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2016 1st Joint International Workshop on Parallel Data Storage and data Intensive Scalable Computing Systems (PDSW-DISCS)最新文献

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Klimatic: A Virtual Data Lake for Harvesting and Distribution of Geospatial Data Klimatic:一个用于地理空间数据收集和分布的虚拟数据湖
Tyler J. Skluzacek, K. Chard, Ian T Foster
Many interesting geospatial datasets are publicly accessible on web sites and other online repositories. However, the sheer number of datasets and locations, plus a lack of support for cross-repository search, makes it difficult for researchers to discover and integrate relevant data. We describe here early results from a system, Klimatic, that aims to overcome these barriers to discovery and use by automating the tasks of crawling, indexing, integrating, and distributing geospatial data. Klimatic implements a scalable crawling and processing architecture that uses an elastic container-based model to locate and retrieve relevant datasets and to extract metadata from headers and within files to build a global index of known geospatial data. In so doing, we create an expansive geospatial virtual data lake that records the location, formats, and other characteristics of large numbers of geospatial datasets while also caching popular data subsets for rapid access. A flexible query interface allows users to request data that satisfy supplied type, spatial, temporal, and provider specifications; in processing such queries, the system uses interpolation and aggregation to combine data of different types, data formats, resolutions, and bounds. Klimatic has so far incorporated more than 10,000 datasets from over 120 sources and has been demonstrated to scale well with data size and query complexity.
许多有趣的地理空间数据集都可以在网站和其他在线存储库上公开访问。然而,数据集和位置的绝对数量,加上缺乏对跨存储库搜索的支持,使得研究人员很难发现和整合相关数据。我们在这里描述了Klimatic系统的早期成果,该系统旨在通过自动化爬行、索引、集成和分发地理空间数据的任务来克服这些发现和使用的障碍。Klimatic实现了一个可扩展的爬行和处理架构,它使用一个弹性的基于容器的模型来定位和检索相关数据集,并从标头和文件中提取元数据,以构建已知地理空间数据的全局索引。通过这样做,我们创建了一个扩展的地理空间虚拟数据湖,它记录了大量地理空间数据集的位置、格式和其他特征,同时还缓存了流行的数据子集,以便快速访问。灵活的查询接口允许用户请求满足所提供的类型、空间、时间和提供者规范的数据;在处理此类查询时,系统使用插值和聚合来组合不同类型、数据格式、分辨率和边界的数据。到目前为止,Klimatic已经整合了来自120多个来源的10,000多个数据集,并且已经证明可以很好地扩展数据大小和查询复杂性。
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引用次数: 21
Parallel I/O Characterisation Based on Server-Side Performance Counters 基于服务器端性能计数器的并行I/O表征
S. E. Sayed, M. Bolten, D. Pleiter, W. Frings
Provisioning of high I/O capabilities for high-end HPC architectures is generally considered a challenge. A good understanding of the characteristics of the utilisation of modern I/O systems can help address the increasing performance gap between I/O and computation. In this paper we present results from an analysis of server-side performance counters that had been collected for multiple years on a parallel file system attached to a peta-scale Blue Gene/P system. We developed a set of general performance characterisation metrics, which we applied to this large dataset.
为高端HPC架构提供高I/O能力通常被认为是一个挑战。很好地理解现代I/O系统的使用特征可以帮助解决I/O和计算之间日益增大的性能差距。在本文中,我们展示了对服务器端性能计数器的分析结果,这些计数器是在附属于一个千兆级Blue Gene/P系统的并行文件系统上收集多年的。我们开发了一套通用的性能表征指标,并将其应用于这个大型数据集。
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引用次数: 1
A Bloom Filter Based Scalable Data Integrity Check Tool for Large-Scale Dataset 基于布隆过滤器的大规模数据集可扩展数据完整性检查工具
Sisi Xiong, Feiyi Wang, Qing Cao
Large scale HPC applications are becoming increasingly data intensive. At Oak Ridge Leadership Computing Facility (OLCF), we are observing the number of files curated under individual project are reaching as high as 200 millions and project data size is exceeding petabytes. These simulation datasets, once validated, often needs to be transferred to archival system for long term storage or shared with the rest of the research community. Ensuring the data integrity of the full dataset at this scale is paramount important but also a daunting task. This is especially true considering that most conventional tools are serial and file-based, unwieldy to use and/or can't scale to meet user's demand.To tackle this particular challenge, this paper presents the design, implementation and evaluation of a scalable parallel checksumming tool, fsum, which we developed at OLCF. It is built upon the principle of parallel tree walk and work-stealing pattern to maximize parallelism and is capable of generating a single, consistent signature for the entire dataset at extreme scale. We also applied a novel bloom-filter based technique in aggregating signatures to overcome the signature ordering requirement. Given the probabilistic nature of bloom filter, we provided a detailed error and trade-off analysis. Using multiple datasets from production environment, we demonstrated that our tool can efficiently handle both very large files as well as many small-file based datasets. Our preliminary test showed that on the same hardware, it outperforms conventional tool by as much as 4×. It also exhibited near-linear scaling properties when provisioned with more compute resources.
大规模HPC应用的数据密集程度越来越高。在橡树岭领导计算设施(Oak Ridge Leadership Computing Facility, OLCF),我们观察到单个项目管理的文件数量高达2亿,项目数据大小超过pb。这些模拟数据集一旦得到验证,通常需要转移到档案系统进行长期存储或与研究界的其他人员共享。在这种规模下确保完整数据集的数据完整性是至关重要的,但也是一项艰巨的任务。考虑到大多数传统工具都是基于串行和文件的,难以使用和/或无法扩展以满足用户需求,这一点尤其正确。为了解决这个特殊的挑战,本文介绍了我们在OLCF开发的可扩展并行校验和工具fsum的设计、实现和评估。它建立在并行树行走和工作窃取模式的原则之上,以最大限度地提高并行性,并且能够在极端规模下为整个数据集生成单个一致的签名。我们还采用了一种新的基于bloom-filter的签名聚合技术来克服签名排序的要求。鉴于布隆过滤器的概率性质,我们提供了详细的误差和权衡分析。通过使用生产环境中的多个数据集,我们证明了我们的工具既可以有效地处理非常大的文件,也可以有效地处理许多基于小文件的数据集。我们的初步测试表明,在相同的硬件上,它的性能比传统工具高出4倍。当提供更多的计算资源时,它还显示出近似线性的缩放特性。
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引用次数: 11
Towards Energy Efficient Data Management in HPC: The Open Ethernet Drive Approach 迈向高效节能的HPC数据管理:开放以太网驱动器方法
Anthony Kougkas, Anthony Fleck, Xian-He Sun
An Open Ethernet Drive (OED) is a new technology that encloses into a hard drive (HDD or SSD) a low-power processor, a fixed-size memory and an Ethernet card. In this study, we thoroughly evaluate the performance of such device and the energy requirements to operate it. The results show that first it is a viable solution to offload data-intensive computations on the OED while maintaining a reasonable performance, and second, the energy consumption savings from utilizing such technology are significant as it only consumes 10% of the power needed by a normal server node. We propose that by using OED devices as storage servers in HPC, we can run a reliable, scalable, cost and energy efficient storage solution.
开放式以太网驱动器(OED)是一种新技术,它将低功耗处理器、固定大小的内存和以太网卡封装在硬盘驱动器(HDD或SSD)中。在本研究中,我们全面评估了这种装置的性能和运行它的能量需求。结果表明,首先,它是一种可行的解决方案,可以在保持合理性能的同时卸载OED上的数据密集型计算;其次,利用这种技术节省的能耗非常显著,因为它只消耗普通服务器节点所需功率的10%。我们建议通过使用OED设备作为HPC中的存储服务器,我们可以运行一个可靠的、可扩展的、成本和节能的存储解决方案。
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引用次数: 5
Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science Using NERSC's Burst Buffer DataWarp-Speed的科学工作流程:使用NERSC的突发缓冲区加速数据密集型科学
A. Ovsyannikov, Melissa Romanus, B. V. Straalen, G. Weber, D. Trebotich
Emerging exascale systems have the ability to accelerate the time-to-discovery for scientific workflows. However, as these workflows become more complex, their generated data has grown at an unprecedented rate, making I/O constraints challenging. To address this problem advanced memory hierarchies, such as burst buffers, have been proposed as intermediate layers between the compute nodes and the parallel file system. In this paper, we utilize Cray DataWarp burst buffer coupled with in-transit processing mechanisms, to demonstrate the advantages of advanced memory hierarchies in preserving traditional coupled scientific workflows. We consider in-transit workflow which couples simulation of subsurface flows with on-the-fly flow visualization. With respect to the proposed workflow, we study the performance of the Cray DataWarp Burst Buffer and provide a comparison with the Lustre parallel file system.
新兴的百亿亿级系统能够加快科学工作流程的发现时间。然而,随着这些工作流变得越来越复杂,它们生成的数据以前所未有的速度增长,使得I/O限制变得具有挑战性。为了解决这个问题,已经提出了高级内存层次结构,如突发缓冲区,作为计算节点和并行文件系统之间的中间层。在本文中,我们利用Cray DataWarp突发缓冲区与传输中的处理机制相结合,来展示先进的内存层次结构在保留传统耦合科学工作流方面的优势。我们考虑将地下流动模拟与动态流动可视化相结合的运输工作流。针对所提出的工作流,我们研究了Cray DataWarp Burst Buffer的性能,并与Lustre并行文件系统进行了比较。
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引用次数: 26
Replicating HPC I/O Workloads with Proxy Applications 使用代理应用程序复制HPC I/O工作负载
J. Dickson, Steven A. Wright, S. Maheswaran, Andy Herdman, Mark C. Miller, S. Jarvis
Large scale simulation performance is dependent on a number of components, however the task of investigation and optimization has long favored computational and communication elements above I/O. Manually extracting the pattern of I/O behavior from a parent application is a useful way of working to address performance issues on a per-application basis, but developing workflows with some degree of automation and flexibility provides a more powerful approach to tackling current and future I/O challenges. In this paper we describe a workload replication workflow that extracts the I/O pattern of an application and recreates its behavior with a flexible proxy application. We demonstrate how simple lightweight characterization can be translated to provide an effective representation of a physics application, and show how a proxy replication can be used as a tool for investigating I/O library paradigms.
大规模模拟性能依赖于许多组件,然而研究和优化任务长期以来更倾向于I/O之上的计算和通信元素。手动从父应用程序中提取I/O行为模式是解决基于每个应用程序的性能问题的一种有用方法,但是开发具有一定程度自动化和灵活性的工作流提供了一种更强大的方法来解决当前和未来的I/O挑战。在本文中,我们描述了一个工作负载复制工作流,该工作流提取应用程序的I/O模式,并使用灵活的代理应用程序重新创建其行为。我们将演示如何将简单的轻量级特性转换为提供物理应用程序的有效表示,并展示如何将代理复制用作研究I/O库范例的工具。
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引用次数: 14
FatMan vs. LittleBoy: Scaling Up Linear Algebraic Operations in Scale-Out Data Platforms 胖子vs小男孩:扩展数据平台中线性代数运算的扩展
Luna Xu, Seung-Hwan Lim, A. Butt, S. Sukumar, R. Kannan
Linear algebraic operations such as matrix manipulations form the kernel of many machine learning and other crucial algorithms. Scaling up as well as scaling out such algorithms are highly desirable to enable efficient processing over millions of data points. To this end, we present a matrix manipulation approach to effectively scale-up each node in a scale-out data parallel platform such as Apache Spark. Specifically, we enable hardware acceleration for matrix multiplications in a distributed Spark setup without user intervention. Our approach supports both dense and sparse distributed matrices, and provides flexible control of acceleration by matrix density. We demonstrate the benefit of our approach for generalized matrix multiplication operations over large matrices with up to four billion elements. To connect the effectiveness of our approach with machine learning applications, we performed Gramian matrix computation via generalized matrix multiplications. Our experiments show that our approach achieves more than 2× performance speed-up, and up to 96.1% computation improvement, compared to a state of the art Spark MLlib for dense matrices.
线性代数运算,如矩阵运算,构成了许多机器学习和其他关键算法的核心。要实现对数百万个数据点的高效处理,这类算法的向上和向外扩展都是非常必要的。为此,我们提出了一种矩阵操作方法,可以在横向扩展数据并行平台(如Apache Spark)中有效地扩展每个节点。具体来说,我们在没有用户干预的情况下为分布式Spark设置中的矩阵乘法启用硬件加速。我们的方法支持密集和稀疏分布矩阵,并通过矩阵密度提供灵活的加速度控制。我们证明了我们的方法对具有多达40亿个元素的大型矩阵的广义矩阵乘法运算的好处。为了将我们的方法与机器学习应用程序的有效性联系起来,我们通过广义矩阵乘法进行了Gramian矩阵计算。我们的实验表明,与目前最先进的Spark MLlib相比,我们的方法实现了2倍以上的性能加速,以及高达96.1%的计算改进。
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引用次数: 3
Can Non-volatile Memory Benefit MapReduce Applications on HPC Clusters? 非易失性内存是否有利于高性能计算集群上的MapReduce应用?
Md. Wasi-ur-Rahman, Nusrat S. Islam, Xiaoyi Lu, D. Panda
Modern High-Performance Computing (HPC) clusters are equipped with advanced technological resources that need to be properly utilized to achieve supreme performance for end applications. One such example, Non-Volatile Memory (NVM), provides the opportunity for fast scalable performance through its DRAM-like performance characteristics. On the other hand, distributed processing engines, such as MapReduce, are continuously being enhanced with features enabling high-performance technologies. In this paper, we present a novel MapReduce framework with NVRAM-assisted map output spill approach. We have designed our framework on top of the existing RDMA-enhanced Hadoop MapReduce to ensure both map and reduce phase performance enhancements to be present for end applications. Our proposed approach significantly enhances map phase performance proven by a wide variety of MapReduce benchmarks and workloads from Intel HiBench [9] and PUMA [18] suites. Our performance evaluation illustrates that NVRAM-based spill approach can improve map execution performance by 2.73x which contributes to the overall execution improvement of 55% for Sort. Our design also guarantees significant performance benefits for other workloads: 54% for TeraSort, 21% for PageRank, 58% for SelfJoin, etc. To the best of our knowledge, this is the first approach towards leveraging NVRAM in MapReduce execution frameworks for applications on HPC clusters.
现代高性能计算(HPC)集群拥有先进的技术资源,需要合理利用这些资源,才能为终端应用提供最高的性能。例如,非易失性内存(NVM)通过其类似dram的性能特性提供了快速可扩展性能的机会。另一方面,分布式处理引擎,如MapReduce,正在不断地增强支持高性能技术的特性。在本文中,我们提出了一种新的MapReduce框架,该框架采用nvram辅助映射输出溢出方法。我们在现有的rdma增强的Hadoop MapReduce之上设计了我们的框架,以确保map和reduce阶段的性能增强在最终应用程序中呈现。我们提出的方法显著提高了地图阶段的性能,并得到了来自英特尔HiBench[9]和PUMA[18]套件的各种MapReduce基准测试和工作负载的证明。我们的性能评估表明,基于nvram的溢出方法可以将映射执行性能提高2.73倍,这使得Sort的总体执行性能提高了55%。我们的设计还保证了其他工作负载的显著性能优势:TeraSort为54%,PageRank为21%,SelfJoin为58%等。据我们所知,这是在高性能计算集群上的应用程序的MapReduce执行框架中利用NVRAM的第一种方法。
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引用次数: 5
A Generic Framework for Testing Parallel File Systems 测试并行文件系统的通用框架
Jinrui Cao, Simeng Wang, Dong Dai, Mai Zheng, Yong Chen
Large-scale parallel file systems are of prime importance today. However, despite of the importance, their failure-recovery capability is much less studied compared with local storage systems. Recent studies on local storage systems have exposed various vulnerabilities that could lead to data loss under failure events, which raise the concern for parallel file systems built on top of them.This paper proposes a generic framework for testing the failure handling of large-scale parallel file systems. The framework captures all disk I/O commands on all storage nodes of the target system to emulate realistic failure states, and checks if the target system can recover to a consistent state without incurring data loss. We have built a prototype for the Lustre file system. Our preliminary results show that the framework is able to uncover the internal I/O behavior of Lustre under different workloads and failure conditions, which provides a solid foundation for further analyzing the failure recovery of parallel file systems.
大规模并行文件系统在今天是非常重要的。然而,尽管它们很重要,但与本地存储系统相比,它们的故障恢复能力研究得很少。最近对本地存储系统的研究暴露了在故障事件下可能导致数据丢失的各种漏洞,这引起了人们对构建在其上的并行文件系统的关注。本文提出了一个测试大规模并行文件系统故障处理的通用框架。该框架捕获目标系统所有存储节点上的所有磁盘I/O命令,以模拟实际的故障状态,并检查目标系统是否可以在不导致数据丢失的情况下恢复到一致状态。我们已经为Lustre文件系统构建了一个原型。初步结果表明,该框架能够揭示Lustre在不同工作负载和故障条件下的内部I/O行为,为进一步分析并行文件系统的故障恢复提供了坚实的基础。
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引用次数: 13
期刊
2016 1st Joint International Workshop on Parallel Data Storage and data Intensive Scalable Computing Systems (PDSW-DISCS)
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