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2012 International Conference for High Performance Computing, Networking, Storage and Analysis最新文献

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4.45 Pflops astrophysical N-body simulation on K computer -- The gravitational trillion-body problem 4.45 Pflops天体物理n体K计算机模拟——引力万亿体问题
T. Ishiyama, Keigo Nitadori, J. Makino
As an entry for the 2012 Gordon-Bell performance prize, we report performance results of astrophysical N-body simulations of one trillion particles performed on the full system of K computer. This is the first gravitational trillion-body simulation in the world. We describe the scientific motivation, the numerical algorithm, the parallelization strategy, and the performance analysis. Unlike many previous Gordon-Bell prize winners that used the tree algorithm for astrophysical N-body simulations, we used the hybrid TreePM method, for similar level of accuracy in which the short-range force is calculated by the tree algorithm, and the long-range force is solved by the particle-mesh algorithm. We developed a highly-tuned gravity kernel for short-range forces, and a novel communication algorithm for long-range forces. The average performance on 24576 and 82944 nodes of K computer are 1.53 and 4.45 Pflops, which correspond to 49% and 42% of the peak speed.
作为2012年Gordon-Bell性能奖的参赛作品,我们报告了在K计算机全系统上执行的1万亿粒子的天体物理n体模拟的性能结果。这是世界上第一个引力万亿体模拟。我们描述了科学动机、数值算法、并行化策略和性能分析。与之前许多使用树算法进行天体物理n体模拟的戈登-贝尔奖获奖者不同,我们使用混合TreePM方法,具有相似的精度水平,其中短程力由树算法计算,而远程力由粒子网格算法求解。我们为短程力开发了一个高度调谐的重力核,并为远程力开发了一个新的通信算法。K计算机24576和82944节点的平均性能分别为1.53和4.45 Pflops,分别相当于峰值速度的49%和42%。
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引用次数: 81
Accelerating MapReduce on a coupled CPU-GPU architecture 在CPU-GPU耦合架构下加速MapReduce
Linchuan Chen, Xin Huo, G. Agrawal
The work presented here is driven by two observations. First, heterogeneous architectures that integrate a CPU and a GPU on the same chip are emerging, and hold much promise for supporting power-efficient and scalable high performance computing. Second, MapReduce has emerged as a suitable framework for simplified parallel application development for many classes of applications, including data mining and machine learning applications that benefit from accelerators. This paper focuses on the challenge of scaling a MapReduce application using the CPU and GPU together in an integrated architecture. We develop different methods for dividing the work, which are the map-dividing scheme, where map tasks are divided between both devices, and the pipelining scheme, which pipelines the map and the reduce stages on different devices. We develop dynamic work distribution schemes for both the approaches. To achieve high load balance while keeping scheduling costs low, we use a runtime tuning method to adjust task block sizes for the map-dividing scheme. Our implementation of MapReduce is based on a continuous reduction method, which avoids the memory overheads of storing key-value pairs. We have evaluated the different design decisions using 5 popular MapReduce applications. For 4 of the applications, our system achieves 1.21 to 2.1 speedup over the better of the CPU-only and GPU-only versions. The speedups over a single CPU core execution range from 3.25 to 28.68. The runtime tuning method we have developed achieves very low load imbalance, while keeping scheduling overheads low. Though our current work is specific to MapReduce, many underlying ideas are also applicable towards intra-node acceleration of other applications on integrated CPU-GPU nodes.
这里介绍的工作是由两个观察结果驱动的。首先,在同一芯片上集成CPU和GPU的异构架构正在出现,并有望支持节能和可扩展的高性能计算。其次,MapReduce已经成为许多应用程序的简化并行应用程序开发的合适框架,包括受益于加速器的数据挖掘和机器学习应用程序。本文主要关注在集成架构中使用CPU和GPU一起扩展MapReduce应用程序的挑战。我们开发了不同的方法来划分工作,即映射划分方案,其中映射任务在两个设备之间划分,以及管道方案,该方案在不同的设备上管道化映射和减少阶段。我们为这两种方法开发了动态工作分配方案。为了在保持低调度成本的同时实现高负载平衡,我们使用运行时调优方法来调整映射划分方案的任务块大小。我们的MapReduce实现基于连续约简方法,这避免了存储键值对的内存开销。我们使用5个流行的MapReduce应用程序评估了不同的设计决策。对于其中4个应用程序,我们的系统比仅cpu和仅gpu的版本实现了1.21到2.1的加速。单个CPU核心执行的加速范围从3.25到28.68。我们开发的运行时调优方法实现了非常低的负载不平衡,同时保持了较低的调度开销。虽然我们目前的工作是针对MapReduce的,但许多潜在的想法也适用于集成CPU-GPU节点上的其他应用程序的节点内加速。
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引用次数: 106
Measuring interference between live datacenter applications 测量实时数据中心应用程序之间的干扰
Melanie Kambadur, Tipp Moseley, R. Hank, Martha A. Kim
Application interference is prevalent in datacenters due to contention over shared hardware resources. Unfortunately, understanding interference in live datacenters is more difficult than in controlled environments or on simpler architectures. Most approaches to mitigating interference rely on data that cannot be collected efficiently in a production environment. This work exposes eight specific complexities of live datacenters that constrain measurement of interference. It then introduces new, generic measurement techniques for analyzing interference in the face of these challenges and restrictions. We use the measurement techniques to conduct the first large-scale study of application interference in live production datacenter workloads. Data is measured across 1000 12-core Google servers observed to be running 1102 unique applications. Finally, our work identifies several opportunities to improve performance that use only the available data; these opportunities are applicable to any datacenter.
由于对共享硬件资源的争夺,应用程序干扰在数据中心非常普遍。不幸的是,与受控环境或更简单的体系结构相比,理解实时数据中心中的干扰要困难得多。大多数减少干扰的方法依赖于无法在生产环境中有效收集的数据。这项工作揭示了限制干扰测量的实时数据中心的八个特定复杂性。然后介绍了新的、通用的测量技术来分析面对这些挑战和限制的干扰。我们使用测量技术对实时生产数据中心工作负载中的应用程序干扰进行了首次大规模研究。数据是在1000个12核谷歌服务器上测量的,这些服务器运行着1102个不同的应用程序。最后,我们的工作确定了仅使用可用数据来提高性能的几个机会;这些机会适用于任何数据中心。
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引用次数: 107
A multithreaded algorithm for network alignment via approximate matching 基于近似匹配的多线程网络对齐算法
Arif M. Khan, D. Gleich, A. Pothen, M. Halappanavar
Network alignment is an optimization problem to find the best one-to-one map between the vertices of a pair of graphs that overlaps as many edges as possible. It is a relaxation of the graph isomorphism problem and is closely related to the subgraph isomorphism problem. The best current approaches are entirely heuristic and iterative in nature. They generate real-valued heuristic weights that must be rounded to find integer solutions. This rounding requires solving a bipartite maximum weight matching problem at each iteration in order to avoid missing high quality solutions. We investigate substituting a parallel, half-approximation for maximum weight matching instead of an exact computation. Our experiments show that the resulting difference in solution quality is negligible. We demonstrate almost a 20-fold speedup using 40 threads on an 8 processor Intel Xeon E7-8870 system and now solve real-world problems in 36 seconds instead of 10 minutes.
网络对齐是一个优化问题,目的是在一对图的顶点之间找到最佳的一对一映射,并尽可能多地重叠边。它是图同构问题的一种松弛,与子图同构问题密切相关。目前最好的方法本质上完全是启发式和迭代式的。它们生成实值启发式权重,必须四舍五入才能找到整数解。这种舍入需要在每次迭代中解决一个二部最大权匹配问题,以避免丢失高质量的解。我们研究用平行的半近似代替最大权重匹配,而不是精确的计算。我们的实验表明,由此产生的溶液质量差异可以忽略不计。我们演示了在8处理器的Intel Xeon E7-8870系统上使用40个线程的速度提高了近20倍,现在在36秒内解决实际问题,而不是10分钟。
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引用次数: 30
Usage behavior of a large-scale scientific archive 大型科学档案的使用行为
I. Adams, B. A. Madden, J. Frank, M. Storer, E. L. Miller, Gene Harano
Archival storage systems for scientific data have been growing in both size and relevance over the past two decades, yet researchers and system designers alike must rely on limited and obsolete knowledge to guide archival management and design. To address this issue, we analyzed three years of filelevel activities from the NCAR mass storage system, providing valuable insight into a large-scale scientific archive with over 1600 users, tens of millions of files, and petabytes of data. Our examination of system usage showed that, while a subset of users were responsible for most of the activity, this activity was widely distributed at the file level. We also show that the physical grouping of files and directories on media can improve archival storage system performance. Based on our observations, we provide suggestions and guidance for both future scientific archival system designs as well as improved tracing of archival activity.
在过去的二十年里,科学数据的档案存储系统在规模和相关性上都在增长,然而研究人员和系统设计者都必须依赖有限和过时的知识来指导档案管理和设计。为了解决这个问题,我们分析了NCAR海量存储系统三年来的文件级活动,对一个拥有1600多名用户、数千万个文件和pb级数据的大型科学档案提供了有价值的见解。我们对系统使用情况的检查表明,虽然一部分用户负责大多数活动,但这些活动在文件级别上广泛分布。我们还表明,在介质上对文件和目录进行物理分组可以提高归档存储系统的性能。在此基础上,为今后科学的档案制度设计和完善档案活动追踪提供建议和指导。
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引用次数: 15
Patus for convenient high-performance stencils: Evaluation in earthquake simulations 方便的高性能模板研究进展:地震模拟中的评估
M. Christen, O. Schenk, Yifeng Cui
PATUS is a code generation and auto-tuning framework for stencil computations targeting modern multi and many-core processors. The goals of the framework are productivity and portability for achieving high performance on the target platform. Its stencil specification language allows the programmer to express the computation in a concise way independently of hardware architecture-specific details. Thus, it increases the programmer productivity by removing the need for manual low-level tuning. We illustrate the impact of the stencil code generation in seismic applications, for which both weak and strong scaling are important. We evaluate the performance by focusing on a scalable discretization of the wave equation and testing complex simulation types of the AWP-ODC code to aim at excellent parallel efficiency, preparing for petascale 3-D earthquake calculations.
PATUS是一个针对现代多核和多核处理器的模板计算的代码生成和自动调优框架。该框架的目标是在目标平台上实现高性能的生产力和可移植性。它的模板规范语言允许程序员以一种简洁的方式表达计算,而不受硬件体系结构特定细节的影响。因此,它通过消除手动低级调优的需要来提高程序员的工作效率。我们说明了模板代码生成在地震应用中的影响,弱尺度和强尺度都很重要。我们通过关注波动方程的可扩展离散化和测试AWP-ODC代码的复杂模拟类型来评估性能,以获得出色的并行效率,为千万亿次三维地震计算做准备。
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引用次数: 37
Hierarchical task mapping of cell-based AMR cosmology simulations 基于细胞的AMR宇宙学模拟的分层任务映射
Jingjin Wu, Z. Lan, Xuanxing Xiong, N. Gnedin, A. Kravtsov
Cosmology simulations are highly communication-intensive, thus it is critical to exploit topology-aware task mapping techniques for performance optimization. To exploit the architectural properties of multiprocessor clusters (the performance gap between inter-node and intra-node communication as well as the gap between inter-socket and intra-socket communication), we design and develop a hierarchical task mapping scheme for cell-based AMR (Adaptive Mesh Refinement) cosmology simulations, in particular, the ART application. Our scheme consists of two parts: (1) an inter-node mapping to map application processes onto nodes with the objective of minimizing network traffic among nodes and (2) an intra-node mapping within each node to minimize the maximum size of messages transmitted between CPU sockets. Experiments on production supercomputers with 3D torus and fat-tree topologies show that our scheme can significantly reduce application communication cost by up to 50%. More importantly, our scheme is generic and can be extended to many other applications.
宇宙学模拟是高度通信密集型的,因此利用拓扑感知任务映射技术进行性能优化是至关重要的。为了利用多处理器集群的架构特性(节点间和节点内通信之间的性能差距以及套接字间和套接字内通信之间的性能差距),我们设计并开发了一种分层任务映射方案,用于基于单元的AMR(自适应网格细化)宇宙学模拟,特别是ART应用。我们的方案由两部分组成:(1)节点间映射,将应用程序进程映射到节点上,目标是最小化节点之间的网络流量;(2)每个节点内的节点内映射,以最小化CPU套接字之间传输的消息的最大大小。在具有三维环面和胖树拓扑结构的生产超级计算机上的实验表明,该方案可以显著降低应用程序通信成本,最高可降低50%。更重要的是,我们的方案是通用的,可以扩展到许多其他应用程序。
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引用次数: 13
A scalable, numerically stable, high-performance tridiagonal solver using GPUs 一个可扩展的,数字稳定的,高性能的三对角线求解器使用gpu
Li-Wen Chang, John A. Stratton, Heehoon Kim, Wen-mei W. Hwu
In this paper, we present a scalable, numerically stable, high-performance tridiagonal solver. The solver is based on the SPIKE algorithm for partitioning a large matrix into small independent matrices, which can be solved in parallel. For each small matrix, our solver applies a general 1-by-1 or 2-by-2 diagonal pivoting algorithm, which is also known to be numerically stable. Our paper makes two major contributions. First, our solver is the first numerically stable tridiagonal solver for GPUs. Our solver provides comparable quality of stable solutions to Intel MKL and Matlab, at speed comparable to the GPU tridiagonal solvers in existing packages like CUSPARSE. It is also scalable to multiple GPUs and CPUs. Second, we present and analyze two key optimization strategies for our solver: a high-throughput data layout transformation for memory efficiency, and a dynamic tiling approach for reducing the memory access footprint caused by branch divergence.
在本文中,我们提出了一个可扩展的,数值稳定的,高性能的三对角求解器。该求解器基于SPIKE算法,将大矩阵划分为独立的小矩阵,可以并行求解。对于每个小矩阵,我们的求解器应用一般的1 × 1或2 × 2对角旋转算法,这也被认为是数值稳定的。我们的论文有两个主要贡献。首先,我们的求解器是gpu的第一个数值稳定的三对角求解器。我们的求解器为英特尔MKL和Matlab提供了相当质量的稳定解决方案,其速度可与现有软件包(如CUSPARSE)中的GPU三对角线求解器相媲美。它还可以扩展到多个gpu和cpu。其次,我们提出并分析了求解器的两个关键优化策略:用于提高内存效率的高吞吐量数据布局转换和用于减少分支发散引起的内存访问占用的动态平铺方法。
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引用次数: 63
Direction-optimizing Breadth-First Search 方向优化宽度优先搜索
S. Beamer, K. Asanović, D. Patterson
Breadth-First Search is an important kernel used by many graph-processing applications. In many of these emerging applications of BFS, such as analyzing social networks, the input graphs are low-diameter and scale-free. We propose a hybrid approach that is advantageous for low-diameter graphs, which combines a conventional top-down algorithm along with a novel bottom-up algorithm. The bottom-up algorithm can dramatically reduce the number of edges examined, which in turn accelerates the search as a whole. On a multi-socket server, our hybrid approach demonstrates speedups of 3.3 -- 7.8 on a range of standard synthetic graphs and speedups of 2.4 -- 4.6 on graphs from real social networks when compared to a strong baseline. We also typically double the performance of prior leading shared memory (multicore and GPU) implementations.
宽度优先搜索是许多图形处理应用程序使用的重要内核。在BFS的许多新兴应用中,例如分析社交网络,输入图是低直径和无标度的。我们提出了一种有利于低直径图的混合方法,它结合了传统的自顶向下算法和一种新颖的自底向上算法。自底向上的算法可以显著减少检查的边的数量,这反过来又加快了整体的搜索速度。在多套接字服务器上,与强基线相比,我们的混合方法在一系列标准合成图上的加速为3.3 - 7.8,在真实社交网络图上的加速为2.4 - 4.6。我们还通常将先前领先的共享内存(多核和GPU)实现的性能提高一倍。
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引用次数: 444
A practical method for estimating performance degradation on multicore processors, and its application to HPC workloads 一种估计多核处理器性能退化的实用方法及其在高性能计算工作负载中的应用
Tyler Dwyer, Alexandra Fedorova, S. Blagodurov, Mark Roth, Fabien Gaud, J. Pei
When multiple threads or processes run on a multi-core CPU they compete for shared resources, such as caches and memory controllers, and can suffer performance degradation as high as 200%. We design and evaluate a new machine learning model that estimates this degradation online, on previously unseen workloads, and without perturbing the execution. Our motivation is to help data center and HPC cluster operators effectively use workload consolidation. Data center consolidation is about placing many applications on the same server to maximize hardware utilization. In HPC clusters, processes of the same distributed applications run on the same machine. Consolidation improves hardware utilization, but may sacrifice performance as processes compete for resources. Our model helps determine when consolidation is overly harmful to performance. Our work is the first to apply machine learning to this problem domain, and we report on our experience reaping the advantages of machine learning while navigating around its limitations. We demonstrate how the model can be used to improve performance fidelity and save energy for HPC workloads.
当多个线程或进程在多核CPU上运行时,它们会竞争共享资源,例如缓存和内存控制器,并且可能遭受高达200%的性能下降。我们设计并评估了一种新的机器学习模型,该模型可以在以前未见过的工作负载上在线估计这种退化,并且不会干扰执行。我们的动机是帮助数据中心和HPC集群运营商有效地使用工作负载整合。数据中心整合是指将许多应用程序放在同一台服务器上,以最大限度地提高硬件利用率。在HPC集群中,相同分布式应用程序的进程运行在同一台机器上。整合提高了硬件利用率,但可能会牺牲性能,因为进程会争夺资源。我们的模型有助于确定合并何时对性能造成过度损害。我们的工作是第一个将机器学习应用于这个问题领域,我们报告了我们的经验,收获了机器学习的优势,同时克服了机器学习的局限性。我们演示了如何使用该模型来提高高性能计算工作负载的性能保真度并节省能源。
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引用次数: 73
期刊
2012 International Conference for High Performance Computing, Networking, Storage and Analysis
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