OpenAtom: Scalable Ab-Initio Molecular Dynamics with Diverse Capability
| Nikhil Jain | Eric Bohm | Eric Mikida | Subhasish Mandal | Minjung Kim | Prateek Jindal | Qi Li | Sohrab Ismail-Beigi | Glenn Martyna | Laxmikant Kale
International Supercomputing Conference (ISC) 2016
Publication Type: Paper
Repository URL: papers/2015-04-openAtom
Abstract
Complex interplay of tightly coupled but disparate computation and communication operations poses several challenges for simulating atomic scale dynamics on multi-petaflops systems. 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 sup- ports 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 functionality 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 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 1.7s is demonstrated for simulating 32-beads of MOF on 262, 144 cores and 768, 432 hardware threads of Blue Gene/Q.
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