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17th International Conference on Enterprise Information Systems, ICEIS 2015

作者： Awasthi, Abhishek Lässig, Jörg Kramer, Oliver Department of Computer Science University of Applied Sciences Zittau/Görlitz Görlitz Germany Department of Computing Science Carl von Ossietzky University of Oldenburg Oldenburg Germany

ISBN: (纸本)9789897580970

This paper considers the un-restricted case of the Common Due-Date (CDD) problem with controllable processing times. The problem consists of scheduling jobs with controllable processing times on a single machine against a common due-date to minimize the overall earliness/tardiness and the compression penalties of the jobs. The objective of the problem is to find the processing sequence of jobs, the optimal reduction in the processing times of the jobs and their completion times. In this work, we first present and prove an essential property for the controllable processing time CDD problem for the un-restricted case along with an exact linear algorithm for optimizing a given job sequence for a single machine with a run-time complexity of O(n), where n is the number of jobs. Henceforth, we implement our polynomial algorithm in conjunction with a modified Simulated Annealing (SA) algorithm and Threshold Accepting (TA) to obtain the optimal/best processing sequence while comparing the two heuristic approaches, as well. The implementation is carried out on appended CDD benchmark instances provided in the OR-library.

关键词： Simulated annealing

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26th Annual Computational Neuroscience Meeting (CNS*2017) of the Organization for Computational Neuroscience Antwerp, Belgium, July 15-20, 2017

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BMC NEUROscience 2017年第SUPPL 1期18卷 59-59页

作者： [Anonymous] Indiana University Purdue University Indianapolis Indianapolis IN 46032 USA Stark Neurosciences Research Institute Indiana University School of Medicine Indianapolis IN 46032 USA Department of Mathematics East Carolina University Greenville NC 27858 USA Jülich Supercomputing Centre Forschungszentrum Jülich 52425 Jülich Germany Future Systems Swiss National Supercomputing Centre 8092 Zurich Switzerland User Engagement and Support Swiss National Supercomputing Centre 6900 Lugano Switzerland Institut de Neurosciences des Systèmes Aix Marseille Univ 13005 Marseille France Simulation Lab Neuroscience Forschungszentrum Jülich Jülich Germany Department of Experimental Psychology Ghent University 9000 Ghent Belgium Donders Center for Cognitive Neuroimaging Radboud University 6525HR Nijmegen The Netherlands Department of Electrical Computer and Energy Engineering University of Colorado Boulder CO 80309 USA Department of Neurosurgery Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Neurology Johns Hopkins School of Medicine Baltimore MD 21287 USA Department of Otolaryngology Johns Hopkins School of Medicine Baltimore MD 21287 USA INSERM U968 Paris France Sorbonne Universités UPMC University Paris 06 UMR_S 968 Institut de la Vision Paris France CNRS UMR_7210 Paris France Department of Computer Architecture and Technology University of Granada (CITIC) Granada Spain Sorbonne Universités UPMC Univ Paris 06 INSERM CNRS Institut de la Vision Paris France Department of Adaptive Machine Systems Osaka University Osaka Japan Department of Computer Science University of Cergy-Pontoise Cergy-Pontoise France Department of Physics and Astronomy College of Charleston Charleston SC 29424 USA School of Physics Faculty of Science University of Sydney Sydney NSW 2006 Australia Center of Excellence for Integrative Brain Function Australian Research Council Sydney Australia Max Planck Institute for Human Cognitive and Brain Sciences Saxony Lei

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Supporting multiple accelerators in high-level programming models 6

Supporting multiple accelerators in high-level programming m...

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6th International Workshop on Programming Models and Applications for Multicores and Manycores, PMAM 2015

作者： Yan, Yonghong Lin, Pei-Hung Liao, Chunhua De Supinski, Bronis R. Quinlan, Daniel J. Department of Computer Science and Engineering Oakland University United States Center of Applied Scientific Computing Lawrence Livermore National Laboratory United States

ISBN: (纸本)9781450334044

Computational accelerators, such as manycore NVIDIA GPUs, Intel Xeon Phi and FPGAs, are becoming common in work-stations, servers and supercomputers for scientific and engineering applications. Efficiently exploiting the massive parallelism these accelerators provide requires the designs and implementations of productive programming models. In this paper, we explore support of multiple accelerators in high-level programming models. We design novel language extensions to OpenMP to support offloading data and computation regions to multiple accelerators (devices). These extensions allow for distributing data and computation among a list of devices via easy-to-use interfaces, including specifying the distribution of multi-dimensional arrays and declaring shared data regions among accelerators. Computation distribution is realized by partitioning a loop iteration space among accelerators. We implement mechanisms to marshal/unmarshal and to move data of non-contiguous array subregions and shared regions between accelerators without involving CPUs. We design reduction techniques that work across multiple accelerators. Combined compiler and runtime support is designed to manage multiple GPUs using asynchronous operations and threading mechanisms. We implement our solutions for NVIDIA GPUs and demonstrate through example OpenMP codes the effectiveness of our solutions for performance improvement. Copyright © 2015 ACM.

关键词： Iterative methods

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An emergent space for distributed data with hidden internal order through manifold learning

arXiv

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arXiv 2017年

作者： Kemeth, Felix P. Haugland, Sindre W. Dietrich, Felix Bertalan, Tom Höhlein, Kevin Li, Qianxiao Bollt, Erik M. Talmon, Ronen Krischer, Katharina Kevrekidis, Ioannis G. Physik-Department Nonequilibrium Chemical Physics Technische Universität München James-Franck-Str. 1 GarchingD-85748 Germany Institute for Advanced Study Technische Universität München Lichtenbergstr. 2a GarchingD-85748 Germany Department of Chemical and Biological Engineering Princeton University PrincetonNJ08544 United States Department of Chemical and Biomolecular Engineering Department of Applied Mathematics and Statistics Johns Hopkins University JHMI Department of Mechanical Engineering MIT CambridgeMA02139 United States Institute of High Performance Computing 1 Fusionopolis Way #16-16 Connexis North Singapore138632 Singapore Department of Mathematics Department of Electrical and Computer Engineering Clarkson Center for Complex Systems Science Clarkson University PotsdamNY13699-5815 United States Department of Electrical Engineering Technion Israel Institute of Technology Technion City Haifa32000 Israel

Manifold-learning techniques are routinely used in mining complex spatiotemporal data to extract useful, parsimonious data representations/parametrizations;these are, in turn, useful in nonlinear model identification tasks. We focus here on the case of time series data that can ultimately be modelled as a spatially distributed system (e.g. a partial differential equation, PDE), but where we do not know the space in which this PDE should be formulated. Hence, even the spatial coordinates for the distributed system themselves need to be identified - to "emerge from"- the data mining process. We will first validate this "emergent space" reconstruction for time series sampled without space labels in known PDEs;this brings up the issue of observability of physical space from temporal observation data, and the transition from spatially resolved to lumped (order-parameter-based) representations by tuning the scale of the data mining kernels. We will then present actual emergent space "discovery" illustrations. Our illustrative examples include chimera states (states of coexisting coherent and incoherent dynamics), and chaotic as well as quasiperiodic spatiotemporal dynamics, arising in partial differential equations and/or in heterogeneous networks. We also discuss how datadriven "spatial" coordinates can be extracted in ways invariant to the nature of the measuring instrument. Such gauge-invariant data mining can go beyond the fusion of heterogeneous observations of the same system, to the possible matching of apparently different systems. For an older version of this article, including other examples, see https://***/abs/1708.05406. Copyright © 2017, The Authors. All rights reserved.

关键词： Data mining

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Automated generation of SADI web services for clinical intelligence using ruled-based semantic mappings 8

Automated generation of SADI web services for clinical intel...

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8th International Conference on Semantic Web Applications and Tools for Life sciences, SWAT4LS 2015

作者： Al Manir, Mohammad Sadnan Riazanov, Alexandre Boley, Harold Klein, Artjom Baker, Christopher J.O. Department of Computer Science and Applied Statistics University of New Brunswick Saint JohnNB Canada IPSNP Computing Inc Canada Faculty of Computer Science University of New Brunswick FrederictonNB Canada

We present a framework that automates the generation of SADI semantic web services from declarative service descriptions and semantic mappings to relational data. Mappings are specified in a Datalog sublanguage of Positional-Slotted Object-Applicative (PSOA) RuleML. We outline a novel methodology, a system architecture, and a prototype implementation for service generation. A proof-of-concept implementation and preliminary evaluation of the approach was conducted by generating a set of SADI services over a database representing a fragment of a hospital research data warehouse. These automatically generated fully functional services are used to answer simple SPARQL queries. © Copyright 2015 for the individual papers by the papers' authors.

关键词： Data warehouses

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Tensor fem for spectral fractional diffusion

arXiv

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arXiv 2017年

作者： Banjai, Lehel Melenk, Jens M. Nochetto, Ricardo H. Otárola, Enrique Salgado, Abner J. Schwab, Christoph Maxwell Institute for Mathematical Sciences School of Mathematical & Computer Sciences Heriot-Watt University EdinburghEH14 4AS United Kingdom Institut für Analysis und Scientific Computing Technische Universität Wien ViennaA-1040 Austria Department of Mathematics Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Departamento de Matemática Universidad Técnica Federico Santa María Valparaíso Chile Department of Mathematics University of Tennessee KnoxvilleTN37996 United States Seminar for Applied Mathematics ETH Zürich ETH Zentrum HG G57.1 ZürichCH8092 Switzerland

We design and analyze several Finite Element Methods (FEMs) applied to the Caffarelli-Silvestre extension that localizes the fractional powers of symmetric, coercive, linear elliptic operators in bounded domains with Dirichlet boundary conditions. We consider open, bounded, polytopal but not necessarily convex domains Ω ⊂ Rd with d = 1, 2. For the solution to the extension problem, we establish analytic regularity with respect to the extended variable y ∈ (0, ∞). We prove that the solution belongs to countably normed, power–exponentially weighted Bochner spaces of analytic functions with respect to y, taking values in corner-weighted Kondat’ev type Sobolev spaces in Ω. In Ω ⊂ R2, we discretize with continuous, piecewise linear, Lagrangian FEM (P1-FEM) with mesh refinement near corners, and prove that first order convergence rate is attained for compatible data f ∈ H1−s(Ω). We also prove that tensorization of a P1-FEM in Ω with a suitable hp-FEM in the extended variable achieves log-linear complexity with respect to NΩ, the number of degrees of freedom in the domain Ω. In addition, we propose a novel, sparse tensor product FEM based on a multilevel P1FEM in Ω and on a P1-FEM on radical–geometric meshes in the extended variable. We prove that this approach also achieves log-linear complexity with respect to NΩ. Finally, under the stronger assumption that the data is analytic in Ω, and without compatibility at ∂Ω, we establish exponential rates of convergence of hp-FEM for spectral, fractional diffusion operators in energy norm. This is achieved by a combined tensor product hp-FEM for the Caffarelli-Silvestre extension in the truncated cylinder Ω × (0, Y) with anisotropic geometric meshes that are refined towards ∂Ω. We also report numerical experiments for model problems which confirm the theoretical results. We indicate several extensions and generalizations of the proposed methods to other problem classes and to other boundary conditions on ∂Ω. Copyright © 2017, The

关键词： Anisotropy

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Commissioning of the J-PET detector for studies of decays of positronium atoms

arXiv

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arXiv 2017年

作者： Czerwinski, E. Dulski, K. Bialas, P. Curceanu, C. Gajos, A. Glowacz, B. Gorgol, M. Hiesmayr, B.C. Jasinska, B. Kisielewska, D. Korcyl, G. Kowalski, P. Kozik, T. Krawczyk, N. Krzemien, W. Kubicz, E. Mohammed, M. Niedzwiecki, Sz. Palka, M. Pawlik-Niedzwiecka, M. Raczynski, L. Rudy, Z. Sharma, N.G. Sharma, S. Shopa, R.Y. Silarski, M. Skurzok, M. Wieczorek, A. Wislicki, W. Zgardzinska, B. Zielinski, M. Moskal, P. Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University Cracow30-348 Poland INFN Laboratori Nazionali di Frascati CP 13 Via E. Fermi 40 FrascatiI-00044 Italy Department of Nuclear Methods Institute of Physics Maria Curie-Sklodowska University Lublin20-031 Poland Faculty of Physics University of Vienna Boltzmanngasse 5 Vienna1090 Austria Swierk Computing Center National Centre for Nuclear Research Otwock-Swierk05-400 Poland High Energy Physics Division National Center for Nuclear Research Otwock-Swierk05-400 Poland Department of Physics College of Education for Pure Sciences University of Mosul Mosul Iraq

The Jagiellonian Positron Emission Tomograph (J-PET) is a detector for medical imaging of the whole human body as well as for physics studies involving detection of electron-positron annihilation into photons. J-PET has high angular and time resolution and allows for measurement of spin of the positronium and the momenta and polarization vectors of annihilation quanta. In this article, we present the potential of the J-PET system for background rejection in the decays of positronium atoms. Copyright © 2017, The Authors. All rights reserved.

关键词： Positrons

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Enhancing domain specific language implementations through ontology 5

Enhancing domain specific language implementations through o...

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5th International Workshop on Domain-Specific Languages and High-Level Frameworks for High Performance computing, WOLFHPC 2015

作者： Liao, Chunhua Lin, Pei-Hung Quinlan, Daniel J. Zhao, Yue Shen, Xipeng Lawrence Livermore National Laboratory Center for Applied Scientific Computing United States Computer Science Department North Carolina State University United States

ISBN: (纸本)9781450340168

Domain specific languages (DSLs) offer an attractive path to program large-scale, heterogeneous parallel computers since application developers can leverage high-level annotations defined by DSLs to efficiently express algorithms without being distracted by low-level hardware details. However, performance of DSL programs heavily relies on how well a DSL implementation, including compilers and runtime systems, can exploit knowledge across multiple layers of software/ hardware environments for optimizations. The knowledge ranges from domain assumptions, high-level DSL semantics, to low-level hardware features. Traditionally, such knowledge is either implicitly assumed or represented using ad-hoc approaches, including narrative text, source-level annotations, or customized software and hardware specifications in high performance computing (HPC). The lack of a formal, uniform, extensible, reusable and scalable knowledge management approach is becoming a major obstacle to efficient DSLs implementations targeting fast-changing parallel architectures. In this paper, we present a novel DSL implementation paradigm using an ontology-based knowledge base to formally and uniformly exploit the knowledge needed for optimizations. An ontology is a formal and explicit knowledge representation to describe concepts, properties, and individuals in a domain. During the past decades, a wide range of ontology standards and tools have been developed to help users capture, share, utilize and reason domain knowledge. Using modern ontology techniques, we design a knowledge base capturing concepts and properties of a problem domain, DSL programs, and hardware architectures. Compiler interfaces are also defined to allow interactions with the knowledge base to assist program analysis, optimization and code generation. Our preliminary evaluation using stencil computation shows the feasibility and benefits of our approach. © 2015 ACM.

关键词： Knowledge representation

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A proposal to OpenMP for addressing the CPU oversubscription challenge

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in computer science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2016年 9903 LNCS卷 187-202页

作者： Yan, Yonghong Hammond, Jeff R. Liao, Chunhua Eichenberger, Alexandre E. Department of Computer Science and Engineering Oakland University Rochester United States Parallel Computing Lab Intel Corp. Santa Clara United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory Livermore United States Thomas J. Watson Research Center IBM Yorktown Heights United States OpenMP Interoperability Language Subcommittee Houston United States

ISBN: (纸本)9783319455495

OpenMP has become a successful programming model for developing multi-threaded applications. However, there are still some challenges in terms of OpenMP’s interoperability within itself and with other parallel programming APIs. In this paper, we explore typical use cases that expose OpenMP’s interoperability challenges and report our proposed solutions for addressing the resource oversubscription issue as the efforts by the OpenMP Interoperability language subcommittee. The solutions include OpenMP runtime routines for changing the wait policies, which include ACTIVE(SPIN BUSY or SPIN PAUSE), PASSIVE (SPIN YIELD or SUSPEND), of idling threads for improved resource management, and routines for supporting contributing OpenMP threads to other thread libraries or tasks. Our initial implementations are being done by extending two OpenMP runtime libraries, Intel OpenMP (IOMP) and GNU OpenMP (GOMP). The evaluation results demonstrate the effectiveness of the proposed approach to address the CPU oversubscription challenge and detailed analysis provide heuristics for selecting an optimal wait policy according to the oversubscription ratios. © Springer International Publishing Switzerland 2016.

关键词： Interoperability

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Opposing Effects of Multivalent Ions on the Flexibility of DNA and RNA

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Physical Review Letters 2016年第2期117卷 028101-028101页

作者： Aleksander V. Drozdetski Igor S. Tolokh Lois Pollack Nathan Baker Alexey V. Onufriev Department of Physics Virginia Tech Blacksburg Virginia 24061 USA Department of Computer Science Virginia Tech Blacksburg Virginia 24061 USA School of Applied and Engineering Physics Cornell University Ithaca New York 14853-3501 USA Advanced Computing Mathematics and Data Division Pacific Northwest National Laboratory Richland Washington 99352 USA Division of Applied Mathematics Brown University Providence Rhode Island 02912 USA Center for Soft Matter and Biological Physics Virginia Tech Blacksburg Virginia 24061 USA

Increasing the concentration of counterions (salt) is known to reduce the bending persistence length of DNA. Here we use atomistic molecular dynamics simulations to predict that multivalent counterions have the opposite effect on double-stranded RNA, increasing its bending rigidity by at least 30%. This counterintuitive effect is observed for various tri- and tetravalent ions alike, and is robust to methodological details and the RNA sequence. In contrast to DNA, multivalent counterions bind inside the RNA major groove, causing significant contraction of the molecule along its helical axis—as a result, its further deformation due to bending becomes energetically more expensive compared to bending without bound multivalent ions. Thus, the relationship between mechanical properties of a charged polymer and its ionic atmosphere may be richer than previously thought.

关键词： Bending Persistence length RNA structure

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