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ACM/IEEE 2005 Supercomputing Conference, SC'05

作者： Gioiosa, Roberto Sancho, José Carlos Song, Jiang Petrini, Fabrizio Davis, Kei Performance and Architecture Laboratory Computer and Computational Sciences Division Los Alamos National Laboratory NM 87545 United States Dipartimento Informatica Sistemi e Produzione Universitá Degli Studi di Roma Tor Vergata 00133 Roma Italy Applied Computer Science Group Computational Sciences and Mathematics Division Pacific Northwest National Laboratory WA 99352 United States

ISBN: (纸本)1595930612

We describe the software architecture, technical features, and performance of TICK (Transparent Incremental Checkpointer at Kernel level), a system-level checkpointer implemented as a kernel thread, specifically designed to provide fault tolerance in Linux clusters. This implementation, based on the 2.6.11 Linux kernel, provides the essential functionality for transparent, highly responsive, and efficient fault tolerance based on full or incremental checkpointing at system level. TICK is completely user-transparent and does not require any changes to user code or system libraries;it is highly responsive: an interrupt, such as a timer interrupt, can trigger a checkpoint in as little as 2.5μs;and it supports incremental and full checkpoints with minimal overhead - less than 6% with full checkpointing to disk performed as frequently as once per minute. © 2005 IEEE.

关键词： Parallel processing systems

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Self-adapting Linear Algebra algorithms and software

Self-adapting Linear Algebra algorithms and software

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作者： Demmel, James Dongarra, Jack Eijkhout, Victor Fuentes, Erika Petitet, Antoine Vuduc, Richard Whaley, R.Clint Yelick, Katherine Computer Science Division Electrical Engineering and Computer Science Department University of California Berkeley CA 94720 United States Computer Science Department University of Tennessee Knoxville TN 37996 United States Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN 37831 United States Computer Science Department Rice University Houston TX United States Innovative Computing Laboratory University of Tennessee Knoxville TN 37996 United States Sun Microsystems Paris 75016 France Center for Applied Scientific Computing Lawrence Livermore National Laboratory Livermore CA 94551 United States Department of Computer Science Florida State University Tallahassee FL 32306-4530 United States Electrical Engineering and Computer Science Department University of California Berkeley CA 94720 United States

One of the main obstacles to the efficient solution of scientific problems is the problem of tuning software, both to the available architecture and to the user problem at hand. We describe approaches for obtaining tuned high-performance kernels and for automatically choosing suitable algorithms. Specifically, we describe the generation of dense and sparse Basic Linear Algebra Subprograms (BLAS) kernels, and the selection of linear solver algorithms. However, the ideas presented here extend beyond these areas, which can be considered proof of concept. © 2005 IEEE.

关键词： Linear algebra

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The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry

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Journal of Bioinformatics and Computational Biology 2005年第2期3卷 455-476页

作者： Fridman, Tema Razumovskaya, Jane Verberkmoes, Nathan Hurst, Greg Protopopescu, Vladimir Xu, Ying Joint Institute for Computer Science University of Tennessee/ORNL ORNL Oak Ridge TN 37831-6164 PO Box 2008 United States Genome Science/Technology Program University of Tennessee Life Sciences Division Oak Ridge TN 37831-6164 United States Genome Science/Technology Program University of Tennessee Chemical Sciences Division Oak Ridge TN 37831-6131 United States Chemical Sciences Division Oak Ridge National Laboratory Oak Ridge TN 37831-6131 United States Computer Sci./Mathematics Division Oak Ridge National Laboratory Oak Ridge TN 37831-6164 United States Biochem./Molecular Biol. Department University of Georgia Athens GA 30602 United States

Proteomic techniques are fast becoming the main method for qualitative and quantitative determination of the protein content in biological systems. Despite notable advances, efficient and accurate analysis of high throughput proteomic data generated by mass spectrometers remains one of the major stumbling blocks in the protein identification problem. We present a model for the number of random matches between an experimental MS-MS spectrum and a theoretical spectrum of a peptide. The shape of the probability distribution is a function of the experimental accuracy, the number of peaks in the experimental spectrum, the length of the interval over which the peaks are distributed, and the number of theoretical spectral peaks in this interval. Based on this probability distribution, a goodness-of-fit tool can be used to yield fast and accurate scoring schemes for peptide identification through database search. In this paper, we describe one possible implementation of such a method and compare the performance of the resulting scoring function with that of SEQUEST. In terms of speed, our algorithm is roughly two orders of magnitude faster than the SEQUEST program, and its accuracy of peptide identification compares favorably to that of SEQUEST. Moreover, our algorithm does not use information related to the intensities of the peaks. © Imperial College Press.

关键词： Database search Mass spectrometry Tandem

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Interaction of a finite-sized particle with wall turbulence

Interaction of a finite-sized particle with wall turbulence

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4th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 4

作者： Zeng, Lanying Balachandar, S. Fischer, Paul Najjar, Fady Department of Theoretical and Applied Mechanics University of Illinois at Urbana-Champaign Urbana IL 61801 United States Mathematics and Computer Science Division Argonne National Laboratory Argonne IL 60439 United States Center for Simulation of Advanced Rockets University of Illinois at Urbana-Champaign Urbana IL 61801 United States

Reliable information on forces on a finite-sized particle in a turbulent boundary layer is lacking. For lack of such knowledge we continue to use standard drag and lift correlations developed for a uniform flow to predict the drag and lift forces. Here we consider direct numerical simulations of a turbulent channel flow over a finite-sized particle. All relevant length and time scales of turbulence, attached boundary layers on the particles, and particle wakes will be faithfully resolved, and thus we consider fully resolved genuine direct numerical simulations. The results from the direct numerical simulation are compared with the corresponding predictions based on standard drag relation.

关键词： Direct numerical simulation

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DRAFT: Not for attribution: Detonation initiation on the microsecond time scale: DDTs

DRAFT: Not for attribution: Detonation initiation on the mic...

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Fall Technical Meeting of the Western States Section of the Combustion Institute 2005, WSS/CI 2005

作者： Kassoy, D.R. Kuehn, J.A. Nabity, M.W. Clarke, J.F. Mechanical Engineering University of Colorado 427 UCB BoulderCO80309 United States Computer Science and Mathematics Division Oak Ridge National Laboratory One Bethel Valley Road MS-6173 Oak RidgeTN37831 United States Applied Mathematics University of Colorado 526 UCB BoulderCO80309 United States Cranfield University Cranfield United Kingdom

ISBN: (纸本)9781617827921

Spatially resolved, thermal power deposition of limited duration into a finite volume of reactive gas is the initiator for a deflagration-to-detonation transition (DDT) on the microsecond time scale. The reactive Euler equations with one-step Arrhenius kinetics are used to derive novel formulas for velocity and temperature variation that describe the physical phenomena characteristic of DDTs. A nonlinear transformation of the variables is shown to yield a canonical equation system, independent of the activation energy. Numerical solutions of the reactive Euler equations are used to describe the detailed sequence of reactive gasdynamic processes leading to an overdriven planar detonation far from the power deposition location. Results are presented for deposition into a region isolated from the planar boundary of the reactive gas as well as for that adjacent to the boundary. The role of compressions and shocks reflected from the boundary into the partially reacted hot gas is described. The quantitative dependences of DDT evolution on the magnitude of thermal power deposition and activation energy are identified. © (2005) by the Western States Section/Combustion Institute. All rights reserved.

关键词： Deposition

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Multi-section freshman classes with laboratories: Lecture as intro vs. lecture as wrap-up

Multi-section freshman classes with laboratories: Lecture as...

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2005 ASEE Annual Conference and Exposition: The Changing Landscape of Engineering and Technology Education in a Global World

作者： Sticklen, Jon Urban-Lurain, Mark Hinds, Timothy Eskil, Taner Amey, Marilyn Michigan State University United States Department of Computer Science and Engineering Michigan State University United States Instructional Technolgy Research and Development Division of Science and Mathematics Education Michigan State University United States MSU Mechanical Engineering Department Department of Educational Administration Higher Adult and Lifelong Education Program Michigan State University United States

An instructional model for Freshman class with laboratories was discussed. The instructional model introduces material of a given unit while laboratory sections are used to provide hands on detailed experience with applying knowledge in assigned readings and lecture. The lecture in the plays the role of wrap up for the unit students including making generalizations. It is suggested that 'lecture as wrap up' should require students to take more responsibility for their own learning, and in the end be more actively engaged in their learning than the 'lecture as introduction' path.

关键词： Laboratories

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Curricular integration of computational tools: A first step

Curricular integration of computational tools: A first step

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2005 ASEE Annual Conference and Exposition: The Changing Landscape of Engineering and Technology Education in a Global World

作者： Hinds, Timothy Urban-Lurain, Mark Sticklen, Jon Amey, Marilyn Eskil, Taner Michigan State University United States Michigan State University Department of Mechanical Engineering United States Instructional Technology Research and Development Division of Science and Mathematics Education Michigan State University United States Department of Computer Science and Engineering Michigan State University United States Department of Educational Administration Higher Adult and Lifelong Education Program MSU United States

A pair of initial studies using an evolutionary approach to curricular reform that capitalize on the strength of both the top-down and bottom-up model, and was built on the science, technology, engineering and mathematics (STEM) reform literature are performed. This approach develop a pairwise linkage among strategic courses in the engineering curricula to promote curricular integration. The results of trial produced higher course grades in both course grades in both courses, though the change was most significant for the mechanical engineering course. Full evaluation of the project cannot be obtained until the study is continued to include statics students who also participated when they were enrolled in the computer science course.

关键词： Curricula

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Radiation-coupled front-tracking simulations for laser-driven shock experiments

Radiation-coupled front-tracking simulations for laser-drive...

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作者： Zhang, Yongmin Drake, R. Paul Glimm, James Grove, John W. Sharp, David H. Department of Applied Mathematics and Statistics University at Stony Brook Stony Brook NY 11974-3600 United States University of Michigan 2455 Hayward St. Ann Arbor MI 48105 United States Center for Data Intensive Computing Brookhaven National Laboratory Upton NY 11793-6000 United States Continuum Dynamics Group Computer and Computational Science Division Los Alamos National Laboratory Los Alamos NM 87545 United States Complex Systems Group Theoretical Division Los Alamos National Laboratory Los Alamos NM 87545 United States

The purpose of this paper is to develop a numerical algorithm to track the preheat interface motion driven by radiation transfer in high-intensity laser experiments. Our front-tracking algorithm is coupled to a radiation process through an inter-package coupling by connecting the output from a radhydro code HYADES to the input of FronTier code of front tracking. Our coupled algorithm is validated by comparing simulation results from both codes in both low and high radiation cases. Significant interface motion and deformation of the harmonic perturbation due to radiation preheat are observed in high radiation heat case. © 2005 Elsevier Ltd. All rights reserved.

关键词： Algorithms

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Analytical approach for calculating the minimally required ranging codes in fixed and mobile broadband wireless access systems based on OFDMA

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WSEAS Transactions on Communications 2005年第10期4卷 989-993页

作者： Chang, Yong Hwang, Gang Uk Lee, Yutae Telecommunication Systems Division Information and Communication Business Samsung Electronics Co. Ltd. Suwon-si Gyeonggi-do Korea Republic of Division of Applied Mathematics and Telecommunication Engineering Program Korea Advanced Institute of Science and Technology Taejeon Korea Republic of Department of Information and Communication Engineering Dongeui University Busanjin-gu Busan 614-714 Korea Republic of

In this paper, we consider a ranging procedure occurred in the fixed and mobile broadband wireless access systems based on the Wireless MAN-OFDMA (Metropolitan Area Network -Orthogonal Frequency division Multiple Access). A ranging procedure is a collection of processes for a Mobile Subscriber Station (MSS) and a Base Station (BS) to maintain the quality of the radio frequency communication link between them. When multiple subscribers select the same ranging codes from the given ranging code pool and range the BS by transmitting those identical ranging codes at the same time frame, the ranging collision may be occurred at BS because the BS can not differentiate two different MSSs since they selected the same ranging code. We propose a mathematical performance model to analyze the probability of ranging collision affected by both the capacity of the ranging code pool and the rate of the MSS arriving to the system and investigate the numerical results of the proposed model. By the proposed model and its numerical results, we can calculate the minimum number of the required ranging codes to be implemented in BS(Base Station). We compare the analytical results with the simulated results to validate the proposed mathematical model is correct.

关键词： Wireless telecommunication systems

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MRA and low-separation rank approximation with applications to quantum electronics structures computations

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Journal of Physics: Conference Series 2005年第1期16卷

作者： G I Fann R J Harrison G Beylkin Computational Mathematics Group Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN 37831 USA Computational Chemical Sciences Group Computer Science and Mathematics Division Oak Ridge National Laboratory Oak Ridge TN 37830 USA Department of Chemistry University of Tennessee at Knoxville USA Department of Applied Mathematics University of Colorado at Boulder 526 UCB Boulder CO 80309-0526 USA

We describe some recent mathematical results in constructing computational methods that lead to the development of fast and accurate multiresolution numerical methods for solving problems in computational chemistry (the so-called multiresolution quantum chemistry). Using low separation rank representations of functions and operators and representations in multiwavelet bases, we developed a multiscale solution method for integral and differential equations and integral transforms. The Poisson equation and the Schrodinger equation, the projector on the divergence free functions, provide important examples with a wide range of applications in computational chemistry, computational electromagnetic and fluid dynamics. We have implemented these ideas that include adaptive representations of operators and functions in the multiwavelet basis and low separation rank approximation of operators and functions. These methods have been implemented into a software package called Multiresolution Adaptive Numerical Evaluation for Scientific Simulation (MADNESS).

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