分子动力学在小型SMP集群中的并行计算

为提高分子动力学的模拟运算效率,在Linux环境下以MPICH技术构建的小型SMP集群系统上,对模拟体系采用改进的原子分解算法进行并行计算.将要模拟的原子平均分配给各个计算节点进行计算,节点间通过MPI进行通信.对进程间的接收和发送进行捆绑操作并采取非阻塞通信取代原有的阻塞通信,从而避免了死锁情况.实验结果表明:优化后的并行算法可以有效地利用计算机资源,提高运算效率,解决了实际测试中出现的死锁问题,在该集群系统上获得3倍以上的加速比.     

MPI集群通信技术浅析

简要介绍了集群系统,指出其用于并行计算的工作原理,重点介绍MPI并行环境及其通信技术,并分析了MPI并行程序中的基本模式及其采用的通信技术。最后对构建MPI并行环境的集群系统进行了展望。     

非平衡进程到达模式下MPI广播的性能优化方法

为了提高非平衡进程到达(unbalanced process arrival,简称UPA)模式下MPI广播的性能,对UPA模式下的广播问题进行了理论分析,证明了在多核集群环境中通过节点内多个MPI进程的竞争可以有效减少UPA对MPI广播性能的影响,并在此基础上提出了一种新的优化方法,即竞争式流水化方法(competitive and pipelined method,简称CP).CP方法通过一种节点内进程竞争机制在广播过程中尽早启动节点间通信,经该方法优化的广播算法利用共享内存在节点内通信,利用由竞争机制产生的引导进程执行原算法在节点间通信.并且,该方法使节点间通信和节点内通信以流水方式重叠执行,能够有效利用集群系统各节点的多核优势,减少了MPI广播受UPA的影响,提高了性能.为了验证CP方法的有效性,基于此方法优化了3种典型的MPI广播算法,分别适用于不同消息长度的广播.在真实系统中,通过微基准测试和两个实际的应用程序对CP广播进行了性能评价,结果表明,该方法能够有效地提高传统广播算法在UPA模式下的性能.在应用程序的负载测试实验结果中,CP广播的性能较流水化广播的性能提高约16%,较MVAPICH21.2中广播的性能提高18%～24%.     

面向多核集群的数据流程序层次流水线并行优化方法

数据流编程语言是一种面向领域的编程语言,它能够将计算与通信分离,暴露应用程序的并行性.多核集群中计算、存储和通信等底层资源的复杂性对数据流程序的性能提出了新的挑战.针对数据流程序在多核集群上执行存在资源利用低和扩展性差等问题,利用同步数据流图作为中间表示,文中提出并实现了面向多核集群的层次性流水线并行优化方法.方法包含任务划分与调度、层次流水线调度和数据局部性优化,经过编译优化后生成基于MPI的可并行执行的目标代码.其中任务划分与调度是利用程序中数据和任务并行性将任务映射到计算核上,实现负载均衡和低通信同步开销;层次性流水线调度是利用程序中的并行性构造低延迟流水线调度;数据局部性优化是针对数据访问存在的Cache伪共享做面向存储的优化.实验以X86架构多核处理器组成的集群为平台,选取媒体处理领域的典型应用算法作为测试程序,对层次流水线优化进行实验分析.实验结果表明了优化方法的有效性.     

蚁群算法的三种并行模型分析

在单机多核下分别构造基于OpenMP和MPI的并行蚁群算法模型,在多核集群机下构造基于MPI和MPI+OpenMP的并行蚁群算法模型,并提出动态蚁群择优策略及分段周期交流策略。基于实际路网的路径寻优问题对上述模型进行比较,实验结果表明,在单机多核下,基于MPI的模型与基于OpenMP的模型相比,运行时间短,加速比高,在多核集群机下,基于MPI+OpenMP的混合模型相比基于MPI的模型,在进程数较多时仍具有较高的加速比。     

基于PC集群的MPI并行环境的搭建

集群是充分利用计算资源的一个重要概念,PC集群是最易构建的分布式并行计算环境。MPI是应用最广的并行程序设计平台。本文通过实例阐述PC集群及PC集群上的MPI并行计算环境的搭建。     

面向Storm的数据流编程模型与编译优化方法研究

数据流编程模型将程序的计算与通信分离,暴露了应用程序潜在的并行性并简化了编程难度。分布式计算框架利用廉价PC构建多核集群解决了大规模并行计算问题,但多核集群层次性存储结构和处理单元对数据流程序的性能提出了新的挑战。针对数据流程序在分布式架构下所面临的问题,设计并实现了数据流编程模型和分布式计算框架的结合——在COStream的基础上提出了面向Storm的编译优化框架。框架包括两个模块:面向Storm的层次性任务划分与调度,以及面向Storm的层次性软件流水与代码生成。层次性任务划分利用Storm的任务调度机制将程序所有子任务分配到Storm集群节点内的多核上。层次性软件流水与代码生成将子任务构造成集群节点间的软件流水和节点内多核间的软件流水,并生成相应的目标代码。实验以多核集群为目标平台,在集群上搭建Storm分布式架构,选取数字媒体处理领域典型程序作为测试程序,对面向Storm的编译优化后的程序进行实验分析。实验结果表明了结合方法的有效性。     

多核集群系统上的混合编程模型研究

对采用多核处理器作为SMP集群系统的计算节点的系统上的一种混合编程模型-MPI+OpenMP混合编程模型进行了深入的研究.建立了两个矩阵乘的混合并行算法,在多核集群平台上与纯MPI算法分别进行了实验,并进行了性能方面的比较.试验表明,混合编程具有更好的性能.     

基于Docker的MPI和OpenMP混合编程

针对当前搭建集群并行系统复杂且耗时等问题,提出基于Docker搭建并行系统。介绍轻量级虚拟化技术Docker的核心概念和基本架构,并基于Docker技术在Linux平台上搭建集群并行开发环境。简要阐述并行计算的思想,叙述MPI和OpenMP并行计算的基本概念和特点,针对矩阵并行乘法的算法建立MPI和OpenMP的混合编程模型,并给出混合编程模型与MPI并行编程模型以及OpenMP并行编程模型的性能对比,分析出现差异的原因。基于该混合编程模型比较Docker与传统物理机两者搭建的并行系统的并行效率。     

关于多核系统并行程序效率的编程因素及其研究

着重分析了多核架构系统中内存对齐技术与cache利用率等因素对并行程序性能的影响。用共享存储环境OpenMP分析了并行计算量与处理器核心数目之间的关系,通过用MPI编程实现的矩阵相乘的行划分和CANNON算法等实例分析,指出了只有综合考虑了多核系统的结构特征、系统软件、多核编程语言环境以及正确运用算法等,才能设计出高效且能耗又小的并行应用程序。     

大规模结构有限元分析程序在多核集群计算环境中的性能分析和优化

通过对基于MPI编程模型实现的开源有限元计算分析软件在多核集群计算平台中的程序性能的分析,找出程序瓶颈及其原因,实现了基于MPI编程模型的并行程序在多核计算环境中的性能优化。根据程序性能瓶颈的分析,提出了基于MPI/OpenMP混合并行编程模型的大规模线性/非线性方程组求解和多线程多进程同时进行消息通信的两种程序性能优化方案。不同计算规模的实验结果表明,在多核集群计算平台中,MPI/OpenMP混合编程模型实现的大规模非线性方程组求解器相对于单纯基于MPI编程模型实现的并行程序,其性能有2倍到3倍的提升;多线程多进程同时消息传递的优化方案虽然对程序能够起到性能优化作用,但是对解决程序消息通信瓶颈的问题不是最好的方法。两个方案总体性能分析结果表明,基于MPI/OpenMP混合编程模型实现的并行程序,在多核集群计算平台中能够更好地发挥硬件系统的计算能力。     

一种实用的并行计算模型

对于当前流行的工作站集群环境和各类并行机系统,文中提出了一种实用的并行计算模型,即基于LogGP的非独占异质同步模型NHBL（Nondedicated Heterogeneous Barrier LogGP）,它旨在反映具有异质性和非独占性的NOW计算环境对并行算法设计和分析的影响,然后用NHBL模型分析了PSRS算法在国家高性能计算中心（合肥）的工作站集群NHPCC-Cluster和曙光－1000MPP由的代价,并用实测结果进行了验证。     

Performance analysis and optimization of MPI collective operations on multi-core clusters

Memory hierarchy on multi-core clusters has twofold characteristics: vertical memory hierarchy and horizontal memory hierarchy. This paper proposes new parallel computation model to unitedly abstract memory hierarchy on multi-core clusters in vertical and horizontal levels. Experimental results show that new model can predict communication costs for message passing on multi-core clusters more accurately than previous models, only incorporated vertical memory hierarchy. The new model provides the theoretical underpinning for the optimal design of MPI collective operations. Aimed at horizontal memory hierarchy, our methodology for optimizing collective operations on multi-core clusters focuses on hierarchical virtual topology and cache-aware intra-node communication, incorporated into existing collective algorithms in MPICH2. As a case study, multi-core aware broadcast algorithm has been implemented and evaluated. The results of performance evaluation show that the above methodology for optimizing collective operations on multi-core clusters is efficient.     

Towards Scalable Java HPC with Hybrid and Native Communication Devices in MPJ Express

MPJ Express is a messaging system that allows application developers to parallelize their compute-intensive sequential Java codes on High Performance Computing clusters and multicore processors. In this paper, we extend MPJ Express software to provide two new communication devices. The first device—called hybrid—enables MPJ Express to exploit hybrid parallelism on cluster of multicore processors by sitting on top of existing shared memory and network communication devices. The second device—called native—uses JNI wrappers in interfacing MPJ Express to native MPI implementations like MPICH and Open MPI. We evaluate performance of these devices on a range of interconnects including 1G/10G Ethernet, 10G Myrinet and 40G InfiniBand. In addition, we analyze and evaluate the cost of MPJ Express buffering layer and compare it with the performance numbers of other Java MPI libraries. Our performance evaluation reveals that the native device allows MPJ Express to achieve comparable performance to native MPI libraries—for latency and bandwidth of point-to-point and collective communications—which is a significant gain in performance compared to existing communication devices. The hybrid communication device—without any modifications at application level—also helps parallel applications achieve better speedups and scalability by exploiting multicore architecture. Our performance evaluation quantifies the cost incurred by buffering and its impact on overall performance of software. We witnessed comparative performance as both new devices improve application performance and achieve upto 90 % of the theoretical bandwidth available without application rewriting effort—including NAS Parallel Benchmarks, point-to-point and collective communication.     

A framework for adaptive collective communications for heterogeneous hierarchical computing systems

Collective communication operations are widely used in MPI applications and play an important role in their performance. However, the network heterogeneity inherent to grid environments represent a great challenge to develop efficient high performance computing applications. In this work we propose a generic framework based on communication models and adaptive techniques for dealing with collective communication patterns on grid platforms. Toward this goal, we address the hierarchical organization of the grid, selecting the most efficient communication algorithms at each network level. Our framework is also adaptive to grid load dynamics since it considers transient network characteristics for dividing the nodes into clusters. Our experiments with the broadcast operation on a real-grid setup indicate that an adaptive framework allows significant performance improvements on MPI collective communications.     

Using hybrid MPI and OpenMP programming to?optimize communications in parallel loop self-scheduling schemes for multicore PC clusters

Recently, a series of parallel loop self-scheduling schemes have been proposed, especially for heterogeneous cluster systems. However, they employed the MPI programming model to construct the applications without considering whether the computing node is multicore architecture or not. As a result, every processor core has to communicate directly with the master node for requesting new tasks no matter the fact that the processor cores on the same node can communicate with each other through the underlying shared memory. To address the problem of higher communication overhead, in this paper we propose to adopt hybrid MPI and OpenMP programming model to design two-level parallel loop self-scheduling schemes. In the first level, each computing node runs an MPI process for inter-node communications. In the second level, each processor core runs an OpenMP thread to execute the iterations assigned for its resident node. Experimental results show that our method outperforms the previous works.     

Optimal software multicast in wormhole-routed multistage networks

Multistage interconnection networks are a popular class of interconnection architecture for constructing scalable parallel computers (SPCs). The focus of this paper is on the multistage network system which supports wormhole routed turnaround routing. Existing machines characterized by such a system model include the IBM SP-1 and SP-2, TMC CM-5, and Meiko CS-2. Efficient collective communication among processor nodes is critical to the performance of SPCs. A system-level multicast service, in which the same message is delivered from a source node to an arbitrary number of destination nodes, is fundamental in supporting collective communication primitives including the application-level broadcast, reduction, and barrier synchronization. This paper addresses how to efficiently implement multicast services in wormhole-routed multistage networks, in the absence of hardware multicast support, by exploiting the properties of the turnaround switching technology. An optimal multicast algorithm is proposed. The results of implementations on a 64-node SP-1 show that the proposed algorithm significantly outperforms the application-level broadcast primitives provided by currently existing collective communication libraries including the public domain MPI     

Explicit formulation of multibody dynamics based on principle of dynamical balance and its parallelization

Efficient computation of dynamics parameters is one of the important issues in simulation and control of the multibody systems as these systems become more complex. Recent advances in computer architecture are toward multiple core systems rather than high-speed single core systems. Therefore, parallel computation algorithms for dynamics parameters should be designed to improve the performance on these multicore architectures. In this paper, a new dynamics computation algorithm is derived using the principle of dynamical balance, which provides explicit computation of dynamic parameters. This new algorithm has the structure to which parallel computation can be easily applicable. Parallel computation methods are then applied so that we can exploit the structure of the proposed dynamics computation algorithm based on the principle of dynamical balance. The parallel algorithm is designed based on task and data-parallelism. The performance of the proposed algorithm is verified on robots with various topologies. The improved speed of parallel computation is demonstrated through these experiments.     

基于主动消息与LogP模型的并行程序设计

主动消息将通信和计算集成为一体，是一种相当有效和高适应性的通信体系结构。ＬｏｇＰ模型是一种面向实际的并行算法设计模型?较好地反映了当前ＭＰＰ的关键性能参数。本文讨论了它的特点，在此基础上着重分析了它在并行程序设计上的互补性。     

三维Navier-Stokes方程分步法的并行算法在异构平台上实现初探

本文选取了三维不可压缩流动方程的分步法(fractional-step method),其中动量方程使用BiCGSTAB算法进行迭代求解,而压力泊松方程使用Fourier变换法进行直接求解。本文研究该算法在集群平台上的并行算法,从区域分解入手,分析一维、两维、三维区域划分三种情况下,各并行处理器上的计算量与通讯量,根据分析结果使用两维区域分解。分析BiCGSTAB算法和泊松Fourier变换法在GPGPU异构平台上的移植方法。最后,本文分析了BiCGSTAB和泊松方程Fourier变换法两种算法在CPU集群和GPGPU异构平台上的并行性能结果。