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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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.

Original languageEnglish (US)
Title of host publicationHigh Performance Computing - 31st International Conference, ISC High Performance 2016, Proceedings
EditorsJack Dongarra, Julian M. Kunkel, Pavan Balaji
PublisherSpringer
Pages139-158
Number of pages20
ISBN (Print)9783319413204
DOIs
StatePublished - 2016
Event31st International Conference on High Performance Computing, ISC High Performance 2016 - Frankfurt, Germany
Duration: Jun 19 2016Jun 23 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9697
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other31st International Conference on High Performance Computing, ISC High Performance 2016
Country/TerritoryGermany
CityFrankfurt
Period6/19/166/23/16

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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