273 research outputs found

    Lattice QCD as a video game

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    The speed, bandwidth and cost characteristics of today's PC graphics cards make them an attractive target as general purpose computational platforms. High performance can be achieved also for lattice simulations but the actual implementation can be cumbersome. This paper outlines the architecture and programming model of modern graphics cards for the lattice practitioner with the goal of exploiting these chips for Monte Carlo simulations. Sample code is also given. (c) 2007 Elsevier B.V. All rights reserved

    Multi-mass solvers for lattice QCD on GPUs

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    Graphical Processing Units (GPUs) are more and more frequently used for lattice QCD calculations. Lattice studies often require computing the quark propagators for several masses. These systems can be solved using multi-shift inverters but these algorithms are memory intensive which limits the size of the problem that can be solved using GPUs. In this paper, we show how to efficiently use a memory-lean single-mass inverter to solve multi-mass problems. We focus on the BiCGstab algorithm for Wilson fermions and show that the single-mass inverter not only requires less memory but also outperforms the multi-shift variant by a factor of two.Comment: 27 pages, 6 figures, 3 Table

    Solving Lattice QCD systems of equations using mixed precision solvers on GPUs

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    Modern graphics hardware is designed for highly parallel numerical tasks and promises significant cost and performance benefits for many scientific applications. One such application is lattice quantum chromodyamics (lattice QCD), where the main computational challenge is to efficiently solve the discretized Dirac equation in the presence of an SU(3) gauge field. Using NVIDIA's CUDA platform we have implemented a Wilson-Dirac sparse matrix-vector product that performs at up to 40 Gflops, 135 Gflops and 212 Gflops for double, single and half precision respectively on NVIDIA's GeForce GTX 280 GPU. We have developed a new mixed precision approach for Krylov solvers using reliable updates which allows for full double precision accuracy while using only single or half precision arithmetic for the bulk of the computation. The resulting BiCGstab and CG solvers run in excess of 100 Gflops and, in terms of iterations until convergence, perform better than the usual defect-correction approach for mixed precision.Comment: 30 pages, 7 figure

    Sorting signed circular permutations by super short reversals

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    We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works.We consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version rema9096272283FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCAPES - COORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIORCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO2013/08293-72014/04718-6306730/2012-0; 477692/2012-5; 483370/2013-411th International Symposium on Bioinformatics Research and Application

    The Effective Particle-Hole Interaction and the Optical Response of Simple Metal Clusters

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    Following Sham and Rice [L. J. Sham, T. M. Rice, Phys. Rev. 144 (1966) 708] the correlated motion of particle-hole pairs is studied, starting from the general two-particle Greens function. In this way we derive a matrix equation for eigenvalues and wave functions, respectively, of the general type of collective excitation of a N-particle system. The interplay between excitons and plasmons is fully described by this new set of equations. As a by-product we obtain - at least a-posteriori - a justification for the use of the TDLDA for simple-metal clusters.Comment: RevTeX, 15 pages, 5 figures in uufiles format, 1 figure avaible from [email protected]

    The Optimal Choice of Trap Type for the Recently Spreading Jewel Beetle Pests Lamprodila festiva and Agrilus sinuatus (Coleoptera, Buprestidae)

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    BACKGROUND: Two jewel beetle species native to Europe, the cypress jewel beetle, Lamprodila (Palmar, Ovalisia) festiva L. (Buprestidae, Coleoptera), and the sinuate pear tree borer, Agrilus sinuatus Olivier (Buprestidae, Coleoptera), are key pests of ornamental thuja and junipers and of orchard and ornamental rosaceous trees, respectively. Although chemical control measures are available, due to the beetles’ small size, agility, and cryptic lifestyle at the larval stage, efficient tools for their detection and monitoring are missing. Consequently, by the time emerging jewel beetle adults are noticed, the trees are typically significantly damaged. METHODS: Thus, the aim of this study was to initiate the development of monitoring traps. Transparent, light green, and purple sticky sheets and multifunnel traps were compared in field experiments in Hungary. RESULTS: Light green and transparent sticky traps caught more L. festiva and A. sinuatus jewel beetles than non-sticky multifunnel traps, regardless of the larger size of the colored surface of the funnel traps. CONCLUSIONS: Although light green sticky sheets turned out to be optimal for both species, using transparent sheets can reduce catches of non-target insects. The key to the effectiveness of sticky traps, despite their reduced suitability for quantitative comparisons, may lie in the behavioral responses of the beetles to the optical features of the traps

    Light Hadron Masses from Lattice QCD

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    This article reviews lattice QCD results for the light hadron spectrum. We give an overview of different formulations of lattice QCD, with discussions on the fermion doubling problem and improvement programs. We summarize recent developments in algorithms and analysis techniques, that render calculations with light, dynamical quarks feasible on present day computer resources. Finally, we summarize spectrum results for ground state hadrons and resonances using various actions.Comment: 53 pages, 24 figures, one table; Rev.Mod.Phys. (published version); v2: corrected typ

    Sorting Signed Circular Permutations by Super Short Reversals

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    International audienceWe consider the problem of sorting a circular permutation by reversals of length at most 2, a problem that finds application in comparative genomics. Polynomial-time solutions for the unsigned version of this problem are known, but the signed version remained open. In this paper, we present the first polynomial-time solution for the signed version of this problem. Moreover, we perform an experiment for inferring distances and phylogenies for published Yersinia genomes and compare the results with the phylogenies presented in previous works
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