کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10357408 | 867869 | 2005 | 13 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Communications overlapping in fast multipole particle dynamics methods
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موضوعات مرتبط
مهندسی و علوم پایه
مهندسی کامپیوتر
نرم افزارهای علوم کامپیوتر
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چکیده انگلیسی
In molecular dynamics the fast multipole method (FMM) is an attractive alternative to Ewald summation for calculating electrostatic interactions due to the operation counts. However when applied to small particle systems and taken to many processors it has a high demand for interprocessor communication. In a distributed memory environment this demand severely limits applicability of the FMM to systems with O(10 K atoms). We present an algorithm that allows for fine grained overlap of communication and computation, while not sacrificing synchronization and determinism in the equations of motion. The method avoids contention in the communication subsystem making it feasible to use the FMM for smaller systems on larger numbers of processors. Our algorithm also facilitates application of multiple time stepping techniques within the FMM. We present scaling at a reasonably high level of accuracy compared with optimized Ewald methods.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Computational Physics - Volume 203, Issue 2, 1 March 2005, Pages 731-743
Journal: Journal of Computational Physics - Volume 203, Issue 2, 1 March 2005, Pages 731-743
نویسندگان
Jakub Kurzak, B. Montgomery Pettitt,