Contribution to a book

FZJ-2021-00075

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png GROMEX: A Scalable and Versatile Fast Multipole Method for Biomolecular Simulation

Kohnke, B. (Corresponding author) ; Ullmann, T. R. ; Beckmann, A.FZJ* ; Kabadshow, I.FZJ* ; Haensel, D.FZJ* ; Morgenstern, L.FZJ* ; Dobrev, P. ; Groenhof, G. ; Kutzner, C. ; Hess, B. ; Dachsel, H.FZJ* ; Grubmüller, H.

2020
Springer International Publishing Cham

Please use a persistent id in citations: http://hdl.handle.net/2128/26688

Abstract: Atomistic simulations of large biomolecular systems with chemical variability such as constant pH dynamic protonation offer multiple challenges in high performance computing. One of them is the correct treatment of the involved electrostatics in an efficient and highly scalable way. Here we review and assess two of the main building blocks that will permit such simulations: (1) An electrostatics library based on the Fast Multipole Method (FMM) that treats local alternative charge distributions with minimal overhead, and (2) A λ-dynamics module working in tandem with the FMM that enables various types of chemical transitions during the simulation. Our λ-dynamics and FMM implementations do not rely on third-party libraries but are exclusively using C++ language features and they are tailored to the specific requirements of molecular dynamics simulation suites such as GROMACS. The FMM library supports fractional tree depths and allows for rigorous error control and automatic performance optimization at runtime. Near-optimal performance is achieved on various SIMD architectures and on GPUs using CUDA. For exascale systems, we expect our approach to outperform current implementations based on Particle Mesh Ewald (PME) electrostatics, because FMM avoids the communication bottlenecks caused by the parallel fast Fourier transformations needed for PME.

Note: DOI: 10.1007/978-3-030-47956-5_17

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. Zivile Sicherheitsforschung (IAS-7)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. SPPEXA - Software for Exascale Computing (214420555) (214420555)
3. PhD no Grant - Doktorand ohne besondere Förderung (PHD-NO-GRANT-20170405) (PHD-NO-GRANT-20170405)

Appears in the scientific report 2020

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