کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
4964555 1447812 2017 29 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Kernel optimization for short-range molecular dynamics
ترجمه فارسی عنوان
بهینه سازی هسته برای دینامیک مولکولی کمینه
موضوعات مرتبط
مهندسی و علوم پایه شیمی شیمی تئوریک و عملی
چکیده انگلیسی
To optimize short-range force computations in Molecular Dynamics (MD) simulations, multi-threading and SIMD optimizations are presented in this paper. With respect to multi-threading optimization, a Partition-and-Separate-Calculation (PSC) method is designed to avoid write conflicts caused by using Newton's third law. Serial bottlenecks are eliminated with no additional memory usage. The method is implemented by using the OpenMP model. Furthermore, the PSC method is employed on Intel Xeon Phi coprocessors in both native and offload models. We also evaluate the performance of the PSC method under different thread affinities on the MIC architecture. In the SIMD execution, we explain the performance influence in the PSC method, considering the “if-clause” of the cutoff radius check. The experiment results show that our PSC method is relatively more efficient compared to some traditional methods. In double precision, our 256-bit SIMD implementation is about 3 times faster than the scalar version.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computer Physics Communications - Volume 211, February 2017, Pages 31-40
نویسندگان
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