Open AccessHeterogeneous CPU+GPU-Enabled Simulations for DFTB Molecular Dynamics of Large Chemical and Biological Systems
Author(s) -
Sarah I. Allec,
Yijing Sun,
Jianan Sun,
Chiaen A. Chang,
Bryan M. Wong
Publication year - 2019
Publication title -
journal of chemical theory and computation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.001
H-Index - 185
eISSN - 1549-9626
pISSN - 1549-9618
DOI - 10.1021/acs.jctc.8b01239
Subject(s) - computer science , bottleneck , molecular dynamics , computational science , symmetric multiprocessor system , implementation , homogeneous , parallel computing , quantum chemical , matrix multiplication , supercomputer , quantum , chemistry , statistical physics , computational chemistry , physics , molecule , embedded system , organic chemistry , quantum mechanics , programming language
We introduce a new heterogeneous CPU+GPU-enhanced DFTB approach for the routine and efficient simulation of large chemical and biological systems. Compared to homogeneous computing with conventional CPUs, heterogeneous computing approaches exhibit substantial performance with only a modest increase in power consumption, both of which are essential to upcoming exascale computing initiatives. We show that DFTB-based molecular dynamics is a natural candidate for heterogeneous computing, since the computational bottleneck in these simulations is the diagonalization of the Hamiltonian matrix, which is performed several times during a single molecular dynamics trajectory. To thoroughly test and understand the performance of our heterogeneous CPU+GPU approach, we examine a variety of algorithmic implementations, benchmarks of different hardware configurations, and applications of this methodology on several large chemical and biological systems. Finally, to demonstrate the capability of our implementation, we conclude with a large-scale DFTB MD simulation of explicitly solvated HIV protease (3974 atoms total) as a proof-of-concept example of an extremely large/complex system which, to the best of our knowledge, is the first time that an entire explicitly solvated protein has been treated at a quantum-based MD level of detail.