本文選題：分子動力學　切入點：負載均衡　出處：《國防科學技術大學》2013年碩士論文　論文類型：學位論文

【摘要】：分子動力學模擬作為一種計算機模擬方法,已廣泛應用于物理、化學、生命科學、材料學以及醫(yī)藥等領域。并且,隨著人類對科學探索的深入,使用高性能計算機進行大規(guī)模分子動力學模擬已成為必然趨勢。然而,高性能計算機在帶來強大計算能力的同時也遇到了各方面的挑戰(zhàn),如負載均衡、通信、可靠性、功耗等問題,其中負載均衡問題帶來的性能損失尤其突出。為了解決該問題,本文提出了面向并行分子動力學模擬的靜動態(tài)負載均衡方法,并基于Open FOAM框架實現(xiàn)。本文的主要工作和創(chuàng)新點包括以下幾個方面:?建立了基于Open FOAM的分子動力學負載均衡框架(第二章)本文深入分析了Open FOAM并行程序框架及其分子動力學的實現(xiàn)方法,發(fā)現(xiàn)負載不均衡會嚴重影響分子動力學的模擬效率。針對該問題,在原有Open FOAM框架的基礎上建立了靜動態(tài)負載均衡機制和相應的數(shù)據(jù)組織、計算流程、框架組成以及與其他模塊的結(jié)合方法。本文提出的面向分子動力學模擬的負載均衡框架對其他粒子方法負載均衡機制的設計具有借鑒意義。?提出了面向并行分子動力學模擬的靜態(tài)負載均衡方法——MDSLB(第三章)本文提出了一種面向大規(guī)模分子動力學模擬的靜態(tài)負載均衡方法——MDSLB。通過對分子動力學中短程力計算特征的深入分析,我們將短程力進一步細分為三類力模型,每類力模型中涉及的計算任務又被拆分為多個細粒度的獨立計算單元,稱為“cell負載”。這些計算單元為MDSLB方法的實現(xiàn)提供了基本的數(shù)據(jù)結(jié)構(gòu)。在MDSLB方法中,模擬區(qū)域被分為多個子區(qū)域,稱為“局部空間”。每個局部空間中的cell負載被均勻地分配給各個處理器。該方法通過在程序開始時執(zhí)行一次,從而保證整個模擬過程中負載的均衡。?提出了面向并行分子動力學模擬的動態(tài)負載均衡方法——MDDLB(第四章)本文針對小規(guī)模分子動力學模擬提出了動態(tài)負載均衡方法——MDDLB。該方法基于Open FOAM的cell結(jié)構(gòu),設計了負載遷移的基本單元——近鄰粒子列表。另外,還引入了閾值檢測機制負責監(jiān)控和衡量每個處理器的負載情況。當負載不均衡的程度超過一定值時,則從負載較重的處理器將負載動態(tài)遷移到負載較輕的處理器上�；谠摲椒�,可以有效解決小規(guī)模分子動力學模擬中的負載均衡問題。?驗證了負載均衡框架及MDSLB方法和MDDLB方法的正確性和有效性(第五章)本文基于Open FOAM設計實現(xiàn)了第二章所提出的分子動力學負載均衡框架,并基于該框架分別實現(xiàn)了第三、四章提出的MDSLB方法和MDDLB方法�；赥ian He-1A子系統(tǒng)使用擴散模型對上述框架和方法進行了測試,實驗結(jié)果表明,分子動力學負載均衡框架及在其上實現(xiàn)的兩個方法是正確有效的。與傳統(tǒng)方法相比,MDSLB方法可以獲得34%-64%的加速,而MDDLB方法則可以獲得更接近理想情況的加速比。
[Abstract]:As a computer simulation method, molecular dynamics simulation has been widely used in the fields of physics, chemistry, life science, materials science and medicine. It has become an inevitable trend to use high performance computer for large-scale molecular dynamics simulation. However, high performance computer not only brings powerful computing power, but also meets various challenges, such as load balancing, communication, reliability, etc. In order to solve this problem, a static and dynamic load balancing method for parallel molecular dynamics simulation is proposed. And based on the implementation of Open FOAM framework. The main work and innovation of this paper include the following aspects:? In this paper, a molecular dynamics load balancing framework based on Open FOAM (Chapter 2) is established. In this paper, the parallel program framework of Open FOAM and its molecular dynamics implementation method are deeply analyzed. It is found that load imbalance will seriously affect the efficiency of molecular dynamics simulation. Based on the original Open FOAM framework, the static and dynamic load balancing mechanism and the corresponding data organization are established. The proposed load balancing framework for molecular dynamics simulation can be used for reference in the design of load balancing mechanism for other particle methods. In this paper, a static load balancing method for parallel molecular dynamics simulation, MDSLB (Chapter 3), is presented. In this paper, a static load balancing method for large-scale molecular dynamics simulation is presented. An in-depth analysis of computational features, We further subdivide the short-range forces into three types of force models, and the computing tasks involved in each force model are split into several fine-grained independent computing units. Called "cell load." these units provide the basic data structure for the implementation of the MDSLB method. In the MDSLB method, the simulation region is divided into multiple subregions, Called "local space". The cell load in each local space is evenly distributed among the processors. This method ensures load balancing throughout the simulation process by executing it once at the beginning of the program. A dynamic load balancing method for parallel molecular dynamics simulation is presented in this paper, which is based on the cell structure of Open FOAM. In addition, a threshold detection mechanism is introduced to monitor and measure the load of each processor. Based on this method, the load balancing problem in small-scale molecular dynamics simulation can be effectively solved. The correctness and validity of the load balancing framework, MDSLB method and MDDLB method are verified (Chapter 5th). The molecular dynamics load balancing framework proposed in chapter 2 is designed and implemented based on Open FOAM, and the third one is implemented based on the framework. The MDSLB method and MDDLB method proposed in the four chapters are tested by using diffusion model based on the Tian He-1A subsystem. The experimental results show that, The molecular dynamics load-balancing framework and the two methods implemented on it are correct and effective. Compared with the traditional method, the MDSLB method can get 34-64% acceleration, while the MDDLB method can obtain a speedup closer to the ideal condition.
【學位授予單位】：國防科學技術大學
【學位級別】：碩士
【學位授予年份】：2013
【分類號】：TP38
，

本文編號：1590434