发布求助
文献互助 智能选刊 最新文献

Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis最新文献

筛选
英文 中文
Diagnosing performance bottlenecks in emerging petascale applications 诊断新兴千兆级应用程序中的性能瓶颈
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654111
Nathan R. Tallent, J. Mellor-Crummey, L. Adhianto, M. Fagan, Mark W. Krentel
{"title":"Diagnosing performance bottlenecks in emerging petascale applications","authors":"Nathan R. Tallent, J. Mellor-Crummey, L. Adhianto, M. Fagan, Mark W. Krentel","doi":"10.1145/1654059.1654111","DOIUrl":"https://doi.org/10.1145/1654059.1654111","url":null,"abstract":"Cutting-edge science and engineering applications require petascale computing. It is, however, a significant challenge to use petascale computing platforms effectively. Consequently, there is a critical need for performance tools that enable scientists to understand impediments to performance on emerging petascale systems. In this paper, we describe HPCToolkit-a suite of multi-platform tools that supports sampling-based analysis of application performance on emerging petascale platforms. HPCToolkit uses sampling to pinpoint and quantify both scaling and node performance bottlenecks. We study several emerging petascale applications on the Cray XT and IBM BlueGene/P platforms and use HPCToolkit to identify specific source lines - in their full calling context - associated with performance bottlenecks in these codes. Such information is exactly what application developers need to know to improve their applications to take full advantage of the power of petascale systems.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124846249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 38
Efficient band approximation of Gram matrices for large scale kernel methods on GPUs 基于gpu的大规模核方法中Gram矩阵的有效带逼近
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654091
Mohamed E. Hussein, W. Abd-Almageed
{"title":"Efficient band approximation of Gram matrices for large scale kernel methods on GPUs","authors":"Mohamed E. Hussein, W. Abd-Almageed","doi":"10.1145/1654059.1654091","DOIUrl":"https://doi.org/10.1145/1654059.1654091","url":null,"abstract":"Kernel-based methods require O(N2) time and space complexities to compute and store non-sparse Gram matrices, which is prohibitively expensive for large scale problems. We introduce a novel method to approximate a Gram matrix with a band matrix. Our method relies on the locality preserving properties of space filling curves, and the special structure of Gram matrices. Our approach has several important merits. First, it computes only those elements of the Gram matrix that lie within the projected band. Second, it is simple to parallelize. Third, using the special band matrix structure makes it space efficient and GPU-friendly. We developed GPU implementations for the Affinity Propagation (AP) clustering algorithm using both our method and the COO sparse representation. Our band approximation is about 5 times more space efficient and faster to construct than COO. AP gains up to 6x speedup using our method without any degradation in its clustering performance.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128882969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
The cat is out of the bag: cortical simulations with 109 neurons, 1013 synapses 谜底揭晓了:大脑皮层模拟了109个神经元，1013个突触
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654124
R. Ananthanarayanan, Steven K. Esser, H. Simon, D. Modha
{"title":"The cat is out of the bag: cortical simulations with 109 neurons, 1013 synapses","authors":"R. Ananthanarayanan, Steven K. Esser, H. Simon, D. Modha","doi":"10.1145/1654059.1654124","DOIUrl":"https://doi.org/10.1145/1654059.1654124","url":null,"abstract":"In the quest for cognitive computing, we have built a massively parallel cortical simulator, C2, that incorporates a number of innovations in computation, memory, and communication. Using C2 on LLNL's Dawn Blue Gene/P supercomputer with 147, 456 CPUs and 144 TB of main memory, we report two cortical simulations -- at unprecedented scale -- that effectively saturate the entire memory capacity and refresh it at least every simulated second. The first simulation consists of 1.6 billion neurons and 8.87 trillion synapses with experimentally-measured gray matter thalamocortical connectivity. The second simulation has 900 million neurons and 9 trillion synapses with probabilistic connectivity. We demonstrate nearly perfect weak scaling and attractive strong scaling. The simulations, which incorporate phenomenological spiking neurons, individual learning synapses, axonal delays, and dynamic synaptic channels, exceed the scale of the cat cortex, marking the dawn of a new era in the scale of cortical simulations.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"80 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116645582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 292
Indexing genomic sequences on the IBM Blue Gene 索引基因组序列上的IBM蓝色基因
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654122
A. Ghoting, K. Makarychev
{"title":"Indexing genomic sequences on the IBM Blue Gene","authors":"A. Ghoting, K. Makarychev","doi":"10.1145/1654059.1654122","DOIUrl":"https://doi.org/10.1145/1654059.1654122","url":null,"abstract":"With advances in sequencing technology and through aggressive sequencing efforts, DNA sequence data sets have been growing at a rapid pace. To gain from these advances, it is important to provide life science researchers with the ability to process and query large sequence data sets. For the past three decades, the suffix tree has served as a fundamental data structure in processing sequential data sets. However, tree construction times on large data sets have been excessive. While parallel suffix tree construction is an obvious solution to reduce execution times, poor locality of reference has limited parallel performance. In this paper, we show that through careful parallel algorithm design, this limitation can be removed, allowing tree construction to scale to massively parallel systems like the IBM Blue Gene. We demonstrate that the entire Human genome can be indexed on 1024 processors in under 15 minutes.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"48 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125669667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 23
Optimal real number codes for fault tolerant matrix operations 最优实数代码的容错矩阵操作
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654089
Zizhong Chen
{"title":"Optimal real number codes for fault tolerant matrix operations","authors":"Zizhong Chen","doi":"10.1145/1654059.1654089","DOIUrl":"https://doi.org/10.1145/1654059.1654089","url":null,"abstract":"It has been demonstrated recently that single fail-stop process failure in ScaLAPACK matrix multiplication can be tolerated without checkpointing. Multiple simultaneous processor failures can be tolerated without checkpointing by encoding matrices using a real-number erasure correcting code. However, the floating-point representation of a real number in today's high performance computer architecture introduces round off errors which can be enlarged and cause the loss of precision of possibly all effective digits during recovery when the number of processors in the system is large. In this paper, we present a class of Reed-Solomon style real-number erasure correcting codes which have optimal numerical stability during recovery. We analytically construct the numerically best erasure correcting codes for 2 erasures and develop an approximation method to computationally construct numerically good codes for 3 or more erasures. Experimental results demonstrate that the proposed codes are numerically much more stable than existing codes.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122700098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 33
FALCON: a system for reliable checkpoint recovery in shared grid environments FALCON:在共享网格环境中用于可靠检查点恢复的系统
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654110
T. Islam, S. Bagchi, R. Eigenmann
{"title":"FALCON: a system for reliable checkpoint recovery in shared grid environments","authors":"T. Islam, S. Bagchi, R. Eigenmann","doi":"10.1145/1654059.1654110","DOIUrl":"https://doi.org/10.1145/1654059.1654110","url":null,"abstract":"In Fine-Grained Cycle Sharing (FGCS) systems, machine owners voluntarily share their unused CPU cycles with guest jobs, as long as their performance degradation is tolerable. However, unpredictable evictions of guest jobs lead to fluctuating completion times. Checkpoint-recovery is an attractive mechanism for recovering from such ”failures”. Today's FGCS systems often use expensive, high-performance dedicated checkpoint servers. However, in geographically distributed clusters, this may incur high checkpoint transfer latencies. In this paper we present a system called FALCON that uses available disk resources of the FGCS machines as shared checkpoint repositories. However, an unavailable storage host may lead to loss of checkpoint data. Therefore, we model failures of storage hosts and develop a prediction algorithm for choosing reliable checkpoint repositories. We experiment with FALCON in the university-wide Condor testbed at Purdue and show improved and consistent performance for guest jobs in the presence of irregular resource availability.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133902478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Early performance evaluation of a "Nehalem" cluster using scientific and engineering applications 使用科学和工程应用程序对“Nehalem”集群进行早期性能评估
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654084
S. Saini, Andrey Naraikin, R. Biswas, D. Barkai, T. Sandstrom
{"title":"Early performance evaluation of a \"Nehalem\" cluster using scientific and engineering applications","authors":"S. Saini, Andrey Naraikin, R. Biswas, D. Barkai, T. Sandstrom","doi":"10.1145/1654059.1654084","DOIUrl":"https://doi.org/10.1145/1654059.1654084","url":null,"abstract":"In this paper, we present an early performance evaluation of a 624-core cluster based on the Intel<sup>®</sup> Xeon<sup>®</sup> Processor 5560 (code named \"Nehalem-EP\", and referred to as Xeon 5560 in this paper)---the third-generation quad-core architecture from Intel. This is the first processor from Intel with a non-uniform memory access (NUMA) architecture managed by on-chip integrated memory controller. It employs a point-to-point interconnect called the Intel<sup>®</sup> QuickPath Interconnect (QPI) between processors and to the input/output (I/O) hub. It also introduces to a quad-core architecture both Intel's hyper-threading technology (or simultaneous multi-threading, \"SMT\") and Intel<sup>®</sup> Turbo Boost Technology (\"Turbo mode\") that automatically allow processor cores to run faster than the base operating frequency if the processor is operating below rated power, temperature, and current specification limits. It can be engaged with any number of cores or logical processors enabled and active. We critically evaluate these features using the High Performance Computing Challenge (HPCC) benchmarks, NAS Parallel Benchmarks (NPB), and four full-scale scientific applications. We compare and contrast the results of a cluster based on the Xeon 5560 with an SGI<sup>®</sup> Altix<sup>®</sup> ICE 8200EX cluster of quad-core Intel<sup>®</sup> Xeon<sup>®</sup> 5472 Processor (\"Xeon 5472\" from here on) and another cluster of Intel<sup>®</sup> Xeon<sup>®</sup> 5462 Processor (\"Xeon 5462\"; the Xeon 5400 Series Processors are previous generation quad-core Intel processors and were code named Harpertown).","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128972122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 20
A scalable method for ab initio computation of free energies in nanoscale systems 纳米系统中自由能从头计算的可扩展方法
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654125
M. Eisenbach, C.-G. Zhou, D. Nicholson, G. Brown, J. Larkin, T. Schulthess
{"title":"A scalable method for ab initio computation of free energies in nanoscale systems","authors":"M. Eisenbach, C.-G. Zhou, D. Nicholson, G. Brown, J. Larkin, T. Schulthess","doi":"10.1145/1654059.1654125","DOIUrl":"https://doi.org/10.1145/1654059.1654125","url":null,"abstract":"Calculating the thermodynamics of nanoscale systems presents challenges in the simultaneous treatment of the electronic structure, which determines the interactions between atoms, and the statistical fluctuations that become ever more important at shorter length scales. Here we present a highly scalable method that combines ab initio electronic structure techniques, we use the Locally Self-Consitent Multiple Scattering (LSMS) technique, with the Wang-Landau (WL) algorithm to compute free energies and other thermodynamic properties of nanoscale systems. The combined WL-LSMS code is targeted to the study of nanomagnetic systems that have anywhere from about one hundred to a few thousand atoms. The code scales very well on the Cray XT5 system at ORNL, sustaining 1.03 Petaflop/s in double precision on 147,464 cores.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117199639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 22
Automating the generation of composed linear algebra kernels 自动生成组合线性代数核
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654119
Geoffrey Belter, E. Jessup, I. Karlin, Jeremy G. Siek
{"title":"Automating the generation of composed linear algebra kernels","authors":"Geoffrey Belter, E. Jessup, I. Karlin, Jeremy G. Siek","doi":"10.1145/1654059.1654119","DOIUrl":"https://doi.org/10.1145/1654059.1654119","url":null,"abstract":"Memory bandwidth limits the performance of important kernels in many scientific applications. Such applications often use sequences of Basic Linear Algebra Subprograms (BLAS), and highly efficient implementations of those routines enable scientists to achieve high performance at little cost. However, tuning the BLAS in isolation misses opportunities for memory optimization that result from composing multiple subprograms. Because it is not practical to create a library of all BLAS combinations, we have developed a domain-specific compiler that generates them on demand. In this paper, we describe a novel algorithm for compiling linear algebra kernels and searching for the best combination of optimization choices. We also present a new hybrid analytic/empirical method for quickly evaluating the profitability of each optimization. We report experimental results showing speedups of up to 130% relative to the GotoBLAS on an AMD Opteron and up to 137% relative to MKL on an Intel Core 2.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"57 4 Suppl 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133281830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 70
PFunc: modern task parallelism for modern high performance computing PFunc:现代高性能计算的现代任务并行
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis Pub Date : 2009-11-14 DOI: 10.1145/1654059.1654103
P. Kambadur, Anshul Gupta, A. Ghoting, H. Avron, A. Lumsdaine
{"title":"PFunc: modern task parallelism for modern high performance computing","authors":"P. Kambadur, Anshul Gupta, A. Ghoting, H. Avron, A. Lumsdaine","doi":"10.1145/1654059.1654103","DOIUrl":"https://doi.org/10.1145/1654059.1654103","url":null,"abstract":"HPC today faces new challenges due to paradigm shifts in both hardware and software. The ubiquity of multi-cores, many-cores, and GPGPUs is forcing traditional serial as well as distributed-memory parallel applications to be parallelized for these architectures. Emerging applications in areas such as informatics are placing unique requirements on parallel programming tools that have not yet been addressed. Although, of all the available parallel programming models, task parallelism appears to be the most promising in meeting these new challenges, current solutions for task parallelism are inadequate. In this paper, we introduce PFunc, a new library for task parallelism that extends the feature set of current solutions for task parallelism with custom task scheduling, task priorities, task affinities, multiple completion notifications and task groups. These features enable PFunc to naturally and efficiently parallelize a wide variety of modern HPC applications and to support the SPMD model of parallel programming. We present three case studies: demand-driven DAG execution, frequent pattern mining and iterative sparse solvers to demonstrate the utility of PFunc's new features.","PeriodicalId":371415,"journal":{"name":"Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis","volume":"138 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2009-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128467660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 42
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信