Kernel Optimization on Short-Range Potentials Computations in Molecular Dynamics Simulations

• 作者: Jianjiang Li Jue Wang Ningming Nie Xianmeng Wang Xinfu He
• 来源期刊: 国际计算机前沿大会会议论文集
• 学科: 社会科学
• 关键词: Molecular dynamics EAM SIMD VECTORIZATION OPENMP SHORT-RANGE potential High-performance computing
• 年，卷（期）: 2015,（B12）
• 页码范围: 67-69
• 页数: 3页
• 分类号: C5

摘要

We present multi-threading and SIMD optimizations on short-range potential calculation kernel in Molecular Dynamics.For the multi-threading optimization,we design a partition-and-two-steps(PTS)method to avoid write conflicts caused by using Newton’s third law.Our method eliminates serialization bottle-neck without extra memory.We implement our PTS method using OpenMP.Afterwards,we discuss the influence of the cutoff if statement on the performance of vectorization in MD simulations.We propose a pre-searching neighbors method,which makes about 70%atoms meet the cutoff check,reducing a large amount of redundant calculation.The experiment results prove our PTS method is scalable and efficient.In double precision,our 256-bit SIMD implementation is about 3×faster than the scalar version.