Parallel molecular dynamics simulation of Lennard-Jones liquids on a small Beowulf cluster

  • Authors:

  • T. E. Karakasidis;A. B. Liakopoulos;N. S. Cholevas

  • Affiliations:

  • Department of Civil Engineering, School of Engineering, University of Thessaly, Pedion Areos, 38834 Volos, Greece;Department of Civil Engineering, School of Engineering, University of Thessaly, Pedion Areos, 38834 Volos, Greece;Department of Mechanical & Industrial Engineering, School of Engineering, University of Thessaly, Pedion Areos, 38834 Volos, Greece

  • Venue:
  • ICCMSE '03 Proceedings of the international conference on Computational methods in sciences and engineering
  • Year:
  • 2003

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Abstract

In the present paper we present results concerning the performance of a parallel Molecular Dynamics simulation of a Lennard-Jones liquid on a PC cluster consisting of four Pentium III processors running under Linux and using the MPI protocol. The methodology for the parallelization was the atom decomposition method in which each processor is assigned to deal with a given group of atoms. We examined the program performance for system sizes 102 to 105 atoms and number of processors varying from 1 to 4. The influence of the communication methods between processors was also examined. It was found that even such a small cluster can be a very useful and cost-effective solution for the realization of MD simulations of small Lennard-Jones liquid systems for real times up to 1 µs within a reasonable computation time.