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1st International Conference on Context-Aware systems and Applications, ICCASA 2012

作者： Pham, Hong Phong Nguyen, Huu Duc Nguyen, Thanh Thuy Department of Information System Hanoi University of Science and Technology NOT Is High Performance Computing Center Viet Nam Department of Computer Science VNU - University of Engineering and Technology Viet Nam

ISBN: (纸本)9783642366413

Implementing Multi Sequence Alignment (MSA) problem using the method of progressive alignment is not feasible on common computing systems;it takes several hours or even days for aligning thousands of sequences if we use sequential versions of the most popular MSA algorithm - Clustal. In this paper, we present our parallel algorithm called CUDAClustal, a MSA parallel program. We have paralleled the first stage of the algorithm Clustal and achieved a significant speedup when compared to the sequential program running on a computer of Pentium 4 3.0 GHz processor. Our tests were performed on one GPU Geforce GTX 295 and they gave a great computing performance: the running time of CUDAClustal is smaller approximately 30 times than Clustal for the first stage. This shows the large benefit of GPU for solving the MSA problem and its high applicability in bioinformatics. © 2013 ICST Institute for Computer Science, Social Informatics and Telecommunications Engineering.

关键词： Graphics processing unit

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Ab Initio Calculation of the Spectrum and Structure of O16

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Physical Review Letters 2014年第10期112卷 102501-102501页

作者： Evgeny Epelbaum Hermann Krebs Timo A. Lähde Dean Lee Ulf-G. Meißner Gautam Rupak Institut für Theoretische Physik II Ruhr-Universität Bochum D-44870 Bochum Germany Institute for Advanced Simulation Institut für Kernphysik and Jülich Center for Hadron Physics Forschungszentrum Jülich D-52425 Jülich Germany Department of Physics North Carolina State University Raleigh North Carolina 27695 USA Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics Universität Bonn D-53115 Bonn Germany JARA-High Performance Computing Forschungszentrum Jülich D-52425 Jülich Germany Department of Physics and Astronomy Mississippi State University Mississippi State Mississippi 39762 USA

We present ab initio lattice calculations of the low-energy even-parity states of O16 using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.

关键词： Ground state

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Reduction of numerical sensitivities in crash simulations on HPC-computers (HPC-10)

Reduction of numerical sensitivities in crash simulations on...

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15th Results and Review Workshop on high performance computing in Science and Engineering, HLRS 2012

作者： Eck, Christiana Mangold, Oliver Prohl, Raphael Tkachuk, Anton Automotive Simulation Center Stuttgart e.V. Nobelstraße 15 70569 Stuttgart Germany High Performance Computing Center Stuttgart Nobelstraße 19 70569 Stuttgart Germany Steinbeis Center of Innovation Simulation in Technology Obere Steinbeisstr. 43/2 75248 Olbronn-Dürrn Germany Institute of Structural Mechanics Pfaffenwaldring 7 70550 Stuttgart Germany

ISBN: (纸本)9783642333736

For practical application in engineering numerical simulations are required to be reliable and reproducible. Unfortunately crash simulations are highly complex and nonlinear and small changes in the initial state can produce big changes in the results. This is caused partially by physical instabilities and partially by numerical instabilities. Aim of the project is to identify the numerical sensitivities in crash simulations and suggest methods to reduce the scatter of the results. Work has been undertaken to identify sources of sensitivities through parameter studies, to improve existing mathematical formulations, e.g. of contact-impact and material models. Furthermore a tool is developed for generation of code from mathematical descriptions of finite elements with the aim to reduce effort required to make modifications of implementations of FEM models. © Springer-Verlag Berlin Heidelberg 2013.

关键词： Numerical methods

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Optimizing MPI Alltoall communications in multicore clusters

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Jisuanji Yanjiu yu Fazhan/Computer Research and Development 2013年第8期50卷 1744-1754页

作者： Li, Qiang Sun, Ninghui Huo, Zhigang Ma, Jie High Performance Computer Research Center Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China Key Laboratory of Computer System and Architecture Chinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100039 China

MPI Alltoall is an important collective operation. In multicore clusters, many processes run in a node. On the one hand, shared memory can be adopted to optimize Alltoall communications of small messages by leader-based schemes. However, as these schemes adopt a fixed number of leader processes, the optimal performance can't be obtained for all small messages. On the other hand, processes within a node contend for the same network resource. In Alltoall communications of large messages, many synchronization messages are used. Nevertheless, the contention makes their latency increase many times and the synchronization overhead can't be ingored. To solve these problems, two optimizations are presented. For small messages, the PLP method adopts changeable numbers of leader processes. For large messages, the LSS method reduces the number of synchronization messages from 3N to 2√N. The evaluations prove two methods. For small messages, the PLP method always obtains optimal performance. For large messages, the LSS method brings almost constant improvement percentage. The performance is improved by 25% for 32 KB and 64 KB messages.

关键词： Synchronization

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Lattice effective field theory for nuclei from A = 4 to A = 28 31

Lattice effective field theory for nuclei from A = 4 to A = ...

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31st International Symposium on Lattice Field Theory, LATTICE 2013

作者： Lähde, Timo A. Epelbaum, Evgeny Krebs, Hermann Lee, Dean Meißner, Ulf-G. Rupak, Gautam Forschungszentrum Jülich Jülich Center for Hadron Physics Institute for Advanced Simulation JülichD-52425 Germany Institut Für Theoretische Physik II Ruhr-Universität Bochum BochumD-44870 Germany Department of Physics North Carolina State University RaleighNC27695 United States Helmholtz-Institut Für Strahlen- Und Kernphysik and Bethe Center for Theoretical Physics Universität Bonn BonnD-53115 Germany Forschungszentrum Jülich JARA - High Performance Computing JülichD-52425 Germany Department of Physics and Astronomy Mississippi State University MississippiMS39762 United States

We present an overview of the extension of Nuclear Lattice Effective Field Theory simulations to the regime of medium-mass nuclei. We focus on the determination of the ground-state energies of the alpha nuclei 16O, 20... 详细信息

关键词： Ground state

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Viability of Carbon-Based Life as a Function of the Light Quark Mass

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Physical Review Letters 2013年第11期110卷 112502-112502页

作者： Evgeny Epelbaum Hermann Krebs Timo A. Lähde Dean Lee Ulf-G. Meißner Institut für Theoretische Physik II Ruhr-Universität Bochum D-44870 Bochum Germany Institut für Kernphysik Institute for Advanced Simulation and Jülich Center for Hadron Physics Forschungszentrum Jülich D-52425 Jülich Germany Department of Physics North Carolina State University Raleigh North Carolina 27695 USA Helmholtz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics Universität Bonn D-53115 Bonn Germany JARA—High Performance Computing Forschungszentrum Jülich D-52425 Jülich Germany

The Hoyle state plays a crucial role in the helium burning of stars that have reached the red giant stage. The close proximity of this state to the triple-alpha threshold is needed for the production of carbon, oxygen, and other elements necessary for life. We investigate whether this life-essential condition is robust or delicately fine-tuned by measuring its dependence on the fundamental constants of nature, specifically the light quark mass and the strength of the electromagnetic interaction. We show that there exist strong correlations between the alpha-particle binding energy and the various energies relevant to the triple-alpha process. We derive limits on the variation of these fundamental parameters from the requirement that sufficient amounts of carbon and oxygen be generated in stars. We also discuss the implications of our results for an anthropic view of the Universe.

关键词： RED giants RESEARCH STARS HELIUM CARBON QUARKS

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An in-network approximate data gathering algorithm exploiting spatial correlation in wireless sensor networks 12

An in-network approximate data gathering algorithm exploitin...

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27th Annual ACM Symposium on Applied computing, SAC 2012

作者： Huang, Chen-Che Huang, Jiun-Long Yan, Jhih-An Yeh, Lo-Yao Department of Computer Science National Chiao Tung University Hsinchu Taiwan System and Network Technology Division National Center for High-Performance Computing Tainan Taiwan

ISBN: (纸本)9781450308571

Recently, several studies have proposed to utilize spatial correlation of sensor readings and approximate answers to select only a subset of representative nodes for reading reporting in the WSN monitoring applications. Although having achieved substantial energy saving, these studies suffered from high control overhead or did not fully exploit spatial correlation. In this paper, we propose an in-network approximate data gathering algorithm exploiting spatial correlation. The proposed algorithm consists of two phases: in-network clustering phase and reading streaming phase. In the former phase, we present an in-network clustering scheme exploiting spatial correlations of sensor readings as well as cluster readings to further reduce the number of representative nodes. On the other hand, the latter phase employs an adaptive cluster maintenance scheme that ensures the user to obtain the reading answers of desired quality despite changing sensor readings. The experimental results show that the proposed algorithm outperforms prior algorithms in terms of network lifetime and number of representative nodes. © 2012 ACM.

关键词： Energy efficiency

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Interactions of charmed mesons with light pseudoscalar mesons from lattice QCD and implications on the nature of the Ds0*(2317)

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Physical Review D 2013年第1期87卷 014508-014508页

作者： Liuming Liu Kostas Orginos Feng-Kun Guo Christoph Hanhart Ulf-G. Meißner School of Mathematics Trinity College Dublin Dublin Ireland Helmholz-Institut für Strahlen- und Kernphysik and Bethe Center for Theoretical Physics Universität Bonn D-53115 Bonn Germany Department of Physics College of William Williamsburg Virginia 23187-8795 USA Thomas Jefferson National Accelerator Facility Newport News Virginia 23606 USA Institute for Advanced Simulation Institut für Kernphysik and Jülich Center for Hadron Physics Forschungszentrum Jülich D-52425 Jülich Germany Institute for Advanced Simulation Institut für Kernphysik Jülich Center for Hadron Physics and JARA-High Performance Computing Forschungszentrum Jülich D-52425 Jülich Germany

We study the scattering of light pseudoscalar mesons (π,K) off charmed mesons (D,Ds) in full lattice QCD. The S-wave scattering lengths are calculated using Lüscher’s finite volume technique. We use a relativistic formulation for the charm quark. For the light quark, we use domain-wall fermions in the valence sector and improved Kogut-Susskind sea quarks. We calculate the scattering lengths of isospin-3/2 Dπ, Dsπ, DsK, isospin-0 DK¯ and isospin-1 DK¯ channels on the lattice. For the chiral extrapolation, we use a chiral unitary approach to next-to-leading order, which at the same time allows us to give predictions for other channels. It turns out that our results support the interpretation of the Ds0*(2317) as a DK molecule. At the same time, we also update a prediction for the isospin breaking hadronic decay width Γ(Ds0*(2317)→Dsπ) to (133±22) keV.

关键词： QUANTUM chromodynamics QUARKS LIGHT -- Scattering MESONS LATTICE theory RELATIVITY (Physics) HADRONS -- Decay PARTICLES (Nuclear physics) -- Chirality

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From laptops to supercomputers: a single highly scalable code base for spiking neuronal network simulations

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BMC Neuroscience 2013年第1期14卷 1-2页

作者： Susanne Kunkel Abigail Morrison Markus Diesmann Maximilian Schmidt Jochen M Eppler Moritz Helias Hans E Plesser Jun Igarashi Tomoki Fukai Gen Masumoto Shin Ishii Simulation Laboratory Neuroscience - Bernstein Facility Simulation and Database Technology Institute for Advanced Simulation Jülich Aachen Research Alliance Jülich Research Centre Germany Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) Jülich Research Centre and JARA Germany Bernstein Center Freiburg Albert-Ludwig University of Freiburg Germany Institute of Cognitive Neuroscience Faculty of Psychology Ruhr-University Bochum Germany Medical Faculty RWTH University Aachen Germany Laboratory for Neural Circuit Theory RIKEN Brain Science Institute Wako Japan Department of Mathematical Sciences and Technology Norwegian University of Life Sciences Aas Norway High-Performance Computing Team RIKEN Computational Science Research Program Kobe Japan Integrated Systems Biology Laboratory Department of Systems Science Graduate School of Informatics Kyoto University Japan

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Hybrid MPI/StarSs -- A Case Study

Hybrid MPI/StarSs -- A Case Study

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International Symposium on Parallel and Distributed Processing with Applications, ISPA

作者： José Gracia Christoph Niethammer Manuel Hasert Steffen Brinkmann Rainer Keller Colin W. Glass High Performance Computing Center Stuttgart (HLRS) University of Stuttgart Stuttgart Germany German Research School for Simulation Sciences GmbH Aachen Germany

Hybrid parallel programming models combining distributed and shared memory paradigms are well established in high-performance computing. The classical prototype of hybrid programming in HPC is MPI/OpenMP, but many other combinations are being investigated. Recently, the data-dependency driven, task parallel model for shared memory parallelisation named StarSs has been suggested for usage in combination with MPI. In this paper we apply hybrid MPI/StarSs to a Lattice-Boltzmann code. In particular, we present the hybrid programming model, the benefits we expect, the challenges in porting, and finally a comparison of the performance of MPI/StarSs hybrid, MPI/OpenMP hybrid and the original MPI-only versions of the same code.

关键词： Tiles Algorithms Computational modeling Synchronization Arrays Programming Runtime

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