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2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing最新文献

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Accurate Scoring of Drug Conformations at the Extreme Scale 极端尺度下药物构象的准确评分
Boyu Zhang, Trilce Estrada, Pietro Cicotti, P. Balaji, M. Taufer
We present a scalable method to extensively search for and accurately select pharmaceutical drug candidates in large spaces of drug conformations computationally generated and stored across the nodes of a large distributed system. For each legend conformation in the dataset, our method first extracts relevant geometrical properties and transforms the properties into a single metadata point in the three-dimensional space. Then, it performs an ochre-based clustering on the metadata to search for predominant clusters. Our method avoids the need to move legend conformations among nodes because it extracts relevant data properties locally and concurrently. By doing so, we can perform accurate and scalable distributed clustering analysis on large distributed datasets. We scale the analysis of our pharmaceutical datasets a factor of 400X higher in performance and 500X larger in size than ever before. We also show that our clustering achieves higher accuracy compared with that of traditional clustering methods and conformational scoring based on minimum energy.
我们提出了一种可扩展的方法,可以在大型分布式系统的节点上计算生成和存储的大量药物构象空间中广泛搜索和准确选择候选药物。对于数据集中的每个图例构象,我们的方法首先提取相关的几何属性,并将这些属性转换为三维空间中的单个元数据点。然后,它在元数据上执行基于赭石的聚类,以搜索主要集群。我们的方法避免了在节点之间移动图例构象的需要,因为它在本地和并发地提取相关的数据属性。通过这样做,我们可以在大型分布式数据集上执行准确且可扩展的分布式聚类分析。我们将制药数据集的分析规模扩大了400倍,比以往任何时候都要大500倍。与传统的聚类方法和基于最小能量的构象评分相比,我们的聚类方法具有更高的准确率。
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引用次数: 6
Analyzing the Impact of CPU Pinning and Partial CPU Loads on Performance and Energy Efficiency 分析CPU固定和部分CPU负载对性能和能效的影响
Pub Date : 2015-05-04 DOI: 10.1109/CCGrid.2015.164
Andrej Podzimek, L. Bulej, L. Chen, Walter Binder, P. Tůma
While workload collocation is a necessity to increase energy efficiency of contemporary multi-core hardware, it also increases the risk of performance anomalies due to workload interference. Pinning certain workloads to a subset of CPUs is a simple approach to increasing workload isolation, but its effect depends on workload type and system architecture. Apart from common sense guidelines, the effect of pinning has not been extensively studied so far. In this paper we study the impact of CPU pinning on performance interference and energy efficiency for pairs of collocated workloads. Besides various combinations of workloads, virtualization and resource isolation, we explore the effects of pinning depending on the level of background load. The presented results are based on more than 1000 experiments carried out on an Intel-based NUMA system, with all power management features enabled to reflect real-world settings. We find that less common CPU pinning configurations improve energy efficiency at partial background loads, indicating that systems hosting collocated workloads could benefit from dynamic CPU pinning based on CPU load and workload type.
虽然工作负载搭配是提高当代多核硬件能源效率的必要条件,但它也增加了由于工作负载干扰而导致性能异常的风险。将某些工作负载固定到cpu子集是增加工作负载隔离的一种简单方法,但其效果取决于工作负载类型和系统架构。除了常识性的指导方针外,到目前为止,钉住的效果还没有得到广泛的研究。本文研究了CPU钉住对并行工作负载的性能干扰和能效的影响。除了工作负载、虚拟化和资源隔离的各种组合之外,我们还探讨了根据后台负载级别绑定的影响。所提出的结果是基于在基于英特尔的NUMA系统上进行的1000多个实验,所有电源管理功能都能反映现实世界的设置。我们发现,不太常见的CPU固定配置可以提高部分后台负载下的能源效率,这表明托管并发工作负载的系统可以从基于CPU负载和工作负载类型的动态CPU固定中受益。
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引用次数: 46
Contiguity and Locality in Backfilling Scheduling 回填调度中的邻近性和局部性
Pub Date : 2015-05-04 DOI: 10.1109/CCGrid.2015.143
Giorgio Lucarelli, F. Mendonca, D. Trystram, Frédéric Wagner
We consider the classical First Come First Served / backfilling algorithm which is commonly used in actual batch schedulers. As HPC platforms grow in size and complexity, an interesting question is how to enhance this algorithm in order to improve global performance by reducing the overall amount of communications. In this direction, we are interested in studying the impact of contiguity and locality allocation constraints on the behavior of batch scheduler. We provide a theoretical analysis of the cost of enforcing contiguity and locality properties. More specifically, we show that both properties do not impose strong limit on achievable make span performance while comparing feasible optimal solutions under different settings, we describe here the existing results on this topic and complete them with all combinations of constraints. We also propose a range of different allocation algorithms for backfilling by choosing between a strict or a soft enforcing of locality and contiguity. Our approach is validated through an extensive series of simulations based on batch scheduler traces. Experiments show that our algorithms do not increase the make span in average when comparing to actual practices. Interestingly, we observe that enforcing contiguity efficiently improves locality.
我们考虑了在实际批调度程序中常用的经典的先到先得/回填算法。随着HPC平台的规模和复杂性的增长,一个有趣的问题是如何通过减少通信总量来增强该算法以提高全局性能。在这个方向上,我们感兴趣的是研究连续性和局部性分配约束对批调度程序行为的影响。我们提供了一个理论分析的成本,强制邻近和局部属性。更具体地说,在比较不同设置下可行最优解时,我们表明这两个属性对可实现的make span性能没有很强的限制,我们在这里描述了关于该主题的现有结果,并使用所有约束组合来完成它们。我们还提出了一系列不同的回填分配算法,通过选择严格或软强制的局部性和连续性。我们的方法通过基于批调度程序跟踪的一系列广泛的模拟进行了验证。实验表明,与实际情况相比,我们的算法在平均上并没有增加制作跨度。有趣的是,我们观察到增强邻近性有效地提高了局部性。
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引用次数: 11
PIONEER: A Solution to Parallel I/O Workload Characterization and Generation 先锋:并行I/O工作负载表征和生成的解决方案
Weiping He, D. Du, Sai B. Narasimhamurthy
The demand for parallel I/O performance continues to grow. However, modelling and generating parallel I/O work-loads are challenging for several reasons including the large number of processes, I/O request dependencies and workload scalability. In this paper, we propose the PIONEER, a complete solution to Parallel I/O workload characterization and gEnERation. The core of PIONEER is a proposed generic workload path, which is essentially an abstract and dense representation of the parallel I/O patterns for all processes in a High Performance Computing (HPC) application. The generic workload path can be built via exploring the inter-processes correlations, I/O dependencies as well as file open session properties. We demonstrate the effectiveness of PIONEER by faithfully generating synthetic workloads for two popular HPC benchmarks and one real HPC application.
对并行I/O性能的需求持续增长。然而,建模和生成并行I/O工作负载是具有挑战性的,原因包括大量的进程、I/O请求依赖关系和工作负载可伸缩性。在本文中,我们提出了PIONEER,一个完整的解决方案并行I/O工作负载的表征和生成。PIONEER的核心是提议的通用工作负载路径,它本质上是高性能计算(HPC)应用程序中所有进程的并行I/O模式的抽象和密集表示。可以通过探索进程间相关性、I/O依赖性以及文件打开会话属性来构建通用工作负载路径。我们通过忠实地为两个流行的HPC基准测试和一个真实的HPC应用程序生成合成工作负载来证明PIONEER的有效性。
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引用次数: 6
A Novel Query Caching Scheme for Dynamic InfiniBand Subnets 一种新的ib动态子网查询缓存方案
Evangelos Tasoulas, Ernst Gunnar Gran, Bjørn Dag Johnsen, T. Skeie
In large InfiniBand subnets the Subnet Manager (SM) is a potential bottleneck. When an InfiniBand subnet grows in size, the number of paths between hosts increases polynomials and the SM may not be able to serve the network in a timely manner when many concurrent path resolution requests are received. This scalability challenge is further amplified in a dynamic virtualized cloud environment. When a Virtual Machine (VM) with InfiniBand interconnect live migrates, the VM addresses change. These address changes result in additional load to the SM as communicating peers send Subnet Administration (SA) path record queries to the SM to resolve new path characteristics. In this paper we benchmark OpenSM to empirically demonstrate the SM scalability problems. Then we show that our novel SA Path Record Query caching scheme significantly reduces the load towards the SM. In particular, we show by using the Reliable Datagram Socket protocol that only a single initial SA path query is needed per communicating peer, independent of any subsequent (re)connection attempts.
在大型ib子网中,子网管理器(SM)是一个潜在的瓶颈。当ib子网规模增大时,主机间的路径数会呈多项式增长,当同时收到很多路径解析请求时,SM可能无法及时为网络提供服务。这种可伸缩性挑战在动态虚拟化云环境中进一步放大。ib热组网的虚拟机迁移时,虚拟机地址会发生变化。这些地址更改会给SM带来额外的负载,因为通信对等体会向SM发送子网管理(SA)路径记录查询,以解析新的路径特征。在本文中,我们对OpenSM进行了基准测试,以经验证明SM的可伸缩性问题。然后,我们证明了我们的新SA路径记录查询缓存方案显着减少了对SM的负载。特别是,我们通过使用可靠数据报套接字协议表明,每个通信对等点只需要一个初始SA路径查询,独立于任何后续(重新)连接尝试。
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引用次数: 4
Towards a High Level Programming Paradigm to Deploy e-Science Applications with Dynamic Workflows on Large Scale Distributed Systems 面向在大规模分布式系统上部署具有动态工作流的电子科学应用的高级编程范式
Pub Date : 2015-05-04 DOI: 10.1109/CCGrid.2015.147
M. B. Belgacem, N. Abdennadher
This papers targeted scientists and programmers who need to easily develop and run e-science applications on large scale distributed systems. We present a rich programming paradigm and environment used to develop and deploy high performance applications (HPC) on large scale distributed and heterogeneous platforms. We particularly target iterative e-science applications where (i) convergence conditions and number of jobs are not known in advance, (ii) jobs are created on the fly and (iii) jobs could be persistent. We propose two programming paradigms so as to provide intuitive statements enabling an easy writing of HPC e-science applications. Non-expert developers (scientific researchers) can use them to guarantee fast development and efficient deployment of their applications.
本文针对需要在大规模分布式系统上轻松开发和运行电子科学应用程序的科学家和程序员。我们提出了一个丰富的编程范例和环境,用于在大规模分布式和异构平台上开发和部署高性能应用程序(HPC)。我们特别针对迭代电子科学应用,其中(i)收敛条件和工作数量事先不知道,(ii)工作是在飞行中创建的,(iii)工作可能是持久的。我们提出了两种编程范例,以便提供直观的语句,使HPC电子科学应用程序易于编写。非专业开发人员(科学研究人员)可以使用它们来保证其应用程序的快速开发和有效部署。
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引用次数: 2
An Availability-on-Demand Mechanism for Datacenters 数据中心的可用性随需应变机制
S. Shen, A. Iosup, A. Israel, W. Cirne, D. Raz, D. Epema
Data enters are at the core of a wide variety of daily ICT utilities, ranging from scientific computing to online gaming. Due to the scale of today's data enters, the failure of computing resources is a common occurrence that may disrupt the availability of ICT services, leading to revenue loss. Although many high availability (HA) techniques have been proposed to mask resource failures, datacenter users' -- who rent datacenter resources and use them to provide ICT utilities to a global population' -- still have limited management options for dynamically selecting and configuring HA techniques. In this work, we propose Availability-on-Demand (AoD), a mechanism consisting of an API that allows datacenter users to specify availability requirements which can dynamically change, and an availability-aware scheduler that dynamically manages computing resources based on user-specified requirements. The mechanism operates at the level of individual service instance, thus enabling fine-grained control of availability, for example during sudden requirement changes and periodic operations. Through realistic, trace-based simulations, we show that the AoD mechanism can achieve high availability with low cost. The AoD approach consumes about the same CPU hours but with higher availability than approaches which use HA techniques randomly. Moreover, comparing to an ideal approach which has perfect predictions about failures, it consumes 13% to 31% more CPU hours but achieves similar availability for critical parts of applications.
从科学计算到在线游戏,数据输入是各种日常信息通信技术实用程序的核心。由于当今数据输入的规模,计算资源的故障是一种常见现象,可能会破坏信息通信技术服务的可用性,导致收入损失。尽管已经提出了许多高可用性(HA)技术来掩盖资源故障,但数据中心用户(租用数据中心资源并使用它们向全球人口提供ICT公用设施)在动态选择和配置HA技术方面的管理选项仍然有限。在这项工作中,我们提出了按需可用性(AoD),这是一种由API组成的机制,允许数据中心用户指定可以动态更改的可用性需求,以及基于用户指定需求动态管理计算资源的可用性感知调度程序。该机制在单个服务实例级别上运行,从而支持对可用性的细粒度控制,例如在突然的需求更改和周期性操作期间。通过真实的、基于轨迹的仿真,我们证明了AoD机制能够以低成本实现高可用性。与随机使用HA技术的方法相比,AoD方法消耗的CPU时间大致相同,但具有更高的可用性。此外,与对故障有完美预测的理想方法相比,它消耗的CPU时间多13%到31%,但在应用程序的关键部分实现了类似的可用性。
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引用次数: 17
Quantifying the Energy Efficiency Challenges of Achieving Exascale Computing 量化实现百亿亿次计算的能源效率挑战
Pub Date : 2015-05-04 DOI: 10.1109/CCGrid.2015.130
J. Mair, Zhiyi Huang, D. Eyers, Yawen Chen
Power and performance are two potentially opposing objectives in the design of a supercomputer, where increases in performance often come at the cost of increased power consumption and vice versa. The task of simultaneously maximising both objectives is becoming an increasingly prominent challenge in the development of future exascale supercomputers. To gain some perspective on the scale of the challenge, we analyse the power and performance trends for the Top500 and Green500 supercomputer lists. We then present the PαPW metric, which we use to evaluate the scalability of power efficiency, projecting the development of an exascale system. From this analysis, we found that when both power and performance are considered, the projected date of achieving an exascale system falls far beyond the current target of 2020.
在超级计算机的设计中,功率和性能是两个潜在的对立目标,性能的提高通常是以功耗的增加为代价的,反之亦然。同时最大化这两个目标的任务正在成为未来百亿亿次超级计算机发展中日益突出的挑战。为了了解挑战的规模,我们分析了Top500和Green500超级计算机列表的功率和性能趋势。然后,我们提出了PαPW度量,我们用它来评估功率效率的可扩展性,预测一个百亿亿级系统的发展。从这一分析中,我们发现,当考虑到功率和性能时,实现百亿亿级系统的预计日期远远超出了目前的2020年目标。
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引用次数: 25
Discovering and Leveraging Content Similarity to Optimize Collective on-Demand Data Access to IaaS Cloud Storage 发现和利用内容相似性来优化对IaaS云存储的集体按需数据访问
Pub Date : 2015-05-04 DOI: 10.1109/CCGrid.2015.156
Bogdan Nicolae, Andrzej Kochut, A. Karve
A critical feature of IaaS cloud computing is the ability to quickly disseminate the content of a shared dataset at large scale. In this context, a common pattern is collective on-demand read, i.e., accessing the same VM image or dataset from a large number of V Minstances concurrently. There are various techniques that avoid I/Ocontention to the storage service where the dataset is located without relying on pre-broadcast. Most such techniques employ peer-to-peer collaborative behavior where the VM instances exchange information about the content that was accessed during runtime, such that it impossible to fetch the missing data pieces directly from each other rather than the storage system. However, such techniques are often limited within a group that performs a collective read. In light of high data redundancy on large IaaS data centers and multiple users that simultaneously run VM instance groups that perform collective reads, an important opportunity arises: enabling unrelated VMinstances belonging to different groups to collaborate and exchange common data in order to further reduce the I/O pressure on the storage system. This paper deals with the challenges posed by such absolution, which prompt the need for novel techniques to efficiently detect and leverage common data pieces across groups. To this end, we introduce a low-overhead fingerprint based approach that we evaluate and demonstrate to be efficient in practice for a representative scenario on dozens of nodes and a variety of group configurations.
IaaS云计算的一个关键特性是能够大规模快速传播共享数据集的内容。在这种情况下,常见的模式是集体按需读取,即从大量V实例并发访问相同的VM映像或数据集。有各种技术可以避免数据集所在存储服务的I/ o争用,而不依赖于预广播。大多数此类技术采用点对点协作行为,其中VM实例交换有关在运行时访问的内容的信息,这样就不可能直接从彼此而不是从存储系统中获取缺失的数据块。然而,这种技术通常仅限于执行集体读取的组。考虑到大型IaaS数据中心的高数据冗余,以及多个用户同时运行执行集体读取的VM实例组,一个重要的机会出现了:允许属于不同组的不相关的VM实例协作和交换公共数据,以进一步减少存储系统的I/O压力。本文讨论了这种赦免带来的挑战,这促使人们需要新的技术来有效地检测和利用跨组的公共数据片段。为此,我们引入了一种低开销的基于指纹的方法,我们在实践中对数十个节点和各种组配置的代表性场景进行了评估和演示,证明该方法是有效的。
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引用次数: 9
Hamiltonian Path Strategy for Deadlock-Free and Adaptive Routing in Diametrical 2D Mesh NoCs 直径二维网格noc中无死锁自适应路由的hamilton路径策略
Pub Date : 2015-05-04 DOI: 10.1109/CCGrid.2015.112
Poona Bahrebar, D. Stroobandt
The overall performance of Network-on-Chip (NoC) is strongly affected by the efficiency of the on-chip routing algorithm. Among the factors associated with the design of a high-performance routing method, adaptivity is an important one. Moreover, deadlock-and live lock-freedom are necessary for a functional routing method. Despite the advantages that the diametrical mesh can bring to NoCs compared with the classical mesh topology, the literature records little research efforts to design pertinent routing methods for such networks. Using the available routing algorithms, the network performance degrades drastically not only due to the deterministic paths, but also to the deadlocks created between the packets. In this paper, we take advantage of the Hamiltonian routing strategy to adaptively route the packets through deadlock-free paths in a diametrical 2D mesh network. The simulation results demonstrate the efficiency of the proposed approach in decreasing the likelihood of congestion and smoothly distributing the traffic across the network.
片上路由算法的效率直接影响到片上网络的整体性能。在设计高性能路由方法的诸多因素中,自适应是一个重要的因素。此外,死锁和活动锁自由对于功能性路由方法是必要的。尽管与经典的网状拓扑结构相比,直径网格可以为noc带来优势,但文献中很少有针对这种网络设计相关路由方法的研究。使用可用的路由算法,不仅由于路径的确定性,而且由于数据包之间产生的死锁,网络性能会急剧下降。在本文中,我们利用哈密顿路由策略在直径二维网格网络中自适应地通过无死锁路径路由数据包。仿真结果证明了该方法在降低网络拥塞可能性和平稳分配网络流量方面的有效性。
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引用次数: 3
期刊
2015 15th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
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