【摘要】：GPU(Graphics Processing Unit,圖形處理器)具有很強(qiáng)的并行計算能力,尤其CUDA(Compute Unified Device Architecture,統(tǒng)一計算設(shè)備架構(gòu))的出現(xiàn)使得GPU在高性能計算中占據(jù)越來越重要的地位。分子動力學(xué)模擬技術(shù)是指利用計算機(jī)來模擬體系中各個粒子隨時間的運(yùn)動變化情況,由于其計算量較大,因此考慮放到GPU上來執(zhí)行。 本文在分析了GPU的并行能力及分子動力學(xué)模擬原理的基礎(chǔ)上,將模擬計算過程中耗時最多的勢函數(shù)計算移至GPU計算,分析勢函數(shù)計算的內(nèi)在并行性,利用CUDA線程與粒子間的一一對應(yīng)關(guān)系,并結(jié)合GPU自身特點,完成計算的加速。本文實現(xiàn)了兩種對勢(Morse勢、Lennard-Jones勢)和兩種多體勢(Tersoff勢、EAM勢)的GPU加速計算。計算結(jié)果表明,在NVIDIA GeForce GTX650的GPU上,相對于Intel Core2E7500的CPU,勢函數(shù)計算的加速比在22-91之間,這也就能極大的縮短整個分子動力學(xué)模擬計算的時間。另外本文還介紹了兩個結(jié)構(gòu)特征量(徑向分布函數(shù)(RDF)、靜態(tài)結(jié)構(gòu)因子(SSF))的GPU加速,計算結(jié)果表明,在與上述相同平臺下,加速比達(dá)到22-27。 最后,本文在Windows平臺下,采用Qt設(shè)計圖形用戶界面,完成了分子動力學(xué)模擬系統(tǒng)的搭建,其中的勢函數(shù)及結(jié)構(gòu)特征量的計算基于GPU運(yùn)行,并對系統(tǒng)進(jìn)行了測試。
[Abstract]:GPU (Graphics Processing Unit, (graphics processor) has a strong parallel computing capability, especially the appearance of CUDA (Compute Unified Device Architecture, unified computing device architecture, which makes GPU play an increasingly important role in high performance computing. Molecular dynamics simulation technology refers to the use of computer to simulate the movement of each particle in the system with time. Due to the large amount of calculation, it is considered to be carried out on GPU. Based on the analysis of the parallel capability of GPU and the principle of molecular dynamics simulation, the potential function calculation, which takes the most time in the simulation calculation, is moved to the GPU calculation, and the inherent parallelism of the potential function calculation is analyzed. Using the one-to-one correspondence between CUDA threads and particles and combining with the characteristics of GPU, the computation is accelerated. In this paper, the GPU acceleration calculations of two pairs of potential (Morse potential, Lennard-Jones potential) and two kinds of multibody potential (Tersoff potential, EAM potential) are realized. The results show that the acceleration ratio calculated by the CPU, potential function relative to that of the Intel Core2E7500 on the GPU of NVIDIA GeForce GTX650 is between 22-91, which can greatly shorten the time of the whole molecular dynamics simulation. In addition, the GPU acceleration of two structural characteristic variables (radial distribution function (RDF), static structure factor (SSF) is also introduced. The calculation results show that the speedup ratio is 22-27 under the same platform. Finally, in this paper, the graphical user interface is designed by using Qt on Windows platform, and the molecular dynamics simulation system is built. The calculation of potential function and structural characteristic is based on GPU, and the system is tested.
【學(xué)位授予單位】：哈爾濱工業(yè)大學(xué)
【學(xué)位級別】：碩士
【學(xué)位授予年份】：2014
【分類號】：TP332;TP391.41

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