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Parallelization of Reaction Dynamics Codes Using P-GRADE: A Case Study

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Computational Science and Its Applications – ICCSA 2004 (ICCSA 2004)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 3044))

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Abstract

P-GRADE, a graphical tool and programming environment was used to parallelize atomic level reaction dynamics codes. In the reported case study a classical trajectory code written in FORTRAN has been parallelized. The selected level was coarse grain parallelization. P-GRADE allowed us to use automatic schemes, out of which the task farm was selected. The FORTRAN code was separated into an input/output and a working section. The former, enhanced by a data transfer section operates on the master, the latter on the slaves. Small sections for data transfer were written in C language. The P-GRADE environment offers a user-friendly way of monitoring the efficiency of the parallelization. On a 20-processor NPACI Rocks cluster the speed-up is 99 percent proportional to the number of processors.

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Author information

Authors and Affiliations

  1. Institute of Chemistry, Chemical Research Center, Hungarian Academy of Sciences, P.O. Box 17, H-1525, Budapest, Hungary

    Ákos Bencsura & György Lendvay

Authors
  1. Ákos Bencsura
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  2. György Lendvay
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Editor information

Editors and Affiliations

  1. Department of Chemistry, University of Perugia, Via Elce di Sotto, 8, I-06123, Perugia, Italy

    Antonio Laganá

  2. Department of Computer Science, University of Calgary, 2500 University Drive N.W., T2N 1N4, Calgary AB, Canada

    Marina L. Gavrilova

  3. William Norris Professor, Head of the Computer Science and Engineering Department, University of Minnesota, USA

    Vipin Kumar

  4. School of Computing, Soongsil University, Seoul, Korea

    Youngsong Mun

  5. OptimaNumerics Ltd., Cathedral House, 23-31 Waring Street, BT1 2DX, Belfast, UK

    C. J. Kenneth Tan

  6. Department of Mathematics and Computer Science, University of Perugia, via Vanvitelli, 1, I-06123, Perugia, Italy

    Osvaldo Gervasi

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© 2004 Springer-Verlag Berlin Heidelberg

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Bencsura, Á., Lendvay, G. (2004). Parallelization of Reaction Dynamics Codes Using P-GRADE: A Case Study. In: Laganá, A., Gavrilova, M.L., Kumar, V., Mun, Y., Tan, C.J.K., Gervasi, O. (eds) Computational Science and Its Applications – ICCSA 2004. ICCSA 2004. Lecture Notes in Computer Science, vol 3044. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24709-8_31

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  • DOI: https://doi.org/10.1007/978-3-540-24709-8_31

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-22056-5

  • Online ISBN: 978-3-540-24709-8

  • eBook Packages: Springer Book Archive

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