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Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: A Comparison of Digital MPI with LAM-MPI and MPICH2

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Recent Advances in Parallel Virtual Machine and Message Passing Interface (EuroPVM/MPI 2005)

Part of the book series: Lecture Notes in Computer Science ((LNPSE,volume 3666))

Abstract

Polarizable Force Fields have a great potential in improving the quality of Molecular Dynamics simulations. Especially for the description of solvents such kind of simulations are greatly appreciated because of the important role solvation plays in all kind of biomedical research. The open source package TINKER is taken for parallelization of a routine made for the proper usage of Polarizable Force Fields. Profiling with the GNU tool gprof identifies the relevant target subroutines to parallelize. MPI is used for the parallelization. Several different parallel platforms and several different versions of MPI are tested and compared. Parallel scalability with reasonable amounts of parallel operating CPUs seems to be limited beyond a factor of 2.5. Appraisal of the present MPI-implementation of the TINKER Molecular Dynamics program using Polarizable Force Fields for large scale computation will heavily depend on the relative availability of computing resources within a given production environment.

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Author information

Authors and Affiliations

  1. Novartis Institutes for BioMedical Research, IK@N Operations and In Silico Sciences, Brunnerstraße 59, A-1235, Vienna, Austria

    Benjamin Almeida & Siegfried Höfinger

  2. Department of Chemical Engineering, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, 16, India

    Reema Mahajan

  3. Joh Kepler University Linz, Altenberger Straße 69, A-4040, Linz, Austria

    Dieter Kranzlmüller & Jens Volkert

Authors
  1. Benjamin Almeida
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  2. Reema Mahajan
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  3. Dieter Kranzlmüller
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  4. Jens Volkert
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  5. Siegfried Höfinger
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Editor information

Editors and Affiliations

  1. Dipartimento di Ingegneria dell’ Informazione, Second University of Naples - Italy, Real Casa dell’Annunziata - via Roma, 29, 81031, Aversa, CE, Italy

    Beniamino Di Martino

  2. GUP, Institute of Graphics and Parallel Processing, Johannes Kepler University, Altenbergerstraße 69, A-4040, Linz, Austria

    Dieter Kranzlmüller

  3. Computer Science Department, University of Tennessee, 37996-3450, Knoxville, TN, USA

    Jack Dongarra

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© 2005 Springer-Verlag Berlin Heidelberg

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Almeida, B., Mahajan, R., Kranzlmüller, D., Volkert, J., Höfinger, S. (2005). Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: A Comparison of Digital MPI with LAM-MPI and MPICH2. In: Di Martino, B., Kranzlmüller, D., Dongarra, J. (eds) Recent Advances in Parallel Virtual Machine and Message Passing Interface. EuroPVM/MPI 2005. Lecture Notes in Computer Science, vol 3666. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557265_55

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  • DOI: https://doi.org/10.1007/11557265_55

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-29009-4

  • Online ISBN: 978-3-540-31943-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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