that scientific software (at least DLA libraries) is often developed by domain experts rather than legions of programmers. For this reason, researchers in SE need to impact the productivity of experts rather than the productivity of the masses. We document this and other lessons learned.
我们叙述了在软件工程(SE)和密集线性代数(DLA)库领域的研究人员之间的合作的见解。我们强调了计算科学的软件开发传统上与其他领域的软件开发的不同之处。我们观察到科学软件(至少是DLA库)通常是由领域专家而不是大批程序员开发的。因此,SE的研究人员需要影响专家的生产力,而不是大众的生产力。我们记录了这些经验教训和其他经验教训。
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引用次数: 3
期刊
2013 5th International Workshop on Software Engineering for Computational Science and Engineering (SE-CSE)
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