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2012 International Conference on High Performance Computing & Simulation (HPCS)最新文献

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Semantic scheduling of virtualized infrastructures for scientific workflows 科学工作流虚拟化基础设施的语义调度
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266994
Idafen Santana-Pérez, M. Pérez-Hernández
Virtualized Infrastructures are a promising way for providing flexible and dynamic computing solutions for resource-consuming tasks. Scientific Workflows are one of these kind of tasks, as they need a large amount of computational resources during certain periods of time. To provide the best infrastructure configuration for a workflow it is necessary to explore as many providers as possible taking into account different criteria like Quality of Service, pricing, response time, network latency, etc. Moreover, each one of these new resources must be tuned to provide the tools and dependencies required by each of the steps of the workflow. Working with different infrastructure providers, either public or private using their own concepts and terms, and with a set of heterogeneous applications requires a framework for integrating all the information about these elements. This work proposes semantic technologies for describing and integrating all the information about the different components of the overall system and a set of policies created by the user. Based on this information a scheduling process will be performed to generate an infrastructure configuration defining the set of virtual machines that must be run and the tools that must be deployed on them.
虚拟化基础设施是一种很有前途的方式,可以为资源消耗任务提供灵活和动态的计算解决方案。科学工作流就是其中一种任务,因为它们在特定时期需要大量的计算资源。为了为工作流提供最佳的基础设施配置,有必要考虑到不同的标准,如服务质量、定价、响应时间、网络延迟等,探索尽可能多的提供商。此外,必须对这些新资源中的每一个进行调优,以提供工作流的每个步骤所需的工具和依赖项。使用不同的基础设施提供者(无论是公共的还是私有的,使用它们自己的概念和术语)以及一组异构应用程序,需要一个框架来集成关于这些元素的所有信息。这项工作提出了语义技术,用于描述和集成有关整个系统的不同组件和用户创建的一组策略的所有信息。基于这些信息,将执行一个调度过程,以生成一个基础架构配置,定义必须运行的一组虚拟机和必须在其上部署的工具。
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引用次数: 1
Deadlock-free routing algorithms for 3-dimension Networks-on-Chip with reduced vertical channel density topologies 降低垂直信道密度拓扑的三维片上网络无死锁路由算法
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266923
Haoyuan Ying, A. Jaiswal, K. Hofmann
3D ICs have emerged as promising solution for scalability, power consumption and performance demands of next generation Systems-on-Chip (SoCs). Along with the advantages, it also imposes lots of challenges in terms of cost, technological reliability, power, thermal budget and so forth. Networks-on-chip (NoCs), which is thoroughly investigated in 2D SoC design as scalable interconnects, is also well relevant to 3D IC Design. The cost of moving from 2D to 3D for any application should be justified with improvements in performance, power, latency and the utilization of Through-Silicon-Via (TSV). In this paper, we present two generalized routing algorithms for different reduced vertical channel density topologies, which can maintain the performance of the NoC and critically improve the utilization of TSV. The experiments for simulation were done in SystemC-RTL which can achieve more flexibility and maintain the cycle accuracy. From the experimental results in aspects of execution time, average throughput, system interconnect and TSV energy consumption, and TSV utilization, 50% vertical channel density topologies achieved the best trade-off for the given constrains.
3D集成电路已成为下一代片上系统(soc)的可扩展性,功耗和性能需求的有前途的解决方案。除了优点之外,它还在成本、技术可靠性、功率、热预算等方面提出了许多挑战。片上网络(noc)在2D SoC设计中作为可扩展互连进行了深入研究,也与3D IC设计密切相关。对于任何应用程序来说,从2D到3D的成本都应该与性能、功耗、延迟和通硅通孔(TSV)利用率的提高相匹配。在本文中,我们针对不同的降低垂直信道密度拓扑提出了两种通用路由算法,可以保持NoC的性能并显著提高TSV的利用率。仿真实验在SystemC-RTL系统中进行,该系统在保持周期精度的同时具有更大的灵活性。从执行时间、平均吞吐量、系统互连和TSV能耗以及TSV利用率等方面的实验结果来看,50%垂直信道密度拓扑在给定约束条件下实现了最佳折衷。
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引用次数: 16
3D dendritic spine automatic detection and segmentation through samples obtained by confocal microscopy 通过共聚焦显微镜获得的样本进行三维树突脊柱的自动检测和分割
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266998
Laura Fernández-Soria, J. Sánchez
Dendritic spines are a small protrusions from a neuron's dendrite that typically receives input from a single synapse of an axon. We propose an automatic method to obtain dendritic spines parameters, in terms of length, volume, angles and density.
树突棘是神经元树突上的一个小突起,通常接收来自轴突单个突触的输入。我们提出了一种自动获取树突棘长度、体积、角度和密度参数的方法。
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引用次数: 0
Energy efficiency of knowledge-free scheduling in Peer-to-Peer Desktop Grids 点对点桌面网格中无知识调度的能源效率
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266898
Aritz Barrondo, Andrei Tchernykh, S. E. Schaeffer, Johnatan E. Pecero
We address knowledge-free Bag-of-Tasks non-preemptive scheduling problem on heterogeneous grids, where scheduling decisions are free from information of resources and application characteristics. We consider a scheduling with task replications to overcome possible random bad resource allocation and ensure good performance. We analyze energy consumption of job allocation strategies based on variations of the replication threshold. In order to provide QoS and minimize energy consumption, we perform a joint analysis of two metrics. A case study is given and corresponding results indicate that proposed strategies reduce energy consumption without significant degradation in performance.
在异构网格中,调度决策不受资源信息和应用特性的影响,研究了无知识的任务袋非抢占调度问题。我们考虑了一种具有任务重复的调度方法,以克服可能出现的随机不良资源分配,并保证良好的性能。我们分析了基于复制阈值变化的作业分配策略的能耗。为了提供QoS和最小化能耗,我们对两个指标进行了联合分析。给出了一个案例研究,结果表明所提出的策略在不显著降低性能的情况下降低了能耗。
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引用次数: 6
Rare event simulation: The RESTART method 罕见事件模拟:RESTART方法
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266888
M. Villén-Altamirano
This paper is a tutorial on RESTART, a widely applicable accelerated simulation technique for estimating rare event probabilities. The method is based on performing a number of simulation retrials when the process enters regions of the state space where the chance of occurrence of the rare event is higher. The paper analyzes its efficiency, showing formulas for the gain obtained with respect to crude simulation and for the parameter values that maximize this gain. It also provides guidelines for the choice of the importance function, the function of the system state used for determining when retrials are made. Several examples on queuing networks and ultra reliable systems are exposed to illustrate the application of the guidelines and the efficiency achieved.
本文是一个关于RESTART的教程,这是一种广泛应用于估计罕见事件概率的加速模拟技术。该方法的基础是,当流程进入状态空间中发生罕见事件的概率较高的区域时,执行大量的模拟重试。本文分析了该方法的有效性,给出了根据原始仿真得到的增益公式和使该增益最大化的参数值。它还为重要性函数的选择提供了指导方针,重要性函数是用于确定何时进行重审的系统状态函数。最后以排队网络和超可靠系统为例,说明了该方法的应用及其效率。
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引用次数: 2
An evaluation of sampling algorithms for estimating the size of a Chord network 估计Chord网络大小的抽样算法的评价
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266933
Gabriele Falace, Paolo Trunfio
Due to the decentralized nature of structured P2P systems, there is no a direct way for a single node of getting aggregate statistics about the whole network, such as its current size. In this paper we focus on the problem of estimating the size of one of the most popular structured P2P networks, Chord, using a sampling-based approach. With this approach, a node calculates an estimate of the network size after having queried a small number of its successors about some of their properties. We formally define three sampling-based algorithms that exploit well-known structural properties of a Chord network to derive an estimate of its size. An experimental evaluation was carried out through simulations to evaluate the accuracy of the three algorithms in different network scenarios. The evaluation allowed us to identify, among the three algorithms, a Ring Density Estimation (RDE) technique that was able to estimate the size of all the Chord networks considered with an average error of 2% or less, using only a few tens of sample nodes. Moreover, the simulation results showed that the RDE accuracy is not affected by dynamic network conditions, even in the presence of high nodes failure rates.
由于结构化P2P系统的分散性,单个节点无法直接获得整个网络的汇总统计信息,例如其当前规模。在本文中,我们重点研究了使用基于抽样的方法估计最流行的结构化P2P网络之一Chord的大小问题。使用这种方法,节点在查询少量后续节点的一些属性后,计算网络大小的估计。我们正式定义了三种基于采样的算法,它们利用Chord网络的众所周知的结构特性来得出其大小的估计。通过仿真对三种算法在不同网络场景下的准确性进行了实验评估。评估使我们能够在三种算法中识别出一种环密度估计(RDE)技术,该技术能够估计所有Chord网络的大小,平均误差为2%或更小,仅使用几十个样本节点。此外,仿真结果表明,即使在高节点故障率的情况下,RDE精度也不受动态网络条件的影响。
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引用次数: 0
Broadcast with mask on a massively parallel processing on a chip 在芯片上进行大规模并行处理的掩码广播
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266924
Hana Krichene, M. Baklouti, M. Abid, P. Marquet, J. Dekeyser
The delay of instructions broadcast has a significant impact on the performance of Single Instruction Multiple Data (SIMD) architecture. This is especially true for massively parallel processing Systems-on-Chip (mppSoC), where the processing stage and that of setting up the communication mechanism need several clock periods. Subnetting is the strategy used to partition a single physical network into more than one smaller logical sub-networks (subnets). This technique better controls the broadcast instructions domain and the data traffic between network nodes. Furthermore, it allows to separate synchronous communications from asynchronous processing which maintains reliable communications and rapid processing through parallel processors. This paper describes the design of a communication model called broadcast with mask. This model is dedicated to mppSoC architecture with a huge number of processor elements because it maintains performances even when the number of processors increases. Simulation results and an FPGA implementation validate our approach.
指令广播的延迟对单指令多数据(SIMD)体系结构的性能影响很大。对于大规模并行处理的片上系统(mppSoC)来说尤其如此,处理阶段和建立通信机制需要几个时钟周期。子网划分是一种将单个物理网络划分为多个较小的逻辑子网(子网)的策略。该技术较好地控制了广播指令域和网络节点间的数据流量。此外,它允许将同步通信与异步处理分离,从而通过并行处理器维护可靠的通信和快速处理。本文介绍了一种基于掩码的广播通信模型的设计。该模型专门用于具有大量处理器元件的mppSoC架构,因为即使处理器数量增加,它也能保持性能。仿真结果和FPGA实现验证了我们的方法。
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引用次数: 6
An energy-aware bioinformatics application for assembling short reads in high performance computing systems 一种能量感知生物信息学应用,用于在高性能计算系统中组装短读取
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266905
Julia D. Warnke-Sommer, Sachin Pawaskar, H. Ali
Current biomedical technologies are producing massive amounts of data on an unprecedented scale. The increasing complexity and growth rate of biological data has made bioinformatics data processing and analysis a key and computationally intensive task. High performance computing (HPC) has been successfully applied to major bioinformatics applications to reduce computational burden. However, a naïve approach for developing parallel bioinformatics applications may achieve a high degree of parallelism while unnecessarily expending computational resources and consuming high levels of energy. As the wealth of biological data and associated computational burden continues to increase, there has become a need for the development of energy efficient computational approaches in the bioinformatics domain. To address this issue, we have developed an energy-aware scheduling (EAS) model to run computationally intensive applications that takes both deadline requirements and energy factors into consideration. An example of a computationally demanding process that would benefit from our scheduling model is the assembly of short sequencing reads produced by next generation sequencing technologies. Next generation sequencing produces a very large number of short DNA reads from a biological sample. Multiple overlapping fragments must be aligned and merged into long stretches of contiguous sequence before any useful information can be gathered. The assembly problem is extremely difficult due to the complex nature of underlying genome structure and inherent biological error present in current sequencing technologies. We apply our EAS model to a newly proposed assembly algorithm called Merge and Traverse, giving us the ability to generate speedup profiles. Our EAS model was also able to dynamically adjust the number of nodes needed to meet given deadlines for different sets of reads.
当前的生物医学技术正在以前所未有的规模产生大量数据。生物数据日益增加的复杂性和增长速度使得生物信息学数据处理和分析成为一项关键的计算密集型任务。高性能计算(HPC)已经成功地应用于主要的生物信息学应用中,以减少计算负担。然而,开发并行生物信息学应用的naïve方法可能在不必要地消耗计算资源和消耗高水平能量的同时实现高度并行性。随着生物数据的丰富和相关计算负担的不断增加,生物信息学领域已经需要开发高效节能的计算方法。为了解决这个问题,我们开发了一个能源感知调度(EAS)模型来运行计算密集型应用程序,该应用程序同时考虑了截止日期要求和能源因素。从我们的调度模型中获益的计算要求较高的过程的一个例子是由下一代测序技术产生的短测序reads的组装。下一代测序从生物样本中产生大量的短DNA读数。在收集到有用的信息之前,必须将多个重叠的片段对齐并合并成一长串连续的序列。由于当前测序技术中潜在基因组结构的复杂性和固有的生物学误差,组装问题非常困难。我们将我们的EAS模型应用于一个新提出的称为合并和遍历的装配算法,使我们能够生成加速配置文件。我们的EAS模型还能够动态调整节点数量,以满足不同读取集的给定截止日期。
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引用次数: 5
Building a virtual cluster using HPC-Europa2 live DVD 使用HPC-Europa2 live DVD构建虚拟集群
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266892
Anthony Sulistio, Alexander Schulz, R. Keller, Panagiotis Kritikakos, Mourtzoukos Kostas, T. Varvarigou
The HPC-Europa2 project aims at uniting European scientists from various research areas with their respective scientific peers and collaborating in their specific fields, while making use of supercomputers at Europe's leading High Performance Computing (HPC) centers, i.e. BSC (Spain), CINECA (Italy), CSC (Finland), EPCC (UK), GENCI-CINES (France), HLRS (Germany), and SARA (Netherlands). In order to attract new fields and scientists from otherwise less HPC-involved scientific areas to the project, a live DVD has been built that provides parallel tools and libraries similar to the ones used by the aforementioned HPC centers (e.g. Torque, Paraver, and MPI). Thus, this live DVD emulates the environment of the platforms available at the HPC-Europa2 centers. By running the HPC-Europa2 live DVD under a hypervisor and/or booting from physical computers, users can build a virtual cluster, where they can learn more about parallel programming with recent tools and libraries without going through time-consuming installation procedures. As a result, the HPC-Europa2 live DVD provides a fool-proof e-learning and teaching experience.
HPC- europa2项目旨在利用欧洲领先的高性能计算(HPC)中心的超级计算机,即BSC(西班牙)、CINECA(意大利)、CSC(芬兰)、EPCC(英国)、GENCI-CINES(法国)、HLRS(德国)和SARA(荷兰),将来自不同研究领域的欧洲科学家与各自的科学同行联合起来,并在各自的领域进行合作。为了吸引新的领域和科学家从其他不太涉及HPC的科学领域到这个项目,已经建立了一个实时DVD,提供类似于前面提到的HPC中心(例如Torque, Paraver和MPI)使用的并行工具和库。因此,这个实时DVD模拟了HPC-Europa2中心可用平台的环境。通过在管理程序下运行HPC-Europa2实时DVD和/或从物理计算机启动,用户可以构建一个虚拟集群,在那里他们可以使用最新的工具和库了解更多关于并行编程的知识,而无需经历耗时的安装过程。因此,HPC-Europa2现场DVD提供了一个万无一失的电子学习和教学经验。
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引用次数: 1
Exploring dynamically reconfigurable multicore designs with NoRC designer 用NoRC设计器探索动态可重构的多核设计
Pub Date : 2012-07-02 DOI: 10.1109/HPCSim.2012.6266921
J. Núñez-Yáñez, A. Beldachi, A. Nabina, Mohammad Hosseinabady
This paper presents a toolset named NoRC (Network on a Reconfigurable Chip) designer and IP infrastructure designed to investigate the effects of partial dynamic reconfiguration in multicore designs mapped to commercial FPGAs. Dynamic reconfiguration means in this context that tiles and communication routers can be modified at run-time adapting to changes in application requirements, operating conditions and/or process variations. The NoRC system is oriented at avoiding any centralized control with functions mapped to tiles at runtime depending on processing capabilities and location. The dynamic nature of the platform means that following a request for an application from an external host any idle tile can be configured as a master able to make additional requests to nearby tiles or as a slave able to service the requests. NoRC designer is used in this paper to investigate possible task mapping strategies suitable for this type of adaptive platform and also the power and partial reconfiguration overheads of commercial FPGAs.
本文提出了一个名为NoRC(可重构芯片上的网络)设计器的工具集和IP基础设施,旨在研究映射到商用fpga的多核设计中的部分动态重构的影响。动态重新配置意味着在这种情况下,瓷砖和通信路由器可以在运行时进行修改,以适应应用程序需求、操作条件和/或过程变化的变化。NoRC系统的目标是避免任何集中控制,在运行时根据处理能力和位置将功能映射到块。平台的动态特性意味着,在外部主机对应用程序发出请求后,可以将任何空闲的tile配置为能够向附近的tile发出额外请求的主节点,或者配置为能够为请求提供服务的从节点。本文使用NoRC设计器来研究适合这种自适应平台的可能的任务映射策略,以及商用fpga的功率和部分重构开销。
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引用次数: 0
期刊
2012 International Conference on High Performance Computing & Simulation (HPCS)
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