Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems
Sorbonne Université, LCT, UMR 7616 CNRS, F-75005, Paris, France
J. Chem. Theory Comput. 2021, arXiv:2011.01207 [physics.comp-ph], (3 Nov 2020)
@misc{adjoua2020tinkerhp,
title={Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems},
author={Olivier Adjoua and Louis Lagardère and Luc-Henri Jolly and Arnaud Durocher and Thibaut Very and Isabelle Dupays and Zhi Wang and Théo Jaffrelot Inizan and Frédéric Célerse and Pengyu Ren and Jay W. Ponder and Jean-Philip Piquemal},
year={2020},
eprint={2011.01207},
archivePrefix={arXiv},
primaryClass={physics.comp-ph}
}
We present the extension of the Tinker-HP package (Lagardère et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single- and multi-GPU architectures ranging from research laboratories to modern pre-exascale supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OpenACC and CUDA, we discuss the various capabilities of the package. Among them, the multi-precision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model and provide illustrative benchmarks of the code for single- and multi-cards simulations on large biosystems encompassing up to millions of atoms.The new code strongly reduces time to solution and offers the best performances ever obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multi-node massive parallelization strategy, unsupervised adaptive sampling and large scale applicability of the Tinker-HP code in biophysics are discussed. The present software has been released in phase advance on GitHub in link with the High Performance Computing community COVID-19 research efforts and is free for Academics.
November 8, 2020 by hgpu
