分子动力学模拟中负载平衡方法的应用

文章针对三维分子动力学并行数值模拟中出现的负载不平衡现象,在静态负载平衡基础上,提出了一种简单有效的动态负载平衡算法。通过对三维分子动力学的并行数值模拟试验,此算法可以使得负载基本达到动态平衡,并进一步提高了并行效率。     

Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

Simulation of in vivo cellular processes with the reaction–diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel efficiency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems.     

基于消息传递的数据交错重分布负载平衡技术

数据重分布是实现消息传递环境下负载平衡的重要手段,提出了数据交错分布的模型问题及模型问题的并行计算模型,分析了模型问题在消息传递环境下的实现,讨论了性能和适用条件,给出了分析结果,讨论了通信与计算的时间重叠问题,将数据交错重分布负载平衡技术应用到非平衡刚性动力学方程组的并行计算中,获得了很好的负载平衡效果。     

并行燃烧数值模拟计算优化——面向自适应非结构网格的动态负载平衡方法

燃烧数值模拟计算通常采用非结构网格模拟计算区域。在非结构网格上进行并行模拟计算时,其自适应方式使得不同进程上的计算负载频繁变动,且差异巨大,导致并行计算效率低下。为了提高并行计算的效率,一个有效的方法是采用动态负载平衡技术。提出一种针对燃烧的化学反应状态的动态负载平衡方法,该方法采用不同策略对化学反应不同阶段各进程上的计算负载进行预测,根据预测结果平均进程间的计算任务,达到负载平衡。实验分析表明,该方法能有效地降低进程间的负载不平衡程度,使得模拟计算的总体运行时间降低了10％。     

Parallel Algorithm Oriented Mesh Database

In this paper, we present a new point of view for efficiently managing general parallel mesh representations. Taking as a slarting point the Algorithm Oriented Mesh Database (AOMD) of [1] we extend the concepts to a parallel mesh representation. The important aspects of parallel adaptivity and dynamic load balancing are discussed. We finally show how AOMD can be effectively interfaced with mesh adaptive partial differential equation solvers. Results of the calculation of an elasticity problem and of a transient fluid dynamics problem involving thousands of mesh refinements, and load balancings are finally presented. ID="A1" Correspondence and offprint requests to: J. Remacle, Scientific Computation Research Center, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA. E-mail: remacle@scorec.rpi.edu     

DSMC并行仿真的数据迁移动态负载平衡技术

针对DSMC并行仿真中的负载变化特点，提出了DSMC并行仿真数据迁移的动态负载平衡技术。测试结果证明该技术能有效提高DSMC并行仿真的计算效率。     

Strategy and Simulation of Adaptive RID for Distributed Dynamic Load Balancing in Parallel Systems

Dynamic load balancing schemes are significant for efficiently executing nonuniform problems in highly parallel multicomputer systems.The objective is to minimize the total exectuion time of single applications.This paper has proposed an ARID strategy for distributed dynamic load balancing.Its principle and control protocol are described,and te communication overhead,the effect on system stability and the performance efficiency are analyzed.Finally,simulation experiments are carried out to compare the adaptive strategy with other dynamic load balancing schemes.     

一维高效动态负载平衡方法：多层均权法

提出了一个适合同构和异构并行计算环境的高效一维动态负载平衡方法;多层均权法,并成功地解决了多物质非定常流体力学Lagrange法并行数值模拟过程中的动态负载不平衡问题。文中给出了详细的理论分析以及两台并行机上结合某实际物理问题组织的并行数值实验。     

大规模并行粒子模拟中基于主从架构的负载平衡策略研究与实现

粒子方法作为一种直观而且普适的模拟方法,在化工、材料、生物等领域得到了广泛的应用。本文采用主从(Master／Slave)并行模型,基于正交递归对分法(recursive coordinate bisection,RCB)和规则网格,设计出一种适用于具有多种复杂粒子的粒子系统并行模拟的负载平衡方法。应用该方法,在集群系统上采用离散元方法模拟了某钢铁公司滚筒系统。模拟采用4个节点,根据是否利用负载平衡模块分别进行测试,计算结果分析表明采用本文的负载平衡策略,计算效率提高了约14％。本文的算法具有较好的通用性,可以方便地应用于其它粒子方法的大规模并行计算问题。     

Simulating Spatially Explicit Problems on High Performance Architectures

This paper addresses issues of implementation and performance optimization of simulations designed to model spatially explicit problems with the use of parallel discrete event simulation. A simulation system is presented that uses the optimistic protocol and runs on a distributed memory machine—the IBM SP. The efficiency of parallel discrete event simulations that use the optimistic protocol is strongly dependent on the overhead incurred by rollbacks. This paper introduces a novel approach to rollback processing which limits the number of events rolled back as a result of a straggler or antimessage. The method, called Breadth-First Rollback (BFR), is suitable for spatially explicit problems where the space is discretized and distributed among processes and simulation objects move freely in the space. The BFR uses incremental state saving, allowing the recovery of causal relationships between events during rollback. These relationships are then used to determine which events need to be rolled back. This paper presents an application of BFR to the simulation of Lyme disease. Our results demonstrate and almost linear speedup—a dramatic improvement over the traditional approach to rollback processing. Additionally, BFR is used as a basis of a dynamic load balancing algorithm that migrates load between the simulation processes. A brief outline of the algorithm and its potential performance are presented.     

基于时间偏差协议的动态负载平衡技术*

对并行VHDL模拟的特殊性进行分析后,建立了一个并行VHDL模拟的动态负载平衡模型。在此模型中,提出动态调节最佳并行规模的动态负载平衡方法来解决系统资源紧张的问题,采用一种新的模拟中负载的度量方法——模拟推进度。此模型还包括基于标准偏差和最小通信变化量的动态负载平衡算法和一个运行中的负载迁移机制。最后对该模型进行可行性分析。     

PLUM : Parallel Load Balancing for Adaptive Unstructured Meshes

Mesh adaption is a powerful tool for efficient unstructured-grid computations but causes load imbalance among processors on a parallel machine. We present a novel method calledPLUMto dynamically balance the processor workloads with a global view. This paper describes the implementation and integration of all major components within our dynamic load balancing strategy for adaptive grid calculations. Mesh adaption, repartitioning, processor assignment, and remapping are critical components of the framework that must be accomplished rapidly and efficiently so as not to cause a significant overhead to the numerical simulation. A data redistribution model is also presented that predicts the remapping cost on the SP2. This model is required to determine whether the gain from a balanced workload distribution offsets the cost of data movement. Results presented in this paper demonstrate thatPLUMis an effective dynamic load balancing strategy which remains viable on a large number of processors.     

Dynamic Load Balancing for Short-range Parallel Molecular Dynamics Simulations

The iterative Multilevel Averaging Weight (MAW) algorithm presented in paper [1] is modified to solve the dynamic load imbalance problems arising from the two-dimensional short-range parallel molecular dynamics simulations in this paper. Firstly, five types of load balancing models are given which allows detailed studies of the algorithm. In particular, it shows that for strip decomposition, the number of iteration needs for the system to converge from an initially unbalanced state to a well balanced state is bounded by 2 log P , where P is the number of processors. This result can permit the algorithm to efficiently track fluctuations in the molecular density as the simulation progresses, and is much better than that of the Cellular Automaton Diffusion (CAD) scheme presented in paper [2] . Secondly, we apply MAW algorithm to solve the load imbalance problem in the parallel molecular dynamics simulation for higher speed wall collisions. At last, the numerical experimental results and parallel computing performance with MPI-1.2 under a PC-Cluster consists of 64 Pentium-III 500 MHz nodes connected by 100 Mbps Switches are given in this paper.     

A Grid-based Virtual Reactor: Parallel performance and adaptive load balancing

We address the problem of porting parallel distributed applications from static homogeneous cluster environments to dynamic heterogeneous Grid resources. We introduce a generic technique for adaptive load balancing of parallel applications on heterogeneous resources and evaluate it using a case study application: a Virtual Reactor for simulation of plasma chemical vapour deposition. This application has a modular architecture with a number of loosely coupled components suitable for distribution over the Grid. It requires large parameter space exploration that allows using Grid resources for high-throughput computing. The Virtual Reactor contains a number of parallel solvers originally designed for homogeneous computer clusters that needed adaptation to the heterogeneity of the Grid. In this paper we study the performance of one of the parallel solvers, apply the technique developed for adaptive load balancing, evaluate the efficiency of this approach and outline an automated procedure for optimal utilization of heterogeneous Grid resources for high-performance parallel computing.     

Tools to support mesh adaptation on massively parallel computers

The scalable execution of parallel adaptive analyses requires the application of dynamic load balancing to repartition the mesh into a set of parts with balanced work load and minimal communication. As the adaptive meshes being generated reach billions of elements and the analyses are performed on massively parallel computers with 100,000??s of computing cores, a number of complexities arise that need to be addressed. This paper presents procedures developed to deal with two of them. The first is a procedure to support multiple parts per processor which is used as the mesh increases in size and it is desirable to partition the mesh to a larger number of computing cores than are currently being used. The second is a predictive load balancing method that sets entity weights before dynamic load balancing steps so that the mesh is well balanced after the mesh adaptation step thus avoiding excessive memory spikes that would otherwise occur during mesh adaptation.     

Customized Dynamic Load Balancing for a Network of Workstations

Load balancing involves assigning to each processor work proportional to its performance, thereby minimizing the execution time of a program. Although static load balancing can solve many problems (e.g., those caused by processor heterogeneity and nonuniform loops) for most regular applications, the transient external load due to multiple users on a network of workstations necessitates a dynamic approach to load balancing. In this paper we show that different load balancing schemes are best for different applications under varying program and system parameters. Therefore, application-driven customized dynamic load balancing becomes essential for good performance. We present a hybrid compile-time and run-time modeling and decision process which selects (customizes) the best scheme, along with automatic generation of parallel code with calls to a run-time library for load balancing.     

Dependency graph approach to load balancing distributed volume visualization

We present a framework that uses data dependency information to automate load balanced volume distribution and ray-task scheduling for parallel visualization of massive volumes. This dependency graph approach improves load balancing for both ray casting and ray tracing. The main bottlenecks in distributed volume rendering involve moving data across the network and loading memory into rendering hardware. Our load balancing solution combines static network distribution with dynamic ray-task scheduling. At the core of the dependency graph approach are the flex-block tree, introduced in this paper, and the cell-tree. The flex-block tree is similar to a kd-tree except that leaf nodes are cells containing a combination of empty space and tightly cropped subvolumes, or flex-blocks. A main contribution of this paper is the moving walls algorithm, which uses dynamic programming to create a flex-block partition. We show results for optimizing distributed ray cast rendering using a time cost function. We compare data distribution using the moving walls algorithm, with distribution using a recursive solution, and with a grid combined with a local kd-tree partition on each render-node.

Agent scheduling model for adaptive dynamic load balancing in agent-based distributed simulations

Agent-based distributed simulations are confronted with load imbalance problem, which significantly affects simulation performance. Dynamic load balancing can be effective in decreasing simulation execution time and improving simulation performance. The characteristics of multi-agent systems and time synchronization mechanisms make the traditional dynamic load balancing approaches not suitable for dynamic load balancing in agent-based distributed simulations. In this paper, an adaptive dynamic load balancing model in agent-based distributed simulations is proposed. Due to the complexity and huge time consuming for solving the model, a distributed approximate optimized scheduling algorithm with partial information (DAOSAPI) is proposed. It integrates the distributed mode, approximate optimization and agent set scheduling approach. Finally, experiments are conducted to verify the efficiency of the proposed algorithm and the simulation performance under dynamic agent scheduling. The experiments indicate that DAOSPI has the advantage of short execution time in large-scale agent scheduling, and the distributed simulation performance under this dynamic agent scheduling outperforms that under static random agent distribution.     

Dynamic workload balancing of parallel applications with user-level scheduling on the Grid

This paper suggests a hybrid resource management approach for efficient parallel distributed computing on the Grid. It operates on both application and system levels, combining user-level job scheduling with dynamic workload balancing algorithm that automatically adapts a parallel application to the heterogeneous resources, based on the actual resource parameters and estimated requirements of the application. The hybrid environment and the algorithm for automated load balancing are described, the influence of resource heterogeneity level is measured, and the speedup achieved with this technique is demonstrated for different types of applications and resources.