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Managing jobs with an interpreted language for dynamic adaptation

Managing jobs with an interpreted language for dynamic adapt...

3rd International Workshop on Middleware for Grid computing, MGC'05, Held at the ACM/IFIP/USENIX International Middleware Conference

作者： Milanés, Anolan Rodriguez, Noemi Schulze, Bruno Pontifícia Universidade Católica Do Rio de Janeiro Computer Science Department Brazil National Laboratory for Scientific Computing Computer Science Dep Brazil LNCC Brazil

ISBN: (纸本)1595932690

In this paper we explore the advantages of using interpreted languages for building submitting engines for the grid. In particular, we discuss an example engine, developed using ALua, for submitting jobs in a cluster, which can be extended to a grid environment. We claim that the flexibility offered by interpreted languages justifies the problems related to the intrinsic loss of efficiency associated with this kind of languages. The focus of this work is on adaptation and ease of use. Copyright 2005 ACM.

关键词： Engines

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A robust content-based image retrieval system using multiple features representations

A robust content-based image retrieval system using multiple...

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2005 IEEE Networking, Sensing and Control, ICNSC2005

作者： Tahoun, Mohamed A. Nagaty, Khaled A. El-Arief, Taha I. A-Megeed, Mohammed Computer Science Dep. Faculty of Computers and Informatics Suez Canal University Egypt Computer Science Dep. Faculty of Computer and Information Science Ain Shams University Egypt Scientific Computing Dep. Faculty of Computer and Information Science Ain Shams University Egypt

The similarity measurements and the representation of the visual features are two important issues in Content-Based Image Retrieval (CBIR). In this paper, we compared between the combination of wavelet-based representations of the texture feature and the color feature with and without using the color layout feature. To represent the color information, we used Global Color Histogram (GCH) beside the color layout feature and with respect to the texture information, we used Haar and Daubechies wavelets. Based on some commonly used Euclidean and Non-Euclidean similarity measures, we tested different categories of images and measured the retrieval accuracy when combining such techniques. The experiments showed that the combination of GCH and 2-D Haar wavelet transform using the cosine distance gives good results while the best results obtained when adding the color layout feature to this combination by using the Euclidean distance. The results reflected the importance of using the spatial information beside the color feature itself and the importance of choosing good similarity distance measurements. © 2005 IEEE.

关键词： Image retrieval

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Efficient and accurate derivatives for a software process chain in airfoil shape optimization

Efficient and accurate derivatives for a software process ch...

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作者： Bischof, C.H. Bücker, H.M. Lang, B. Rasch, A. Slusanschi, E. Institute for Scientific Computing RWTH Aachen University D-52056 Aachen Germany Applied Computer Science Group University of Wuppertal D-42097 Wuppertal Germany Institute for Scientific Computing RWTH Aachen University Seffenterweg 23 D-52074 Aachen Germany

When using a Newton-based numerical algorithm to optimize the shape of an airfoil with respect to certain design parameters, a crucial ingredient is the derivative of the objective function with respect to the design parameters. In large-scale aerodynamics, this objective function is an output of a computational fluid dynamics program written in a high-level programming language such as Fortran or C. Numerical differentiation is commonly used to approximate derivatives but is subject to truncation and subtractive cancellation errors. For a particular two-dimensional airfoil, we instead apply automatic differentiation to compute accurate derivatives of the lift and drag coefficients with respect to geometric shape parameters. In automatic differentiation, a given program is transformed into another program capable of computing the original function together with its derivatives. In the problem at hand, the objective function consists of a sequence of programs: a MATLAB program followed by two Fortran 77 programs. It is shown how automatic differentiation is applied to a sequence of programs while keeping the computational complexity within reasonable limits. The derivatives computed by automatic differentiation are compared with approximations based on divided differences. © 2004 Elsevier B.V. All rights reserved.

关键词： Airfoils

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Topology-based simplification for feature extraction from 3D scalar fields

Topology-based simplification for feature extraction from 3D...

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VIS 05: IEEE Visualization 2005, Proceedings

作者： Gyulassy, Attila Natarajan, Vijay Pascucci, Valerio Bremer, Peer-Timo Hamann, Bernd Institute for Data Analysis and Visualization Dept. of Computer Science University of California Davis Center for Applied Scientific Computing Lawrence Livermore National Laboratory Dept. of Computer Science University of Illinois Urbana Champaign

ISBN: (纸本)0780394623

In this paper, we present a topological approach for simplifying continuous functions defined on volumetric domains. We introduce two atomic operations that remove pairs of critical points of the function and design a combinatorial algorithm that simplifies the Morse-Smale complex by repeated application of these operations. The Morse-Smale complex is a topological data structure that provides a compact representation of gradient flow between critical points of a function. Critical points paired by the Morse-Smale complex identify topological features and their importance. The simplification procedure leaves important critical points untouched, and is therefore useful for extracting desirable features. We also present a visualization of the simplified topology. © 2005 IEEE.

关键词： Feature extraction

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The versioning system balancing data amount and access frequency on distributed storage system

The versioning system balancing data amount and access frequ...

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21st International Conference on Data Engineering Workshops 2005

作者： Nakano, Mana Kobayashi, Dai Watanabe, Akitsugu Uehara, Toshihiro Taguchi, Ryo Yokota, Haruo Department of Computer Science Tokyo Institute of Technology Japan Science and Technical Research Laboratories Japan Broadcasting Corporation Japan Global Scientific Information and Computing Center Tokyo Institute of Technology Japan

ISBN: (纸本)0769526578

In this paper, a method of balancing both access frequency and data amount for a distributed parallel storage system under version management is discussed. We assume the version management method keeps the latest version of file and a number of differential information sets to access previous versions. Since the access frequency for an aged version is tend to be lower than that for the latest version, we control the access frequency distribution by the placement of the latest versions, while the data amount distribution is managed by the placement of the differential information whose size is enough small to adjust the subtle difference of data amount. We propose a distributed directory structure and data placement algorithm, and evaluate its effect on the access frequency and data amount distribution. © 2005 IEEE.

关键词： Distributed database systems

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Tree wavelet approximations with applications

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science China Mathematics 2005年第5期48卷 680-702页

作者： XU Yuesheng & ZOU Qingsong Department of Mathematics, Syracuse University, Syracuse, NY 13244, USA Institute of Mathematics, Academy of Mathematics and System sciences, Chinese Academy of sciences, Beijing 100080, China Department of scientific computing and computer science, Zhongshan University, Guangzhou 510275, China 1. Department of Mathematics Syracuse University 13244 Syracuse NY USA 2. Institute of Mathematics Academy of Mathematics and System Sciences Chinese Academy of Sciences 100080 Beijing China 3. Department of Scientific Computing and Computer Science Zhongshan University 510275 Guangzhou China

We construct a tree wavelet approximation by using a constructive greedy scheme (CGS). We define a function class which contains the functions whose piecewise polynomial approximations generated by the CGS have a prescribed global convergence rate and establish embedding properties of this class. We provide sufficient conditions on a tree index set and on bi-orthogonal wavelet bases which ensure optimal order of convergence for the wavelet approximations encoded on the tree index set using the bi-orthogonal wavelet bases. We then show that if we use the tree index set associated with the partition generated by the CGS to encode a wavelet approximation, it gives optimal order of convergence.

关键词： greedy algorithms tree wavelet approximations Besov spaces.

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Approximating anatomical brain connectivity with diffusion tensor MRI using kernel-based diffusion simulations

Approximating anatomical brain connectivity with diffusion t...

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19th International Conference on Information Processing in Medical Imaging, IPMI 2005

作者： Zhang, Jun Kang, Ning Rose, Stephen E. Laboratory for High Performance Scientific Computing and Computer Simulation Department of Computer Science University of Kentucky Lexington KY 40506-0046 United States Centre for Magnetic Resonance University of Queensland Brisbane QLD 4072 Australia

We present a new technique for noninvasively tracing brain white matter fiber tracts using diffusion tensor magnetic resonance imaging (DT-MRI). This technique is based on performing diffusion simulations over a series of overlapping three dimensional diffusion kernels that cover only a small portion of the human brain volume and are geometrically centered upon selected starting voxels where a seed is placed. Synthetic and real DT-MRI data are employed to demonstrate the tracking scheme. It is shown that the synthetic tracts can be accurately replicated, while several major white matter fiber pathways in the human brain can be reproduced noninvasively as well. The primary advantages of the algorithm lie in the handling of fiber branching and crossing and its seamless adaptation to the platform established by new imaging techniques, such as high angular, q-space, or generalized diffusion tensor imaging. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Brain

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Multiple structural RNA alignment with Lagrangian relaxation

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5th International Workshop on Algorithms in Bioinformatics, WABI 2005

作者： Bauer, Markus Klau, Gunnar W. Reinert, Knut Institute of Computer Science Free University of Berlin Germany International Max Planck Research School for Computational Biology and Scientific Computing Germany Institute of Mathematics Free University of Berlin Germany

ISBN: (纸本)3540290087

Many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure. Hence, it is clear that any method that relates RNA sequences in form of (multiple) alignments should take structural features into account. Since multiple: alignments are of great importance for subsequent data analysis, research in improving the speed and accuracy of such alignments benefits many other analysis problems. We present a formulation for computing provably optimal, structure-based, multiple RNA alignments and give an algorithm that finds such an optimal (or near-optimal) solution. To solve the resulting computational problem we propose an algorithm based on Lagrangian relaxation which already proved successful in the two-sequence case. We compare our implementation, mLARA, to three programs (clustalW, MARNA, and pmmulti) and demonstrate that we can often compute multiple alignments with consensus structures that have a significant lower minimum free energy term than computed by the other programs. Our prototypical experiments show that our new algorithm is competitive and, in contrast to other methods, is applicable to long sequences where standard dynamic programming approaches must fail. Furthermore, the Lagrangian method is capable of handling arbitrary pseudoknot structures. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Lagrange multipliers

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A hybrid hardware/software approach to efficiently determine cache coherence bottlenecks 05

A hybrid hardware/software approach to efficiently determine...

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ICS05 - 19th ACM International Conference on Supercomputing

作者： Marathe, Jaydeep Mueller, Frank De Supinski, Bronis Department of Computer Science North Carolina State University Raleigh NC 27695-7534 Lawrence Livermore National Laboratory Center for Applied Scientific Computing L-561 Livermore CA 94551

ISBN: (纸本)9781595931672

High-end computing increasingly relies on shared-memory multiprocessors (SMPs), such as clusters of SMPs, nodes of chipmultiprocessors (CMP) or large-scale single-system image (SSI) SMPs. In such systems, performance is often affected by the sharing pattern of data within applications and its impact on cache coherence. Sharing patterns that result in frequent invalidations followed by subsequent coherence misses create cache coherence bottlenecks with significant performance penalties. Past work on identifying coherence bottlenecks based on tracing memory accesses incurs considerable runtime overhead and does not scale well with increasing problem sizes, which makes it infeasible to use with real-world programs. In this paper, we introduce a novel low-cost, hardware-assisted approach to determine coherence bottlenecks in shared-memory OpenMP applications. We assess the merits of our approach on a contemporary SMP platform. Specifically, we assess the feasibility of lossy tracing to pin-point coherence problems in applications. We evaluate the qualitative and quantitative trade-offs between tracing overhead and accuracy of the generated coherence traffic metrics, correlated to memory access points at the program source level. Our lossy tracing mechanism closely approximates the degree of accuracy of determining coherence misses in full traces for most of the benchmarks we study while reducing run-time execution overhead and trace sizes by one to two orders of magnitude. To the best of our knowledge, this novel method significantly outperforms any of the prior approaches and, for the first time, makes cache coherence analysis feasible for long-running applications. Copyright © 2005 ACM.

关键词： Buffer storage

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Improving scientific software component quality through assertions

Improving scientific software component quality through asse...

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2nd International Workshop on Software Engineering for High Performance computing System Applications, SE-HPCS '05, Co-located with the International Conference on Software Engineering, ICSE 2005

作者： Dahlgren, Tamara L. Devanbu, Premkumar T. Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States Centre for Software Systems Research Dept. of Computer Science University of California Davis CA United States

ISBN: (纸本)1595931171

We are proposing research on self-adaptive interface assertion enforcement for the purposes of improving scientific software component quality. Demonstrating software correctness through assertions is a well-known technique for quality improvement. However, the performance penalty is often considered too high for deployment. In order to determine if partial enforcement based on adaptive sampling is a viable solution in performance critical environments, we are pursuing research on mechanisms combining static and dynamic analyses to efficiently maximize assertion checking within performance constraints. This paper gives an overview of our initial experiments, current work, and plans. Copyright 2005 ACM.

关键词： Babel constrained enforcement interface assertions SIDL

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