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2006 ACM/IEEE Conference on Supercomputing, SC'06

作者： Narumi, Tetsu Ohno, Yousuke Okimoto, Noriaki Koishi, Takahiro Suenaga, Atsushi Futatsugi, Noriyuki Yanai, Ryoko Himeno, Ryutaro Fujikawa, Shigenori Taiji, Makoto Ikei, Mitsuru Intel K.K. High Performance Molecular Simulation Team Genomic Sciences Center Innovative Nanopatterning Laboratory Topochemical Design Laboratory Frontier Research System Advanced Center for Computing and Communication Software and Solutions Group Parallel and Distributed Solutions Group

ISBN: (纸本)0769527000

We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system - -a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for Coulomb force calculations;this is the highest-ever performance reported for classical molecular dynamics simulations. Amyloid fibril formation is known to be related to the occurrence of severe diseases such as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob diseases. The Sup35 protein is a "yeast prion protein," which forms mini-crystals due to aggregation;it forms an effective platform for studying the formation process of amyloid fibrils. In these simulations, we first elucidate that the amyloid-forming peptides GNNQQNY aggregate at a higher frequency than non-amyloid-forming peptides SQNGNQQRG;further, the GNNQQNY peptides tend to form parallel two-stranded -sheets that would grow into a cross- amyloid nucleus. The results are consistent with those obtained experimentally. Furthermore, we could observe an early elongation of the amyloid nucleus. This result is expected to contribute toward a deeper understanding of the amyloid growth mechanism. © 2006 IEEE.

关键词： Peptides

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A distributed Multi-Storage Resource Architecture and I/O Performance Prediction for Scientific computing

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Cluster computing 2003年第3期6卷 189-200页

作者： Shen, X. Choudhary, A. Matarazzo, C. Sinha, P. Center for Parallel and Distributed Computing Department of Electrical and Computer Engineering Northwestern University Evanston USA Lawrence Livermore National Laboratory Livermore USA

I/O intensive applications have posed great challenges to computational scientists. A major problem of these applications is that users have to sacrifice performance requirements in order to satisfy storage capacity requirements in a conventional computing environment. Further performance improvement is impeded by the physical nature of these storage media even when state-of-the-art I/O optimizations are employed. In this paper, we present a distributed multi-storage resource architecture, which can satisfy both performance and capacity requirements by employing multiple storage resources. Compared to a traditional single storage resource architecture, our architecture provides a more flexible and reliable computing environment. This architecture can bring new opportunities for high performance computing as well as inherit state-of-the-art I/O optimization approaches that have already been developed. It provides application users with high-performance storage access even when they do not have the availability of a single large local storage archive at their disposal. We also develop an Application Programming Interface (API) that provides transparent management and access to various storage resources in our computing environment. Since I/O usually dominates the performance in I/O intensive applications, we establish an I/O performance prediction mechanism which consists of a performance database and a prediction algorithm to help users better evaluate and schedule their applications. A tool is also developed to help users automatically generate performance data stored in databases. The experiments show that our multi-storage resource architecture is a promising platform for high performance distributed computing.

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Optimizing Batched Small Matrix Multiplication on Multi-core DSP Architecture 22

Optimizing Batched Small Matrix Multiplication on Multi-core...

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22nd IEEE International Symposium on parallel and distributed Processing with Applications, ISPA 2024

作者： Zuo, Xiaohan Xiao, Chunhua Wang, Qinglin Shi, Chen Chongqing University College of Computer Science Chongqing China Ministry of Education Key Laboratory of Dependable Service Computing in Cyber Physical Society China National University of Defense Technology National Key Laboratory of Parallel and Distributed Computing Changsha410073 China National University of Defense Technology Laboratory of Digitizing Software for Frontier Equipment Changsha410073 China

ISBN: (纸本)9798331509712

General Matrix Multiplication (GEMM) is a critical computational operation in scientific computing and machine learning domains. While traditional GEMM performs well on large matrices, it is inefficient in terms of data transfer and computation for small matrices. Many High-Performance computing (HPC) tasks can be decomposed into large batches of small matrix multiplication operations. Multi-core Digital Signal Processors (DSPs) are commonly used to accelerate high-performance computing. We present a design for batched fusion small matrix multiplication (BFMM) tailored for multi-core DSP architecture. To address the inefficiencies and redundancy in storage and computational operations associated with batch small matrix multiplications, we designed several strategies. We design a matrix fusion concatenation strategy, an access coordination mechanism, and a mechanism for fragment aggregation. BFMM supports an efficient K-dimension multi-core parallelization strategy. The parameter constraint model makes BFMM highly portable. BFMM also includes a performance evaluation model that facilitates assessment and verification. Experimental results demonstrate that, compared to traditional GEMM (TGEMM) on multi-core DSP and traditional GEMM with concatenated data access (TGEMM Op), BFMM exhibits superior performance. For large batches of small matrices, our design achieves 1.21x to 18x higher performance than TGEMM Op on single-core DSP, while on multi-core DSP, it outperforms TGEMM Op by 1.14x to 18.1x. © 2024 IEEE.

关键词： Network security

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Assessment of two pressure-velocity coupling strategies for local meshless numerical method

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9th International Conference on Advances in Fluid Mechanics - Advances in Fluid Mechanics IX, AFM 2012

作者： Kosec, G. Vertnik, R. Šarler, B. Jožef Stefan Institute Laboratory for Parallel and Distributed Computing Slovenia University of Nova Gorica Laboratory for Multiphase Processes Slovenia Štore steel d.o.o. Research Slovenia Centre of Excellence for Biosensors Automation and Process Control Laboratory for Advanced Materials Systems Slovenia

ISBN: (纸本)9781845646004

The performance of two pressure-velocity coupling strategies, associated with the primitive variable solution of incompressible Newtonian fluid with the meshless Local Radial Basis Function Collocation Method (LRBFCM), is compared with respect to computational efficiency, stability, accuracy and spatial convergence. The LRBFCM is structured with multiquadrics on five noded support domains. The explicit time stepping is used. The Backward- Facing Step problem (BFS) has been selected as a benchmark problem, previously tackled by several numerical methods. The semi-local fractional step method (FSM) and completely local pressure-velocity couplings (LPVC) are compared. The numerical results are validated against previously published data. The results are represented and compared in terms of a convergence plot of the reattachment position. We show that both approaches provide reasonable results;however, LVPC is less computationally complex and less stable in comparison to FSM. © 2012 WIT Press.

关键词： Computational efficiency

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Security mechanisms for legacy code applications in GT3 environment

Security mechanisms for legacy code applications in GT3 envi...

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Euromicro Conference on parallel, distributed and Network-Based Processing

作者： G. Terstyanszky T. Delaitre A. Goyeneche T. Kiss K. Sajadah S.C. Winter P. Kacsuk Centre of Parallel Computing Universitv of Westminster London Centre of Parallel Computing Cavendish School of Computer Science University of Westminster London UK MTA SZTAKI Laboratory of Parallel and Distributed Systems Budapest Hungary

There are many legacy code applications that cannot be run in grid environment without significant modifications. To avoid reengineering of legacy code, we developed the grid execution management for legacy code architecture (GEMLCA) that enables deployment of legacy code applications as grid services. GEMLCA is an OGSI grid service layer that supports submitting jobs, getting their results and status back. Security requirements are essential to any grid application to preserve the confidentiality and integrity of data. To meet these requirements the GT3 security model was implemented in GEMLCA. The paper introduces GEMLCA and how grid security infrastructure (GSI) components have been added to GEMLCA in order to enable secure execution of jobs in grid. The paper also presents how a legacy code traffic simulator was transformed into a grid service using GEMLCA and gives some simulation results.

关键词： Java Data security Computational modeling Wrapping Application software Testing Grid computing Computer architecture Concurrent computing distributed computing

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On construction of a large computing farm using multiple linux PC clusters

On construction of a large computing farm using multiple lin...

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5th International Conference, PDCAT 2004

作者： Yang, Chao-Tung Liao, Chun-Sheng Li, Kuan-Ching High-Perf. Computing Laboratory Department of Computer Science Tunghai University Taichung Taichung 407 Taiwan Parallel and Distributed Proc. Ctr. Department of Computer Science Providence University Shalu Taichung 433 Taiwan

In addition to the traditional massively parallel computers, distributed workstation clusters now play an important role in scientific computing, due to the advent of commodity high performance processors, low-latency/high-bandwidth networks and powerful development tools. In a cluster environment, we add more and more workstations for reaching more computing performance. Unfortunately, in general case, we don't have enough space for setting up many PCs to form a large-scale PC cluster, and more questions we are concerned about, for example, network topology, electric power, and management question etc. Thus, we can use several places for setting up a number of machines on each place, and enabling networking for transparent computing on each cluster node for enable an enormous node cluster. In this paper, we use some routing policy and a kernel module named Netfilter to enable three or more clusters to be connected as a big one. In our experimental environment we use three different quantities of nodes in each PC cluster connected via a Fast-Ethernet network environment. As experiment, we performed matrix multiplication for performance analysis.

关键词： parallel processing systems

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Routing with uncertainty in wireless mesh networks

Routing with uncertainty in wireless mesh networks

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2010 IEEE 18th International Workshop on Quality of Service, IWQoS 2010

作者： Chen, Fajun Liu, Jiangchuan Li, Zongpeng Wang, Yijie Key Laboratory of Science and Technology for National Defence of Parallel and Distributed Processing School of Computer National University of Defense Technology China School of Computing Science Simon Fraser University Canada Department of Computer Science University of Caglary Canada

ISBN: (纸本)9781424459889

Existing routing protocols for Wireless Mesh Networks (WMNs) are generally optimized with statistical link measures, while not addressing on the intrinsic uncertainty of wireless links. We show evidence that, with the transient link uncertainties at PHY and MAC layers, a pseudo-deterministic routing protocol that relies on average or historic statistics can hardly explore the full potentials of a multi-hop wireless mesh. We study optimal WMN routing using probing-based online anypath forwarding, with explicit consideration of transient link uncertainties. We show the underlying connection between WMN routing and the classic Canadian Traveller Problem (CTP) [1]. Inspired by a stochastic recoverable version of CTP (SRCTP), we develop a practical SRCTP-based online routing algorithm under link uncertainties. We study how dynamic next hop selection can be done with low cost, and derive a systematic selection order for minimizing transmission delay. We conduct simulation studies to verify the effectiveness of the SRCTP algorithms under diverse network configurations. In particular, compared to deterministic routing, reduction of end-to-end delay (51:15∼73:02%) and improvement on packet delivery ratio (99:76%) are observed.

关键词： Routing protocols

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Design and evaluation of an environment APE for automatic parallelization of programs

Design and evaluation of an environment APE for automatic pa...

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International Symposium on parallel Architectures, Algorithms and Networks (ISPAN)

作者： V. Chaudhary Chengzhong Xu S. Roy Jialin Ju V. Sinha Laiwu Luo Parallel and Distributed Computing Laboratory Department of Electrical and Computer Engineering Wayne State University MI USA

In this paper, we present the design and evaluation of a compiler system, called APE, for automatic parallelization of scientific and engineering applications on distributed memory computers. APE is built on top of SUIF compiler. It extends SUIF with capabilities in parallelizing loops with non-uniform cross-iteration dependencies, and in handling loops that have indirect access patterns. We have evaluated the effectiveness of SUIF with several CFD test codes, and found that SUIF handles uniform loops over dense and regular data structures very well. For non-uniform loops, an innovative and efficient parallelization approach based on convex theory have been proposed and is being implemented. We have also presented a class of scalable algorithms for parallel distribution and redistribution of unstructured data structures during parallelizing irregular loops.

关键词： Program processors distributed computing Concurrent computing Computational fluid dynamics Data structures Quantum computing Programming profession parallel processing Design engineering Optimizing compilers

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A resource broker for computing nodes selection in grid computing environments 3rd

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3rd International Conference on Grid and Cooperative computing, GCC2004

作者： Yang, Chao-Tung Lai, Chuan-Lin Shih, Po-Chi Li, Kuan-Ching High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung407 Taiwan Parallel and Distributed Processing Center Department of Computer Science and Information Management Providence University Shalu Taichung433 Taiwan

ISBN: (纸本)3540235647

As Grid computing is becoming a reality, there is a need for managing and monitoring the available resources worldwide, as well as the need for conveying these resources to the everyday user. This paper describes a resource broker with its main function as to match the available resources to the user’s needs. The use of the resource broker provides a uniform interface to access any of the available and appropriate resources using user’s credentials. The resource broker runs on top of the Globus Toolkit. Therefore, it provides security and current information about the available resources and serves as a link to the diverse systems available in the Grid. © Springer-Verlag Berlin Heidelberg 2004.

关键词： Grid computing

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parallel image processing in heterogeneous computing network systems

Parallel image processing in heterogeneous computing network...

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IEEE International Conference on Image Processing

作者： P. Chalermwat N. Alexandridis P. Piamsa-Nga M. O'Connell Parallel and Distributed Computing Laboratory George Washington University Washington D.C. DC USA

We present a uniform construct of parallel programming for a set of image processing tasks based on our distributed computing primitive (DCP) concept. Our target architecture is a heterogeneous computing network system consisting of various high performance workstations connected through a local area network. We show that DCP has advantages over non-primitive PVM-based parallel approaches in three aspects: ease-of-use, automation, and optimization.

关键词： Image processing Computer networks Concurrent computing parallel programming distributed computing Computer architecture High performance computing Workstations Local area networks Automation

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