Tinker-HP : Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields using GPUs and Multi-GPUs systems
| Autor: | Olivier Adjoua, Louis Lagardère, Luc-Henri Jolly, Arnaud Durocher, Zhi Wang, Thibault Very, Isabelle Dupays, Théo Jaffrelot Inizan, Frederic Célerse, Pengyu Ren, Jay Ponder, Jean-Philip Piquemal |
|---|---|
| Přispěvatelé: | Laboratoire de chimie théorique (LCT), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Parisien de Chimie Physique et Théorique (IP2CT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Sorbonne Université-Centre National de la Recherche Scientifique (CNRS), INEOS, Washington University in Saint Louis (WUSTL), Institut du développement et des ressources en informatique scientifique (IDRIS), Centre National de la Recherche Scientifique (CNRS), Institut Parisien de Chimie Moléculaire (IPCM), Chimie Moléculaire de Paris Centre (FR 2769), Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Biomedical Engineering [Austin], University of Texas at Austin [Austin], Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), ANR: 11-LABX-0037,CALSIMLAB,LABEX pour la modélisation et la simulation scientifiques en recherche(2011), European Project: 810367,EMC2(2019), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Chemical Physics (physics.chem-ph)
FOS: Computer and information sciences Molecular dynamics MD simulation HPC Systems GPUs Polarizable force field [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph] FOS: Physical sciences Computational Physics (physics.comp-ph) Molecular dynamics Polarizable force field AMOEBA Article [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry Computer Science - Distributed Parallel and Cluster Computing [SDV.SP.MED]Life Sciences [q-bio]/Pharmaceutical sciences/Medication Physics - Chemical Physics Graphics Card [CHIM]Chemical Sciences Computer Science - Mathematical Software Distributed Parallel and Cluster Computing (cs.DC) High performance computing [INFO.INFO-DC]Computer Science [cs]/Distributed Parallel and Cluster Computing [cs.DC] Mathematical Software (cs.MS) Physics - Computational Physics |
| Zdroj: | Journal of Chemical Theory and Computation Journal of Chemical Theory and Computation, American Chemical Society, 2021, 17 (4), pp.2034-2053. ⟨10.1021/acs.jctc.0c01164⟩ HAL ArXiv Journal of Chemical Theory and Computation, 2021, 17 (4), pp.2034-2053. ⟨10.1021/acs.jctc.0c01164⟩ |
| ISSN: | 1549-9618 1549-9626 |
| DOI: | 10.1021/acs.jctc.0c01164⟩ |
| Popis: | International audience; We present the extension of the Tinker-HP package (Lagardere, 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 highperformance module allows for an efficient use of single-and multiple-GPU architectures ranging from research laboratories to modern 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 multiprecision 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. Testing various NVIDIA platforms including 2080Ti, 3090, V100, and A100 cards, we provide illustrative benchmarks of the code for single-and multicards simulations on large biosystems encompassing up to millions of atoms. The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multinode 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 (see https://github.com/ TinkerTools/tinker-hp). |
| Databáze: | OpenAIRE |
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