WILEY Journal Home Page
Papers under review through 2007
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | The Parallel Image Processing Environment (PIPE): automated parallelization of satellite data analyses | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 1 | ||||||||
| Date | 01 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1058 | ||||||||
| Article ID | CPE1058 | ||||||||
| Author Name(s) | James J. Simpson1Timothy J. McIntire2Jared S. Berg3Yueh Lung (Ben) Tsou4 | ||||||||
| Author Email(s) | jsimpson@ucsd.ed1 | ||||||||
| Affiliation(s) | Digital Image Analysis Laboratory (DIAL), Scripps Institution of Oceanography, La Jolla, CA 92093-0237, U.S.A. 1 2 3 4 | ||||||||
| Keyword(s) | parallel computing, embarrassingly parallel, remote sensing, data-intensive and I/O demanding computing, image classification, neural networks, signal analysis, | ||||||||
Abstract |
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| A Beowulf-type cluster can: (1) mitigate many issues associated with the analysis of large, complex remotely sensed data sets; (2) shorten the response time of operational agencies to crisis-management situations; and (3) expedite the reanalysis of large archives of satellite data. Whereas most Beowulf-type designs support modeling applications, the Parallel Image Processing Environment (PIPE) addresses the unique requirements of remote sensing applications. PIPE has four hierarchical layers: hardware, operating system, middleware and applications. Rocks, a middleware sublayer, manages the cluster. DIAL-developed interprocess communication and control daemons form the second middleware sublayer. They encapsulate user-defined applications and thereby support automated, user-transparent parallelization of satellite data analyses, implemented in the applications layer using generalized constructs. The daemons also monitor resource (computational and I/O) utilization on a node/thread basis, a feature not supported by other generally available monitoring utilities. The application support libraries are fully extensible, facilitate the reuse of modular and commonly used software functions in new applications and thereby reduce both the cost and time to implement new applications. Two applications (signal analysis, image classification) show PIPE's versatility and performance characteristics. PIPE is intrinsically scalable, reliable and can be incrementally implemented. A comparison with other embarrassingly parallel systems is also provided. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Performance and effectiveness trade-off for checkpointing in fault-tolerant distributed systems | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 1 | ||||||||
| Date | 01 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1059 | ||||||||
| Article ID | CPE1059 | ||||||||
| Author Name(s) | Panagiotis Katsaros1Lefteris Angelis2Constantine Lazos3 | ||||||||
| Author Email(s) | katsaros@csd.auth.gr1 | ||||||||
| Affiliation(s) | Department of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece 1 2 3 | ||||||||
| Keyword(s) | checkpointing and recovery, fault tolerance, distributed systems, performance evaluation, statistical analysis, | ||||||||
Abstract |
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| Checkpointing has a crucial impact on systems' performance and fault-tolerance effectiveness: excessive checkpointing results in performance degradation, while deficient checkpointing incurs expensive recovery. In distributed systems with independent checkpoint activities there is no easy way to determine checkpoint frequencies optimizing response-time and fault-tolerance costs at the same time. The purpose of this paper is to investigate the potentialities of a statistical decision-making procedure. We adopt a simulation-based approach for obtaining performance metrics that are afterwards used for determining a trade-off between checkpoint interval reductions and efficiency in performance. Statistical methodology including experimental design, regression analysis and optimization provides us with the framework for comparing configurations, which use possibly different fault-tolerance mechanisms (replication-based or message-logging-based). Systematic research also allows us to take into account additional design factors, such as load balancing. The method is described in terms of a standardized object replication model (OMG FT-CORBA), but it could also be applied in other (e.g. process-based) computational models. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Parallel four-dimensional Haralick texture analysis for disk-resident image datasets | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 1 | ||||||||
| Date | 01 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1073 | ||||||||
| Article ID | CPE1073 | ||||||||
| Author Name(s) | Brent Woods1Bradley Clymer2Johannes Heverhagen3Michael Knopp4Joel Saltz5Tahsin Kurc6 | ||||||||
| Author Email(s) | kurc@bmi.osu.edu6 | ||||||||
| Affiliation(s) | Department of Electrical and Computer Engineering, Ohio State University, Columbus, OH 43210, U.S.A. 1 2 Department of Radiology, Ohio State University, Columbus, OH 43210, U.S.A. 3 4 Department of Biomedical Informatics, Ohio State University, Columbus, OH 43210, U.S.A. 5 6 | ||||||||
| Keyword(s) | biomedical image processing, texture analysis, distributed computing, | ||||||||
Abstract |
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| Texture analysis is one possible method of detecting features in biomedical images. During texture analysis, texture-related information is found by examining local variations in image brightness. Four-dimensional (4D) Haralick texture analysis is a method that extracts local variations along space and time dimensions and represents them as a collection of 14 statistical parameters. However, application of the 4D Haralick method on large time-dependent image datasets is hindered by data retrieval, computation, and memory requirements. This paper describes a parallel implementation using a distributed component-based framework of 4D Haralick texture analysis on PC clusters. The experimental performance results show that good performance can be achieved for this application via combined use of task- and data-parallelism. In addition, we show that our 4D texture analysis implementation can be used to classify imaged tissues. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Grid benchmarking: vision, challenges, and current status | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 1 | ||||||||
| Date | 01 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1086 | ||||||||
| Article ID | CPE1086 | ||||||||
| Author Name(s) | Marios D. Dikaiakos1 | ||||||||
| Author Email(s) | mdd@cs.ucy.ac.cy1 | ||||||||
| Affiliation(s) | Department of Computer Science, University of Cyprus, 1678 Nicosia, Cyprus 1 | ||||||||
| Keyword(s) | Grid benchmarking, ontologies, performance evaluation, | ||||||||
Abstract |
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| Grid benchmarking is an important and challenging topic of Grid computing research. In this paper, we present an overview of the key challenges that need to be addressed for the integration of benchmarking practices, techniques, and tools in emerging Grid computing infrastructures. We discuss the problems of performance representation, measurement, and interpretation in the context of Grid benchmarking, and propose the use of ontologies for organizing and describing benchmarking metrics. Finally, we present a survey of ongoing research efforts that develop benchmarks and benchmarking tools for the Grid. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | An optimization approach for decentralized QoS-based scheduling based on utility and pricing in Grid computing | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 1 | ||||||||
| Date | 01 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1106 | ||||||||
| Article ID | CPE1106 | ||||||||
| Author Name(s) | Li Chunlin1Li Layuan2 | ||||||||
| Author Email(s) | chunlin74@tom.com1 | ||||||||
| Affiliation(s) | Department of Computer Science, Wuhan University of Technology, Wuhan 430063, People's Republic of China 1 2 | ||||||||
| Keyword(s) | Quality of Service QoS, scheduling optimization, Grid, utility, | ||||||||
Abstract |
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| This paper presents an optimization approach for decentralized Quality of Service (QoS)-based scheduling based on utility and pricing in Grid computing. The paper assumes that the quality dimensions can be easily formulated as utility functions to express quality preferences for each task agent. The utility values are calculated by the user-supplied utility function that can be formulated with the task parameters. The QoS constraint Grid resource scheduling problem is formulated into a utility optimization problem. The QoS-based Grid resource scheduling optimization is decomposed into two subproblems by applying the Lagrangian method. In the Grid, a Grid task agent acts as a consumer paying for the Grid resource and the resource providers receive profits from task agents. A pricing-based QoS scheduling algorithm is used to perform optimally decentralized QoS-based resource scheduling. The experiments investigate the effect of the QoS metrics on the global utility and compare the performance of the proposed algorithm with other economical Grid resource scheduling algorithms. Copyright 2006 John Wiley Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | The importance of locality in the visualization of large datasets | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1042 | ||||||||
| Article ID | CPE1042 | ||||||||
| Author Name(s) | J. M. Brooke1J. Marsh2S. Pettifer3L. S. Sastry4 | ||||||||
| Author Email(s) | james.marsh@manchester.ac.uk2 | ||||||||
| Affiliation(s) | School of Computer Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K. 1 2 3 CCLRC, Rutherford Appleton Laboratory, Didcot, Oxon, U.K. 4 | ||||||||
| Keyword(s) | Grid computing, visualization, Web services, oceanography, | ||||||||
Abstract |
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| Many scientific phenomena in large high-resolution datasets such as the U.K. Ocean Circulation and Advanced Modelling (OCCAM) ocean model are better discovered through visualization than by algorithmic analysis: it is often more straightforward to see a feature than it is to characterize it numerically. Using traditional rendering techniques, the size of modern datasets presents a challenge for even high-end graphical supercomputers, and the cost of such hardware limits its availability for day-to-day analysis. We present an architecture that brings visual analysis to the desktop by exploiting consumer-grade graphics hardware in order to provide initial interactive exploration and Web services to enable finer-grained analysis and interoperability with traditional visualization tools. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Applying the Grid to 3D capture technology | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1043 | ||||||||
| Article ID | CPE1043 | ||||||||
| Author Name(s) | Lewis Mackenzie1Paul Cockshott2Viktor Yarmolenko3Ewan Borland4Paul Graham5Kostas Kavoussanakis6 | ||||||||
| Author Email(s) | wpc@dcs.gle.ac.uk2 | ||||||||
| Affiliation(s) | Department of Computing Science, 17 Lilybank Gardens, University of Glasgow, Glasgow G12 8QQ, U.K. 1 2 3 4 Edinburgh Parallel Computing Center, The University of Edinburgh, James Clerk Maxwell Building, Mayfield Road, Edinburgh EH9 3JZ, U.K. 5 6 | ||||||||
| Keyword(s) | Grid, pi calculus, Java, animation, 3D capture, | ||||||||
Abstract |
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| The PGPGrid project aims to parallelize the process of extracting range data from an experimental 3D scanner using the Grid as a vehicle for accessing necessary resources. The application is potentially highly parallel but has some unusual features such as rapid spawning of processes in real time and a dynamic inter-process network topology. These characteristics are such as to require enhancement of the usual task migration capabilities of the Globus toolkit. The present paper initially discusses attempts to estimate the real parallelizability of the scanner application. It then describes a new Java application programming interface, based on Milner's -calculus, which could be used to extend Globus in a manner capable of supporting systems with this kind of dynamic parallel structure. The location of processing resources for the -calculus is done using a Web-services-based resource locator. The article also describes the pipeline of processing from initial stereo photogrametry to the final production of animation models. A key step in this is the conformation of animators models to the data obtained by the real-time scanner. Algorithmic innovations in this process are described. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Catalyzer: a novel tool for integrating, managing and publishing heterogeneous bioscience data | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1044 | ||||||||
| Article ID | CPE1044 | ||||||||
| Author Name(s) | F. W. Howell1R. C. Cannon2N. H. Goddard3 | ||||||||
| Author Email(s) | fwh@inf.ed.ac.uk1 | ||||||||
| Affiliation(s) | Institute for Adaptive and Neural Computation, Informatics, University of Edinburgh, 5 Forrest Hill, Edinburgh EH1 2QL, U.K. 1 2 3 | ||||||||
| Keyword(s) | XML, semantic Web, e-Science, biological databases, data publication, data sharing, | ||||||||
Abstract |
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| The integrative ambitions of systems biology and neuroinformatics-to construct working models of the machinery of living cells and brains-will flounder unless researchers have access to the huge amounts of diverse experimental data being collected. However, the vast majority of bioscience research data that is gathered is never made available to other researchers, partly for the want of an adequate software for annotating experimental data, and partly for social reasons (researchers are rarely rewarded for publishing the actual data sets-just for journal articles summarizing findings). Catalyzer ad hoc | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | e-Science and artificial neural networks in cancer management | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1045 | ||||||||
| Article ID | CPE1045 | ||||||||
| Author Name(s) | S. D. Dolgobrodov1R. Marshall2P. Moore3R. Bittern4R. J. C. Steele5A. Cuschieri6 | ||||||||
| Author Email(s) | robin.marshall@manchester.ac.uk2 | ||||||||
| Affiliation(s) | School of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, U.K. 1 2 3 Department of Surgery and Molecular Oncology, The University of Dundee, Dundee DD1 9SY, U.K. 4 5 Scuola Superiore S'Anna di Studi Universitari e di Perfezionamento, Piazza dei Martiri della Libertá n. 33, 56127 Pisa, Italy 6 | ||||||||
| Keyword(s) | cancer management, artificial neural network, e-Science, | ||||||||
Abstract |
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| We describe the origins of this project, its aims and its relevance to e-Science research. Particle physicists at the University of Manchester with experience of artificial neural networks (ANNs) have collaborated with clinicians at the University of Dundee to produce an ANN that is intended to predict survival rates and to indicate management profiles for cancer patients. Comparisons are made between typical data handling problems in particle physics and health care. The problems associated with data procurement, namely reliability and censoring are described, together with a discussion of how these problems were addressed. The inputs to the ANN and its decision output are discussed. The reliability of the ANN is assessed quantitatively. The prototype secure Web-based interface, which allows clinicians to input new patient data to the central node at the University of Manchester and to obtain prognoses from anywhere in the world is presented. For each topic, the e-Science relevance is described and underlined. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Optimization of integrated Earth System Model components using Grid-enabled data management and computation | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1046 | ||||||||
| Article ID | CPE1046 | ||||||||
| Author Name(s) | A. R. Price1G. Xue2A. Yool3D. J. Lunt4P. J. Valdes5T. M. Lenton6J. L. Wason7G. E. Pound8S. J. Cox9 | ||||||||
| Author Email(s) | a.r.price@soton.ac.uk1 | ||||||||
| Affiliation(s) | Southampton Regional e-Science Centre, University of Southampton, Southampton SO17 1BJ, U.K. 1 2 National Oceanography Centre, University of Southampton, Southampton SO14 3ZH, U.K. 3School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, U.K. 4 5 School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, U.K. 6 7 8 9 | ||||||||
| Keyword(s) | optimization, Grid, data management, Earth System Model, Kriging, Genetic Algorithm, | ||||||||
Abstract |
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| In this paper, we present the Grid enabled data management system that has been deployed for the Grid ENabled Integrated Earth system model (GENIE) project. The database system is an augmented version of the Geodise Database Toolbox and provides a repository for scripts, binaries and output data in the GENIE framework. By exploiting the functionality available in the Geodise toolboxes we demonstrate how the database can be employed to tune parameters of coupled GENIE Earth System Model components to improve their match with observational data. A Matlab client provides a common environment for the project Virtual Organization and allows the scripting of bespoke tuning studies that can exploit multiple heterogeneous computational resources. We present the results of a number of tuning exercises performed on GENIE model components using multi-dimensional optimization methods. In particular, we find that it is possible to successfully tune models with up to 30 free parameters using Kriging and Genetic Algorithm methods. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Developing LHCb Grid software: experiences and advances | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1048 | ||||||||
| Article ID | CPE1048 | ||||||||
| Author Name(s) | I. Stokes-Rees1A. Tsaregorodtsev2V. Garonne3R. Graciani4M. Sanchez5M. Frank6J. Closier7 | ||||||||
| Author Email(s) | i.stokes-rees1@physics.ox.ac.uk1 | ||||||||
| Affiliation(s) | Department of Particle Physics, University of Oxford, Oxford OX1 3RH, U.K. 1Centre de Physique des Particules de Marseille, 163 avenue de Luminy, Case 902, 13288 Marseille cedex 09, France 2 3 Departamento de Estructura y Constituyentes de la Materia, Facultat de Fisica, Universidad de Barcelona, Diagonal 647, 08028 Barcelona, Spain 4Departamento de Física de Particulas, Facultade de Física, Campus Universitario Sur, E-15782 Santiago de Compostela, Spain 5CERN, CH-1211 Genève 23, Switzerland 6 7 | ||||||||
| Keyword(s) | Grid, scheduling, workload management, service-oriented architecture (SOA), physics computing, | ||||||||
Abstract |
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| The LHCb Grid software has been used for two Physics Data Challenges, with the latter producing over 98 TB of data and consuming over 650 processor-years of computing power. This paper discusses the experience of developing a Grid infrastructure, interfacing to an existing Grid (LCG) and traditional computing centres simultaneously, running LHCb experiment software and jobs on the Grid, and the integration of a number of new technologies into the Grid infrastructure. Our experience and utilization of the following core technologies will be discussed: OGSI, XML-RPC, Grid services, LCG middleware and instant messaging. Specific attention will be given to analysing the behaviour of over 100 000 jobs executed through the LCG Grid environment, providing insight into the performance, failure modes and scheduling efficiency over a period of several months for a large computational Grid incorporating over 40 sites and thousands of nodes. © Crown copyright 2006. Reproduced with the permission of Her Majesty's Stationery Office. Published by John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Supporting scientific discovery processes in Discovery Net | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1049 | ||||||||
| Article ID | CPE1049 | ||||||||
| Author Name(s) | Jameel Syed1Moustafa Ghanem2Yike Guo3 | ||||||||
| Author Email(s) | jasyed@acm.org1 | ||||||||
| Affiliation(s) | Imperial College London, South Kensington Campus, 180 Queen's Gate, London SW7 2AZ, U.K. 1 2 3 | ||||||||
| Keyword(s) | Workflow, e-Science, preservation, provenance, audit, Web services, | ||||||||
Abstract |
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| The activity of e‐Science involves making discoveries by analysing data to find new knowledge. Discoveries of value cannot be made by simply performing a pre‐defined set of steps to produce a result. Rather, there is an original, creative aspect to the activity that by its nature cannot be automated. In addition to finding new knowledge, discovery therefore also concerns finding a process to find new knowledge. How discovery processes are modelled is therefore key to effectively practicing e‐Science. We argue that since a discovery process instance serves a similar purpose to a mathematical proof it should have similar properties, namely it allows results to be deterministically reproduced when re‐executed and that intermediate results can be viewed to aid examination and comprehension. We examine the issues involved for software environments used to make discoveries to preserve these properties, and show how they are tackled in the Discovery Net system. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Recycling workflows and services through discovery and reuse | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1050 | ||||||||
| Article ID | CPE1050 | ||||||||
| Author Name(s) | Chris Wroe1Carole Goble2Antoon Goderis3Phillip Lord4Simon Miles5Juri Papay6Pinar Alper7Luc Moreau8 | ||||||||
| Author Email(s) | carole@cs.man.ac.uk2 | ||||||||
| Affiliation(s) | School of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, U.K. 1 2 3 4 School of Electronics and Computer Science, University of Southampton, Southampton SO17 1BJ, U.K. 5 6 7 8 | ||||||||
| Keyword(s) | workflow, reuse, semantic discovery, | ||||||||
Abstract |
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| Scientific workflows are becoming a valuable tool for scientists to capture and automate e-Science procedures. Their success brings the opportunity to publish, share, reuse and re-purpose this explicitly captured knowledge. Within the Grid project, we have identified key resources that can be shared including complete workflows, fragments of workflows and constituent services. We have examined the alternative ways that these resources can be described by their authors (and subsequent users) and developed a unified descriptive model to support their later discovery. By basing this model on existing standards, we have been able to extend existing Web service and Semantic Web service infrastructure whilst still supporting the specific needs of the e-Scientist. The Grid components enable a workflow life-cycle that extends beyond execution to include the discovery of previous relevant designs, the reuse of those designs and their subsequent publication. Experience with example groups of scientists indicates that this cycle is valuable. The growing number of workflows and services mean more work is needed to support the user in effective ranking of search results and to support the re-purposing process. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Editorial | ||||||||
| Article Title | Special Issue: Selected Papers from the 2004 U.K. e-Science All Hands Meeting (AHM 2004) | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 2 | ||||||||
| Date | 02 00 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1051 | ||||||||
| Article ID | CPE1051 | ||||||||
| Author Name(s) | D. W. Walker1M. P. Atkinson2I. Sommerville3 | ||||||||
| Author Email(s) | |||||||||
| Affiliation(s) | School of Computer Science, Cardiff University, Cardiff CF24 3AA, U.K. 1e-Science Institute, 15 South College Street, Edinburgh EH8 9AA, U.K. 2Computing Department, Lancaster University, Lancaster LA1 4WA, U.K. 3 | ||||||||
| Keyword(s) | ., | ||||||||
Abstract |
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| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Editorial | ||||||||
| Article Title | Special Issue: Parallel and Distributed Systems: Testing and Debugging (PADTAD) | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 3 | ||||||||
| Date | 03 10 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1061 | ||||||||
| Article ID | CPE1061 | ||||||||
| Author Name(s) | Shmuel Ur1 | ||||||||
| Author Email(s) | |||||||||
| Affiliation(s) | IBM Haifa Research Laboratory, Haifa 31905, Israel 1 | ||||||||
| Keyword(s) | ., | ||||||||
Abstract |
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| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | Choosing among alternative pasts | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 3 | ||||||||
| Date | 03 10 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1062 | ||||||||
| Article ID | CPE1062 | ||||||||
| Author Name(s) | Marina Biberstein1Eitan Farchi2Shmuel Ur3 | ||||||||
| Author Email(s) | ur@il.ibm.com3 | ||||||||
| Affiliation(s) | IBM Haifa Research Laboratory, Haifa University Campus, Haifa 31905, Israel 1 2 3 | ||||||||
| Keyword(s) | multithreading, software testing, | ||||||||
Abstract |
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| The primary difficulty with testing concurrent programs is their non-determinism, where two executions with the same input can yield different results due to a changed thread schedule (also known as interleaving). This problem is aggravated by the fact that most thread schedulers are almost deterministic, and generate the same interleavings over and over for a given testing environment. The traditional approach to testing concurrent programs is to identify and examine the race conditions. A different solution involves noise-making, which generates different interleavings at runtime, for example, using embedded sleep statements. This paper proposes a totally different technique for generating a rich set of interleavings. In this approach, operations on shared variables are tracked. Every time a shared variable is read, the value to be read is selected from the set of values that were held by this variable during the program execution. The algorithm identifies those values that the variable could hold in some interleaving consistent with the past observed events. Within this subset, the value choice can be random, biased-random, based on coverage, etc. The problem of identifying read values that are consistent with the past observations is far from simple, since past decisions on value selection affect future ones. Our solution is computationally intensive and, therefore, impractical as is. However, insights gained from this solution lead to new heuristics for noise-making. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | A method for verifying concurrent Java components based on an analysis of concurrency failures | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 3 | ||||||||
| Date | 03 10 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1063 | ||||||||
| Article ID | CPE1063 | ||||||||
| Author Name(s) | Brad Long1Paul Strooper2Luke Wildman3 | ||||||||
| Author Email(s) | pstroop@itee.uq.edu.au2 | ||||||||
| Affiliation(s) | School of Information Technology and Electrical Engineering, The University of Queensland, Brisbane, Queensland 4072, Australia 1 2 3 | ||||||||
| Keyword(s) | concurrency, verification, testing, component, Java, | ||||||||
Abstract |
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| The Java programming language supports concurrency. Concurrent programs are harder to verify than their sequential counterparts due to their inherent non-determinism and a number of specific concurrency problems, such as interference and deadlock. In previous work, we have developed the ConAn testing tool for the testing of concurrent Java components. ConAn has been found to be effective at testing a large number of components, but there are certain classes of failures that are hard to detect using ConAn. Although a variety of other verification tools and techniques have been proposed for the verification of concurrent software, they each have their strengths and weaknesses. In this paper, we propose a method for verifying concurrent Java components that includes ConAn and complements it with other static and dynamic verification tools and techniques. The proposal is based on an analysis of common concurrency problems and concurrency failures in Java components. As a starting point for determining the concurrency failures in Java components, a Petri-net model of Java concurrency is used. By systematically analysing the model, we come up with a complete classification of concurrency failures. The classification and analysis are then used to determine suitable tools and techniques for detecting each of the failures. Finally, we propose to combine these tools and techniques into a method for verifying concurrent Java components. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||
| Publisher | John Wiley & Sons, Ltd. Chichester, UK | ||||||||
| Category | Research Article | ||||||||
| Article Title | MultiRace: efficient on-the-fly data race detection in multithreaded C++ programs | ||||||||
| Volume ID | 19 | ||||||||
| Issue ID | 3 | ||||||||
| Date | 03 10 2007 | ||||||||
| DOI(URI) | http://dx.doi.org/10.1002/cpe.1064 | ||||||||
| Article ID | CPE1064 | ||||||||
| Author Name(s) | Eli Pozniansky1Assaf Schuster2 | ||||||||
| Author Email(s) | assaf@cs.technion.ac.il2 | ||||||||
| Affiliation(s) | Computer Science Department, Technion-Israel Institute of Technology, Haifa 32000, Israel 1 2 | ||||||||
| Keyword(s) | data race, concurrency, multithreading, instrumentation, synchronization, | ||||||||
Abstract |
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| Data race detection is highly essential for debugging multithreaded programs and assuring their correctness. Nevertheless, there is no single universal technique capable of handling the task efficiently, since the data race detection problem is computationally hard in the general case. Thus, all currently available tools, when applied to some general case program, usually result in excessive false alarms or in a large number of undetected races. Another major drawback of many currently available tools is that they are restricted, for performance reasons, to detection units of fixed size. Thus, they all suffer from the same problem-choosing a small unit might result in missing some of the data races, while choosing a large one might lead to false detection. We present a novel testing tool, called MultiRace, which combines improved versions of Djit and Lockset-two very powerful on-the-fly algorithms for dynamic detection of apparent data races. Both extended algorithms detect races in multithreaded programs that may execute on weak consistency systems, and may use two-way as well as global synchronization primitives. By employing novel technologies, MultiRace adjusts its detection to the native granularity of objects and variables in the program under examination. In order to monitor all accesses to each of the shared locations, MultiRace instruments the C++ source code of the program. It lets the user fine-tune the detection process, but otherwise is completely automatic and transparent. This paper describes the algorithms employed in MultiRace, gives highlights of its implementation issues, and suggests some optimizations. It shows that the overheads imposed by MultiRace are often much smaller (orders of magnitude) than those obtained by other existing tools. Copyright © 2006 John Wiley & Sons, Ltd. | |||||||||