RP Bruin

University of Cambridge, Cambridge, England, United Kingdom

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Publications (41)24.92 Total impact

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    ABSTRACT: Grid‐based simulation usually involves large quantities of data at each stage of the simulation process. These data include simulation input and output files, intermediate results files, log and error files, associated metadata, and information capturing the processes that generate the data. The question of how to effectively store and manage data files within a Grid computing environment is increasingly becoming an important issue. This paper illustrates how we built a lightweight e‐Science infrastructure for data management within a Grid computing environment, including the integration of data curation activities into the entire Grid‐based simulation process. Rather than focusing on specific implementation details, we aim to identify the key issues and research challenges, describing how various existing technologies and tools can be best integrated to address these requirements and challenges. Although the case of quantum mechanical simulation of materials properties is used in the paper, much of the discussion is as generic as possible so that approaches, methods and practice (e.g. integrated approach, workflow taxonomy and development approach, simple but useful semantic annotation approach) can be applied to wider domains and disciplines to facilitat the digital research. A comparison between our approach and Cloud computing, and lessons learned in data management within the Grid computing environment, are also presented. Copyright © 2012 John Wiley & Sons, Ltd.
    Concurrency and Computation Practice and Experience 01/2013; 25(3). · 0.85 Impact Factor
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    ABSTRACT: In this paper, a service-oriented framework for running quantum mechanical simulation of material properties over Grids is proposed, and a prototype framework has been developed. The framework consists of portal and workflow systems, a set of class libraries and application programming interfaces, defined service specifications, schemas, and configuration files. The framework can be instantiated to submit specific quantum mechanical simulation (e.g., CASTEP) jobs to a Grid from a Web browser with the required tasks managed and coordinated by the workflow without human interaction. The paper details analysis, design, and implementation of a prototype framework. In the test case, the prototype framework is instantiated to submit a CASTEP simulation job to available Grid resources in order to calculate the equation of state of a material.
    IEEE Transactions on Systems Man and Cybernetics Part C (Applications and Reviews) 08/2010; · 2.55 Impact Factor
  • Xiaoyu Yang, R.P. Bruin, M.T. Dove
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    ABSTRACT: Grid-based simulation usually involves sequences of activities such as resource discovery, job submission, file transfer, analysis and simulation, and data harvesting. We can use service-oriented workflow to automate task coordination without direct human control, where each task and legacy scientific code can be presented as a Web service and thereby simplifying workflow development and maintenance. Because each service is described using Web Service Description Language, workflow manager works only with the WSDL interface rather than specific implementations.
    Computing in Science and Engineering 07/2010; · 1.73 Impact Factor
  • Xiaoyu Yang, Martin T. Dove, Richard P. Bruin
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    ABSTRACT: e-Science promotes global research collaboration based on Grid, hence building a user infrastructure that can facilitate the use of physical Grids to improve the Grid usability and accessibility becomes critical. This paper proposes to use a user-centered design approach to build a user level infrastructure for running Grid-enabled simulations, and reviews associated technologies. In a case study, a user infrastructure formulated by encompassing the user-centered design approach for running quantum mechanical simulation of material properties in a Grid environment is discussed.
    New Generation Computing 01/2010; 28:147-159. · 0.80 Impact Factor
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    ABSTRACT: We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 01/2009; 367(1890):967-85. · 2.89 Impact Factor
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    ABSTRACT: We describe RMCS as one of the first tools for grid computing that integrates data and metadata management into a single job submission system. The system is easy to use, with client tools that are easy to install. Although the RMCS system was developed as a prototype, it is now in production use and a number of scientific studies have been completed using it.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 01/2009; 367(1890):1047-50. · 2.89 Impact Factor
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    ABSTRACT: A collaborative environmental eScience project produces a broad range of data, notable as much for its diversity, in source and format, as its quantity. We find that extensible markup language (XML) and associated technologies are invaluable in managing this deluge of data. We describe F o X, a toolkit for allowing Fortran codes to read and write XML, thus allowing existing scientific tools to be easily re-used in an XML-centric workflow.
    Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences 12/2008; 367(1890):1041-6. · 2.89 Impact Factor
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    ABSTRACT: The problem of enabling scientist users to submit jobs to grid computing environments will eventually limit the usability of grids. The eMinerals project has tackled this problem by developing the ‘my_condor_submit’ (MCS) tool, which provides a simple scriptable interface to Globus, a flexible interaction with the storage resource broker, metascheduling with load balancing within a grid environment, and automatic metadata harvesting. This paper provides an overview of MCS together with a use case. We also describe the use of MCS within parameter-sweep studies. Copyright © 2008 John Wiley & Sons, Ltd.
    Concurrency and Computation Practice and Experience 08/2008; 20(11):1329 - 1340. · 0.85 Impact Factor
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    ABSTRACT: The structure of diopside (CaMgSi2O6) has been calculated at pressures between 0 and 25GPa using the planewaves and pseudopotentials approach to density functional theory. After applying a pressure correction of 4.66GPa to allow for the under-binding usually associated with the generalized gradient approximation, cell parameters are in good agreement with experiment. Fitting to the third-order Birch–Murnaghan equation of state yields values of 122GPa and 4.7 for the bulk modulus and its pressure derivative. In addition to cell parameters, our calculations provide all atomic positional parameters to pressures considerably beyond those currently available from experiment. We have analyzed these data in terms of polyhedral rigidity and regularity and find that the most compressible Ca polyhedron becomes markedly less anisotropic above 10GPa.
    Physics and Chemistry of Minerals 07/2008; 35(7):359-366. · 1.30 Impact Factor
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    ABSTRACT: We propose an explanation for the anomalous compressibility maximum in amorphous silica based on rigidity arguments. The model considers the fact that a network structure will be rigidly compressed in the high-pressure limit, and rigidly taut in the negative pressure limit, but flexible and hence softer at intermediate pressures. We validate the plausibility of this explanation by the analysis of molecular dynamics simulations. In fact this model is quite general, and will apply to any network solid, crystalline or amorphous; there are experimental indications that support this prediction. In contrast to other ideas concerning the compressibility maximum in amorphous silica, the model presented here does not invoke the existence of polyamorphic phase transitions in the glass phase.
    Journal of Physics Condensed Matter 06/2007; · 2.22 Impact Factor
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    ABSTRACT: Escience technologies are designed to address problems arising in the practice of computational science. The outcome of computational science is the generation of data, and a significant portion of these problems concern Information Delivery: the process of disseminating data across virtual organizations, and of contextualizing that data so that relevant quantities may be extracted and examined with the minimum of difficulty. This paper describes some of these issues encountered in the particular field of computational mineral science, and the solutions that the eMinerals consortium has developed to address them.
    e-Science and Grid Computing, 2006. e-Science '06. Second IEEE International Conference on; 01/2007
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    ABSTRACT: The use of atomic scale computer simulation of minerals to obtain information for geophysics and environmental science has grown enormously over the past couple of decades. It is now routine to probe mineral behavior in the Earth's deep interior and in the surface environment by borrowing methods and simulation codes from computational chemistry and physics. It is becoming increasingly important to use methods embodied in more than one of these codes to solve any single scientific problem. However, scientific codes are rarely designed for easy interoperability and data exchange; data formats are often code-specific, poorly documented and fragile, liable to frequent change between software versions, and even compiler versions. This means that the scientist's simple desire to use the methodological approaches offered by multiple codes is frustrated, and even the sharing of data between collaborators becomes fraught with difficulties. The eMinerals consortium was formed in the early stages of the UK eScience program with the aim of developing the tools needed to apply atomic scale simulation to environmental problems in a grid-enabled world, and to harness the computational power offered by grid technologies to address some outstanding mineralogical problems. One example of the kind of problem we can tackle is the origin of the compressibility anomaly in silica glass. By passing data directly between simulation and analysis tools we were able to probe this effect in more detail than has previously been possible and have shown how the anomaly is related to the details of the amorphous structure. In order to approach this kind of problem we have constructed a mini-grid, a small scale and extensible combined compute- and data-grid that allows the execution of many calculations in parallel, and the transparent storage of semantically-rich marked-up result data. Importantly, we automatically capture multiple kinds of metadata and key results from each calculation. We believe that the lessons learned and tools developed will be useful in many areas of science beyond the computational mineralogy. Key tools that will be described include: a pure Fortran XML library (FoX) that presents XPath, SAX and DOM interfaces as well as permitting the easy production of valid XML from legacy Fortran programs; a job submission framework that automatically schedules calculations to remote grid resources, handles data staging and metadata capture; and a tool (AgentX) that map concepts from an ontology onto locations in documents of various formats that we use to enable data exchange.
    AGU Fall Meeting Abstracts. 12/2006;
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    ABSTRACT: Grid computing has the potential to revolutionise how small groups of simulation scientists work together to tackle new science problems. In this paper we report how the eMinerals project has developed a small scale integrated compute and data grid infrastructure - the eMinerals minigrid - and developed generic job submission tools that exploit this infrastructure and which enable the science users to also access other grid systems.
    Second International Conference on e-Science and Grid Technologies (e-Science 2006), 4-6 December 2006, Amsterdam, The Netherlands; 12/2006
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    ABSTRACT: We use the example of a study of the compressibility anomaly in amourphous silica to illustrate how molecular-scale simulations can be performed using grid computing. The potential for running many simulations within a single study requires the use of new data management methods, which are discussed in this paper. The example of silica highlightd the advantage of the use of grid computing for studying subtle effects.
    01/2006;
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    ABSTRACT: A report is presented on the use of eScience tools to parameterise a quantum mechanical model of an environmentally important organic molecule. eScience tools are shown to enable better model parameterisation by facilitating broad parameter sweeps that would otherwise, were more conventional methods used, be prohibitive in both time required to set up, submit and evaluate the calculations, and in the volume of data storage required. In this case, the broad parameter sweeps performed highlighted the existence of a computational artefact that was not expected affect this system to such an extent, and which is unlikely to have been observed had fewer data points been taken. The better parameterisation of the model leads to more accurate results and the better identification of the applicability of aspects of the model to the system, such that great confidence can be put in the results of the research, which is of environmental importance.
    01/2006;
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    ABSTRACT: This article describes the configuration, monitoring, management, and use of compute clusters in an environment in which users access resources via grid middleware tools rather than direct logins. The work described here shows that setting up and managing clusters within grid environments is feasible without large investments in support or user training.
    Computing in Science and Engineering 12/2005; · 1.73 Impact Factor
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    ABSTRACT: This paper describes a prototype grid infrastructure, called the “eMinerals minigrid”, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.
    Molecular Simulation 04/2005; 31(5):303-313. · 1.06 Impact Factor
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    ABSTRACT: Collaboratories provide an environment where researchers at distant locations work together at tackling important scientific and industrial problems. In this paper we outline the tools and principles used to form the eMinerals collaboratory, and discuss the experience, from within, of working towards establishing the eMinerals project team as a functioning virtual organisation. Much of the emphasis of this paper is on experience with the IT tools. We introduce a new application sharing tool.
    Molecular Simulation 04/2005; 31(5):329-337. · 1.06 Impact Factor
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    ABSTRACT: This article describes the techniques and mechanisms that have been used to tackle workflow problems encountered in the eMinerals project. We examine how established tools and technologies can be brought together to specify and deploy a computational process, consisting of a set of jobs and tasks, on our production level mini-grid infrastructure, with respect to a specific problem—the distribution of calculations required to determine, in a systematic way, the mechanisms by which pollutant molecules such as DDT, dioxins and biphenyls, become bound to soil minerals. We also briefly discuss the use of data standards such as the Chemical Mark-up Language (CML) and web-service based grid standards as a means to facilitate workflow specification.
    Molecular Simulation 01/2005; 31(5):323-328. · 1.06 Impact Factor
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    ABSTRACT: We present the structural as well as elastic properties of the alkaline earth oxides and FeO, calculated using hybrid exchange functionals within DFT. We show that by empirically fitting the amount of Fock-exchange in the hybrid functionals, we can accurately reproduce the pressure-induced phase transitions for MgO, CaO, SrO and BaO. For FeO the hybrid functionals predict an insulator $ metal transition at ca. 150 GPa, associated with an i-B8 $ B8 structural phase transition. The structural phase transition is accompanied by a spin transition from a high-to low-spin electron configuration on the Fe 2þ ions. Hence, FeO undergoes a magnetic phase transition from an anti-ferromagnetic to non-magnetic structure. We also find that as the ionicity of the polymorphs increases a higher fraction of Fock-exchange is required to reproduce the structural volumes reported from experiments.
    Molecular Simulation 01/2005; 31(5). · 1.06 Impact Factor