Job submission to grid computing environments

Bruin, R. P.; White, T. O. H.; Walker, Andrew; Austen, Kat; Dove, MT; Tyer, R. P.; Couch, PA; Todorov, IT; Blanchard, Marc

doi:10.1002/cpe.1290

Cited by 14 publications

(11 citation statements)

References 4 publications

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“…Job submission was carried out using the my_condor_ submit (MCS) tool [15,16,21], which was specifically developed by one of the authors (RPB) to facilitate job submission to Globus grid computing environments with a high degree of usability as the key design requirement. As a result, the user only needs to supply a very simple script.…”

Section: Job Submission and Managementmentioning

confidence: 99%

“…In addition to handling job submission, MCS is also designed to enable interaction with the SRB, in order to enable downloading of files from the SRB to the actual grid resource on which the simulation is performed and the subsequent upload of output files. Many of the details of MCS are described in detail elsewhere [21].…”

Section: Job Submission and Managementmentioning

confidence: 99%

“…Although MCS manages the running of jobs, there is also the challenge of preparing all the input files. This is accomplished by a separate tool developed by one of the authors (RPB) [21]. At its heart, the tool has a script that takes a template and generates a set of input files and MCS Figure 2.…”

Section: Job Submission and Managementmentioning

confidence: 99%

See 2 more Smart Citations

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within theeMinerals escience project

Dove

Sullivan

Walker

et al. 2006

Molecular Simulation

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We use the example of a study of the compressibility anomaly in amorphous 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 highlights the advantages of the use of grid computing for studying subtle effects.

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Section: Job Submission and Managementmentioning

confidence: 99%

Section: Job Submission and Managementmentioning

confidence: 99%

See 1 more Smart Citation

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within theeMinerals escience project

Dove

Sullivan

Walker

et al. 2006

Molecular Simulation

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“…We use the GLOBUS TOOLKIT, with user authentication handled by X.509 certificates. However, GLOBUS commands are not easy for researchers to work with, and so we originally developed a grid job submission tool called my_condor_submit (MCS; Calleja et al 2005;Bruin et al 2008), which uses the CONDOR_G interface to GLOBUS and CONDOR's DAGMAN workflow system. This tool required the user to supply a simple script that closely resembles the scripts used with the CONDOR system, and which our experience showed users were more comfortable with.…”

Section: Escience Developments Within the Eminerals Project (A ) Gridmentioning

confidence: 99%

eScience for molecular-scale simulations and the e Minerals project

Salje

Artacho

Austen

et al. 2008

Phil. Trans. R. Soc. A.

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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.

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“…By contrast, the eMinerals [34] and Materials Grid [35] projects sought to develop automated scientific workflows forhigh-throughput computation in atomic-scale mineralogy and materials science. Theseworkflows combined distributed grid computing [26, 27] with tools to generate input files, extract and analyse output data, andcreate and store key items of metadata [28]. An important aspect of this work was the generation of a representationof the key data in a CML document.…”

Section: Introductionmentioning

confidence: 99%

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

2013

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BackgroundMultidisciplinary integrated research requires the ability to couple thediverse sets of data obtained from a range of complex experiments andcomputer simulations. Integrating data requires semantically richinformation. In this paper an end-to-end use of semantically rich data incomputational chemistry is demonstrated utilizing the Chemical MarkupLanguage (CML) framework. Semantically rich data is generated by the NWChemcomputational chemistry software with the FoX library and utilized by theAvogadro molecular editor for analysis and visualization.ResultsThe NWChem computational chemistry software has been modified and coupled tothe FoX library to write CML compliant XML data files. The FoX library wasexpanded to represent the lexical input files and molecular orbitals used bythe computational chemistry software. Draft dictionary entries and a formatfor molecular orbitals within CML CompChem were developed. The Avogadroapplication was extended to read in CML data, and display molecular geometryand electronic structure in the GUI allowing for an end-to-end solutionwhere Avogadro can create input structures, generate input files, NWChem canrun the calculation and Avogadro can then read in and analyse the CML outputproduced. The developments outlined in this paper will be made available infuture releases of NWChem, FoX, and Avogadro.ConclusionsThe production of CML compliant XML files for computational chemistrysoftware such as NWChem can be accomplished relatively easily using the FoXlibrary. The CML data can be read in by a newly developed reader in Avogadroand analysed or visualized in various ways. A community-based effort isneeded to further develop the CML CompChem convention and dictionary. Thiswill enable the long-term goal of allowing a researcher to run simple“Google-style” searches of chemistry and physics and have theresults of computational calculations returned in a comprehensible formalongside articles from the published literature.Electronic supplementary materialThe online version of this article (doi:10.1186/1758-2946-5-25) contains supplementary material, which is available to authorized users.

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Job submission to grid computing environments

Cited by 14 publications

References 4 publications

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within theeMinerals escience project

Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within theeMinerals escience project

eScience for molecular-scale simulations and the e Minerals project

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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