Efficient parallelization of perturbative Monte Carlo QM/MM simulations in heterogeneous platforms. (November 2017)

• Record Type: Journal Article
• Authors: Miranda, Sebastião; Feldt, Jonas; Pratas, Frederico; Mata, Ricardo A; Roma, Nuno; Tomás, Pedro
• Is Part Of: International journal of high performance computing applications. Volume 31:Number 6(2017)
• Page Start: 499
• Page End: 516
• Publication Date: 2017-11
• Subjects: Quantum mechanics -- molecular mechanics -- Monte Carlo simulations -- parallel computing -- openCL -- GPGPU -- heterogeneous systems; High performance computing -- Periodicals; Supercomputers -- Periodicals; 004.1105
• DOI: 10.1177/1094342016649420
• Languages: English
• ISSNs: 1094-3420

Abstract

A novel perturbative Monte Carlo mixed quantum mechanics (QM)/molecular mechanics (MM) approach has been recently developed to simulate molecular systems in complex environments. However, the required accuracy to efficiently simulate such complex molecular systems is usually granted at the cost of long executing times. To alleviate this problem, a new parallelization strategy of multi-level Monte Carlo molecular simulations is herein proposed for heterogeneous systems. It simultaneously exploits fine-grained (at the data level), coarse-grained (at the Markov chain level) and task-grained (pure QM, pure MM and QM/MM procedures) parallelism to ensure an efficient execution in heterogeneous systems composed of central processing units and multiple and possibly different graphical processing units. This is achieved by making use of the OpenCL library, together with appropriate dynamic load balancing schemes. From the conducted evaluation with real benchmarking data, a speed-up of 56x in the computational bottleneck part was observed, which results in a global speed-up of 38x for the whole simulation, reducing the time of a typical simulation from 80 hours to only 2 hours.