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研究生:陳權
研究生(外文):Chuan Chen
論文名稱:平行分子動力學應用於個人電腦叢集系統分析與效能研究
論文名稱(外文):The Parallel Molecular Dynamics Simulation Performance and System Analysis on PC Cluster
指導教授:黃吉川黃吉川引用關係
指導教授(外文):Chi-Chuan Hwang
學位類別:博士
校院名稱:國立成功大學
系所名稱:工程科學系碩博士班
學門:工程學門
學類:綜合工程學類
論文種類:學術論文
論文出版年:2009
畢業學年度:97
語文別:中文
論文頁數:108
中文關鍵詞:平行演算法平行計算分子動力學個人電腦叢集系統
外文關鍵詞:PC cluster systemmolecular dynamicsparallel computingparallel algorithm
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近幾十年來,利用分子動力學方法模擬研究各種奈米材料已非常普遍,並且能夠成功地分析各項物理與化學之性質。通常模擬系統之粒子數有可能從數萬顆至數億顆,且執行步階數可能達到千萬步,其需要之計算資源非常大,在一般之序列程式執行需要甚多時日,所以許多研究學者發展了多種平行化之演算法來減少整體執行之時間。一般將平行化之切割法分類為三種:粒子切割法、力切割法與空間切割法。此三種基本之演算法各有其優劣點,且限制條件會隨我們所選擇之勢能函數而異;例如假設我們選取之勢能是二體勢能,力切割法中各粒子間之力陣列運算可以節省一半時間,但如果勢能變成REBO時,此種方法便不能適用。為了探討各種勢能函數在各種計算平台不同之平行策略,本篇論文先從分子動力學基本之勢能函數分析,再探究目前常用之平行計算硬體架構之差異。透過平行計算基本理論,包括各種平行運算環境硬體架構的分析、程式執行之相對效能(performance)、系統產能(throughput) 與擴充性 (scalability)分析,找出適合各式勢能函數之演算法,並作各種運用於分子動力學常用之平行計算切割演算法、各式演算法效能分析與適用範圍討論。除了分析研究個人電腦叢集分類與建置方法,也分析利用(Message Passing Interface,MPI)函數發展空間切割法平行程式模組之步驟。最後之例子是利用此平行模組產生任意形狀隨機網點之LCD導光板網點設計,也發展適合REBO勢能平行化之快速搜尋演算法,並分析比較各類平行演算法之優劣點。
Molecular dynamics (MD) simulation method is widely applied to study various nano materials and successfully analyze their physical and chemical properties in the recent decades. The MD simulations usually including a great number of particles (104-108) as well as numerous simulation time steps up to ten millions are computation intensive, especially with serial algorithms. Therefore, parallel algorithms have been developed to reduce the simulation time. Traditionally, the parallelized MD algorithms divide into three decomposition strategies: particle decomposition, force decomposition and spatial decomposition. Although there are some advantages by using these three basic strategies, there still have different limitations which may be changed according to what potential we use. For example, the force decomposition method can be used and save computer time very well to calculate force matrixes between the particles if we chose the 2-body potential, but this stage is not suitable when the potential energy form changes to REBO. In order to find the suitable method to parallelize the serial code in many cases of MD simulation, in this thesis, we analyze the foundation of MD method and the difference of potential energy form first. Then we discuss the different architecture of parallel system used nowadays. By studying the basic theory of parallel computing and analyzing the performance, throughput and scalability of different program, we hope to find suitable algorithm for different potential form. It also mentioned the classification of PC cluster and method to build the PC cluster. In the final chapter we discuss the steps to develop spatial decomposition module using the (Message Passing Interface, MPI) function and apply this program to generate random dot in LCD light guide. In addition, we also develop a new algorithm to search neighbor particle in REBO potential form.
第一章 序論 1
1-1 研究動機與目的 1
1-2 研究背景 2
1-3 文獻回顧 3
1-4 論文架構 4
第二章 分子動力學理論與數值模擬方法 6
2-1 分子動力學模擬簡介 6
2-2 原子勢能函數分析 7
2-2-1 Lennard-Jones勢能 7
2-2-2 EAM 勢能 9
2-2-3 Tight Binding 勢能 12
2-2-4 Tersoff 勢能 12
2-2-5 REBO 勢能 15
2-3 運動方程式 20
第三章 平行理論與高速計算平台系統分析 21
3-1 平行計算系統硬體架構分類 22
3-1-1 依控制機制分類 22
3-1-2 依位址空間架構分類 29
3-1-3 依互聯網路架構分類 33
3-1-4 依處理器粒度分類 33
3-2 平行系統之記憶體架構 34
3-2-1 訊息傳遞模式 34
3-3 程序平行化之模式 35
3-4 平行運算之效率與可擴充性 37
3-5 擴充(Scaling)模式 42
3-5-1 固定問題尺寸擴充模式 42
3-5-2 記憶限制擴充模式 43
3-5-3 時間限制擴充模式 44
第四章 分子動力學平行計算演算法 47
4-1 前言 47
4-2 粒子分割法 49
4-3 力切割法 53
4-4 空間切割法 60
第五章 個人電腦叢集平行計算平台建置 62
5-1 叢集系統節點之種類 62
5-2 電腦叢集硬體建置之規劃 64
5-3 網路介面差異 68
5-4 系統軟體 70
5-5 平行檔案系統 70
5-6 工作排程軟體 72
第六章 分子動力學平行計算軟體之開發 74
6-1 分散空間切割法平行模組開發 74
6-2 利用平行空間切割法之網點設計 83
6-3 利用樹狀串列遞迴演算法加速REBO勢能計算 91
6-4. 結論與未來展望 94
參考文獻 96
論文著作 105
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