OpenAtom: Scalable Ab-Initio Molecular Dynamics with Diverse Capabilities

  • Nikhil Jain
  • Eric Bohm
  • Eric Mikida
  • Subhasish Mandal
  • Minjung Kim
  • Prateek Jindal
  • Qi Li
  • Sohrab Ismail-Beigi
  • Glenn J. Martyna
  • Laxmikant V. Kale
Conference paper

DOI: 10.1007/978-3-319-41321-1_8

Part of the Lecture Notes in Computer Science book series (LNCS, volume 9697)
Cite this paper as:
Jain N. et al. (2016) OpenAtom: Scalable Ab-Initio Molecular Dynamics with Diverse Capabilities. In: Kunkel J., Balaji P., Dongarra J. (eds) High Performance Computing. ISC High Performance 2016. Lecture Notes in Computer Science, vol 9697. Springer, Cham

Abstract

The complex interplay of tightly coupled, but disparate, computation and communication operations poses several challenges for simulating atomic scale dynamics on multi-petaflops architectures. OpenAtom addresses these challenges by exploiting overdecomposition and asynchrony in Charm++, and scales to thousands of cores for realistic scientific systems with only a few hundred atoms. At the same time, it supports several interesting ab-initio molecular dynamics simulation methods including the Car-Parrinello method, Born-Oppenheimer method, k-points, parallel tempering, and path integrals. This paper showcases the diverse functionalities as well as scalability of OpenAtom via performance case studies, with focus on the recent additions and improvements to OpenAtom. In particular, we study a metal organic framework (MOF) that consists of 424 atoms and is being explored as a candidate for a hydrogen storage material. Simulations of this system are scaled to large core counts on Cray XE6 and IBM Blue Gene/Q systems, and time per step as low as \(1.7\,s\) is demonstrated for simulating path integrals with 32-beads of MOF on 262,144 cores of Blue Gene/Q.

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Nikhil Jain
    • 1
  • Eric Bohm
    • 1
  • Eric Mikida
    • 1
  • Subhasish Mandal
    • 2
  • Minjung Kim
    • 2
  • Prateek Jindal
    • 1
  • Qi Li
    • 3
  • Sohrab Ismail-Beigi
    • 2
  • Glenn J. Martyna
    • 3
  • Laxmikant V. Kale
    • 1
  1. 1.Department of Computer ScienceUniversity of Illinois at Urbana-ChampaignChampaignUSA
  2. 2.Department of Applied PhysicsYale UniversityNew HavenUSA
  3. 3.IBM TJ Watson LaboratoryYorktown HeightsUSA

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