Extension of the AMBER molecular dynamics software to Intel’s Many Integrated Core (MIC) architecture

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• 作者：Perri J. Needham^a ; Ashraf Bhuiyan^b ; Ross C. Walker^a ; ^c ; ^{ross@rosswalker.co.uk" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Xeon Phi ; Molecular dynamics ; Code optimization ; Acceleration ; MIC
• 刊名：Computer Physics Communications
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：201
• 期：Complete
• 页码：95-105
• 全文大小：1808 K

文摘

We present an implementation of explicit solvent particle mesh Ewald (PME) classical molecular dynamics (MD) within the PMEMD molecular dynamics engine, that forms part of the AMBER v14 MD software package, that makes use of Intel Xeon Phi coprocessors by offloading portions of the PME direct summation and neighbor list build to the coprocessor. We refer to this implementation as pmemd MIC offload   and in this paper present the technical details of the algorithm, including basic models for MPI and OpenMP configuration, and analyze the resultant performance. The algorithm provides the best performance improvement for large systems (>$>$400,000 atoms), achieving a ∼35% performance improvement for satellite tobacco mosaic virus (1,067,095 atoms) when 2 Intel E5-2697 v2 processors (2 ×12 cores, 30M cache, 2.7 GHz) are coupled to an Intel Xeon Phi coprocessor (Model 7120P—1.238/1.333 GHz, 61 cores). The implementation utilizes a two-fold decomposition strategy: spatial decomposition using an MPI library and thread-based decomposition using OpenMP. We also present compiler optimization settings that improve the performance on Intel Xeon processors, while retaining simulation accuracy.