JINR CICC in computational chemistry and nanotechnology problems

DL_POLY performance for different communication architectures

E. Dushanov, Kh Kholmurodov, G. Aru, V. Korenkov, W. Smith, Y. Ohno, T. Narumi, G. Morimoto, M. Taiji, Kenji Yasuoka

Research output: Contribution to journalArticle

Abstract

This report compares the performance of the DL_POLY general-purpose molecular dynamics simulation package on the LIT JINR computing cluster CICC with various communication systems. The comparison involved two cluster architectures: Gigabit Ethernet and InfiniBand technologies, respectively. The code performance tests include some comparison of the CICC cluster with the special-purpose computer MDGRAPE-3 developed at RIKEN for a high-speed acceleration of the MD (molecular dynamics) without a fixed cutoff. The DL_POLY benchmark covers a set of typical MD system simulations detailed below.

Original languageEnglish
Pages (from-to)251-259
Number of pages9
JournalPhysics of Particles and Nuclei Letters
Volume6
Issue number3
DOIs
Publication statusPublished - 2009

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computational chemistry
Nanotechnology
Molecular Dynamics Simulation
nanotechnology
communication
molecular dynamics
Benchmarking
systems simulation
Ethernet
performance tests
telecommunication
cut-off
high speed
Technology
simulation

ASJC Scopus subject areas

  • Nuclear and High Energy Physics
  • Atomic and Molecular Physics, and Optics
  • Radiation
  • Radiology Nuclear Medicine and imaging

Cite this

JINR CICC in computational chemistry and nanotechnology problems : DL_POLY performance for different communication architectures. / Dushanov, E.; Kholmurodov, Kh; Aru, G.; Korenkov, V.; Smith, W.; Ohno, Y.; Narumi, T.; Morimoto, G.; Taiji, M.; Yasuoka, Kenji.

In: Physics of Particles and Nuclei Letters, Vol. 6, No. 3, 2009, p. 251-259.

Research output: Contribution to journalArticle

Dushanov, E. ; Kholmurodov, Kh ; Aru, G. ; Korenkov, V. ; Smith, W. ; Ohno, Y. ; Narumi, T. ; Morimoto, G. ; Taiji, M. ; Yasuoka, Kenji. / JINR CICC in computational chemistry and nanotechnology problems : DL_POLY performance for different communication architectures. In: Physics of Particles and Nuclei Letters. 2009 ; Vol. 6, No. 3. pp. 251-259.
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