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arXiv 2019年

作者： Arenas, Diego Atkins, Jon Austin, Claire Beavan, David Egea, Alvaro Cabrejas Carlysle-Davies, Steven Carter, Ian Clarke, Rob Cunningham, James Doel, Tom Forrest, Oliver Gabasova, Evelina Geddes, James Hetherington, James Jersakova, Radka Kiraly, Franz Lawrence, Catherine Manser, Jules O'Reilly, Martin T. Robinson, James Sherwood-Taylor, Helen Tierney, Serena Vallejos, Catalina A. Vollmer, Sebastian Whitaker, Kirstie University of St Andrews KY16 9SX United Kingdom Alan Turing Institute 96 Euston Rd Kings Cross LondonNW1 2DB United Kingdom MRC Human Genetics Unit Institute of Genetics & Molecular Medicine University of Edinburgh Western General Hospital Crewe Road EdinburghEH4 2XU United Kingdom Department of Psychiatry University of Cambridge Herchel Smith Buidling for Brain & Mind Sciences Forvie Site Robinson Way CambridgeCB2 0SZ United Kingdom VWV LLP 24 King William Street LondonEC4R 9AT United Kingdom Division of Informatics Imaging and Data Sciences School of Health Sciences Faculty of Biology Medicine and Health University of Manchester Oxford Road ManchesterM13 9PL United Kingdom Warwick Mathematics Institute Department of Statistics University of Warwick CV4 7AL United Kingdom MathSys Centre for Doctoral Training Warwick Mathematics Institute University of Warwick CV4 7AL United Kingdom British Library 96 Euston Road LondonNW1 2DB United Kingdom Edinburgh Parallel Computing Centre University of Edinburgh Bayes Centre 47 Potterrow EdinburghEH8 9BT United Kingdom

We present a policy and process framework for secure environments for productive data science research projects at scale, by combining prevailing data security threat and risk profiles into five sensitivity tiers, and, at each tier, specifying recommended policies for data classification, data ingress, software ingress, data egress, user access, user device control, and analysis environments. By presenting design patterns for security choices for each tier, and using software defined infrastructure so that a different, independent, secure research environment can be instantiated for each project appropriate to its classification, we hope to maximise researcher productivity and minimise risk, allowing research organisations to operate with confidence. Copyright © 2019, The Authors. All rights reserved.

关键词： Risk assessment

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Verification of Electromagnetic Physics Models for parallel computing Architectures in the GeantV Project

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Journal of Physics: Conference Series 2017年第4期898卷

作者： G Amadio J Apostolakis M Bandieramonte S P Behera R Brun P Canal F Carminati G Cosmo L Duhem D Elvira G Folger A Gheata M Gheata I Goulas F Hariri S Y Jun D Konstantinov H Kumawat V Ivantchenko G Lima T Nikitina M Novak W Pokorski A Ribon R Seghal O Shadura S Vallecorsa S Wenzel Parallel Computing Center at Sao Paulo State University (UNESP) Sao Paulo Brazil CERN Route de Meyrin Meyrin Switzerland Bhabha Atomic Research Centre (BARC) Mumbai India Fermilab MS234 P.O. Box 500 Batavia IL 60510 USA Intel Corporation Santa Clara CA 95052 USA Institute of Space Sciences Bucharest-Magurele Romania

An intensive R&D and programming effort is required to accomplish new challenges posed by future experimental high-energy particle physics (HEP) programs. The GeantV project aims to narrow the gap between the performance of the existing HEP detector simulation software and the ideal performance achievable, exploiting latest advances in computing technology. The project has developed a particle detector simulation prototype capable of transporting in parallel particles in complex geometries exploiting instruction level microparallelism (SIMD and SIMT), task-level parallelism (multithreading) and high-level parallelism (MPI), leveraging both the multi-core and the many-core opportunities. We present preliminary verification results concerning the electromagnetic (EM) physics models developed for parallel computing architectures within the GeantV project. In order to exploit the potential of vectorization and accelerators and to make the physics model effectively parallelizable, advanced sampling techniques have been implemented and tested. In this paper we introduce a set of automated statistical tests in order to verify the vectorized models by checking their consistency with the corresponding Geant4 models and to validate them against experimental data.

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Multi-scale CAFE Framework for Simulating Fracture in Heterogeneous Materials Implemented in Fortran Co-arrays and MPI

Multi-scale CAFE Framework for Simulating Fracture in Hetero...

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PGAS Applications Workshop (PAW)

作者： Anton Shterenlikht Lee Margetts Jose D. Arregui-Mena Luis Cebamanos Mech Eng Dept The University of Bristol Bristol UK School of Mechanical The University of Manchester Manchester UK Edinburgh Parallel Computing Centre (EPCC) The University of Edinburgh Edinburgh UK

ISBN: (纸本)9781509052158

Fortran coarrays have been used as an extension to the standard for over 20 years, mostly on Cray systems. Their appeal to users increased substantially when they were standardised in 2010. In this work we show that coarrays offer simple and intuitive data structures for 3D cellular automata (CA) modelling of material microstructures. We show how coarrays can be used together with an MPI finite element (FE) library to create a two-way concurrent hierarchical and scalable multi-scale CAFE deformation and fracture framework. Design of a coarray cellular automata microstructure evolution library CGPACK is described. A highly portable MPI FE library ParaFEM was used in this work. We show that independently CGPACK and ParaFEM programs can scale up well into tens of thousands of cores. Strong scaling of a hybrid ParaFEM/CGPACK MPI/coarray multi-scale framework was measured on an important solid mechanics practical example of a fracture of a steel round bar under tension. That program did not scale beyond 7 thousand cores. Excessive synchronisation might be one contributing factor to relatively poor scaling. Therefore we conclude with a comparative analysis of synchronisation requirements in MPI and coarray programs. Specific challenges of synchronising a coarray library are discussed.

关键词： Iron Microstructure Three-dimensional displays Finite element analysis Libraries Electronic mail Automata

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Pulsar Searches with the SKA

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Proceedings of the International Astronomical Union 2017年第S337期13卷 171-174页

作者： Levin, L. Armour, W. Baffa, C. Barr, E. Cooper, S. Eatough, R. Ensor, A. Giani, E. Karastergiou, A. Karuppusamy, R. Keith, M. Kramer, M. Lyon, R. Mackintosh, M. Mickaliger, M. Van Nieuwpoort, R Pearson, M. Prabu, T. Roy, J. Sinnen, O. Spitler, L. Spreeuw, H. Stappers, B.W. Van Straten, W. Williams, C. Wang, H. Wiesner, K. Jodrell Bank Centre for Astrophysics University of Manchester Oxford Road Manchester M13 9PL United Kingdom University of Oxford Denys Wilkinson Building Keble Road Oxford OX1 3RH United Kingdom INAF Osservatorio Astrofisico di Arcetri Largo E. Fermi 5 Firenze 50125 Italy Max-Planck-Institut fur Radioastronomie Auf dem Hügel 69 Bonn D-53121 Germany Institute for Radio Astronomy and Space Research Auckland University of Technology Private Bag 92006 Auckland 1142 New Zealand Science and Technology Facilities Council Polaris House North Star Avenue Swindon SN2 1SZ United Kingdom Netherlands Institute for Radio Astronomy (ASTRON) Postbus 2 Dwingeloo NL-7990 AA Netherlands NCRA-TIFR Pune University Campus Pune 411007 India Parallel and Reconfigurable Computing (PARC) Lab University of Auckland Private Bag 92019 Auckland 1142 New Zealand

The Square Kilometre Array will be an amazing instrument for pulsar astronomy. While the full SKA will be sensitive enough to detect all pulsars in the Galaxy visible from Earth, already with SKA1, pulsar searches will discover enough pulsars to increase the currently known population by a factor of four, no doubt including a range of amazing unknown sources. Real time processing is needed to deal with the 60 PB of pulsar search data collected per day, using a signal processing pipeline required to perform more than 10 POps. Here we present the suggested design of the pulsar search engine for the SKA and discuss challenges and solutions to the pulsar search venture. © 2018 International Astronomical Union.

关键词： (stars:) pulsars: general methods: data analysis telescopes

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Development of cloud software services for computational analysis of blood flows

Development of cloud software services for computational ana...

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作者： Kaceniauskas, A. Pacevic, R. Staškuniene, M. Starikovicius, V. Davidavicius, G. Laboratory of Parallel Computing Vilnius Gediminas Technical University Lithuania Centre of Cardiology and Angiology Vilnius University Hospital Santariškiu Klinikos Lithuania

This paper presents the development of the cloud software services for computational analysis of blood flows on a private university cloud. The main focus is on the software service level built on the top of the computational platform provided. Moreover, user friendly management tools have been developed by using the Apache jclouds API to enhance the management of OpenStack cloud infrastructure and to increase the accessibility of engineering software. The blood flow through an aortic valve is considered as a pilot application of the private cloud infrastructure. The investigated flows can be described using numerical models based on viscous incompressible Navier-Stokes equations. The modelling software environment based on ANSYS Fluent is developed as a software service (SaaS) for the numerical analysis of low flow, low pressure gradient aortic stenosis. The performance of the developed cloud infrastructure has been assessed testing CPU, memory IO, disk IO, network and the developed software service for computations of blood flow through an aortic valve. The results obtained have been compared with the performance obtained using the native hardware. © Civil-Comp Press, 2015.

关键词： Navier Stokes equations

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Stochastic optimization of GeantV code by use of genetic algorithms

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Journal of Physics: Conference Series 2017年第4期898卷

作者： G. Amadio J. Apostolakis M. Bandieramonte S.P. Behera R. Brun P. Canal F. Carminati G. Cosmo L. Duhem D. Elvira G. Folger A. Gheata M. Gheata I. Goulas F. Hariri S.Y. Jun D. Konstantinov H. Kumawat V. Ivantchenko G. Lima T. Nikitina M. Novak W. Pokorski A. Ribon R. Seghal O. Shadura S. Vallecorsa S. Wenzel Parallel Computing Center at Sao Paulo State University (UNESP) Sao Paulo Brazil CERN Route de Meyrin Meyrin Switzerland Bhabha Atomic Research Centre (BARC) Mumbai India Fermilab MS234 P.O. Box 500 Batavia IL 60510 USA Intel Corporation Santa Clara CA 95052 USA Institute of Space Sciences Bucharest-Magurele Romania

GeantV is a complex system based on the interaction of different modules needed for detector simulation, which include transport of particles in fields, physics models simulating their interactions with matter and a geometrical modeler library for describing the detector and locating the particles and computing the path length to the current volume boundary. The GeantV project is recasting the classical simulation approach to get maximum benefit from SIMD/MIMD computational architectures and highly massive parallel systems. This involves finding the appropriate balance between several aspects influencing computational performance (floating-point performance, usage of off-chip memory bandwidth, specification of cache hierarchy, etc.) and handling a large number of program parameters that have to be optimized to achieve the best simulation throughput. This optimization task can be treated as a black-box optimization problem, which requires searching the optimum set of parameters using only point-wise function evaluations. The goal of this study is to provide a mechanism for optimizing complex systems (high energy physics particle transport simulations) with the help of genetic algorithms and evolution strategies as tuning procedures for massive parallel simulations. One of the described approaches is based on introducing a specific multivariate analysis operator that could be used in case of resource expensive or time consuming evaluations of fitness functions, in order to speed-up the convergence of the black-box optimization problem.

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Performance of GeantV EM Physics Models

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Journal of Physics: Conference Series 2017年第7期898卷

作者： G Amadio A Ananya J Apostolakis A Aurora M Bandieramonte A Bhattacharyya C Bianchini R Brun P Canal F Carminati G Cosmo L Duhem D Elvira G Folger A Gheata M Gheata I Goulas R Iope S Y Jun G Lima A Mohanty T Nikitina M Novak W Pokorski A Ribon R Seghal O Shadura S Vallecorsa S Wenzel Y Zhang Parallel Computing Center at São Paulo State University (UNESP) São Paulo Brazil CERN EP Department Geneva Switzerland Bhabha Atomic Research Centre (BARC) Mumbai India Mackenzie Presbyterian University São Paulo Brazil Fermilab† MS234 P.O. Box 500 Batavia IL 60510 USA Intel Corporation Santa Clara CA 95052 USA Institute of Space Sciences Bucharest-Magurele Romania

The recent progress in parallel hardware architectures with deeper vector pipelines or many-cores technologies brings opportunities for HEP experiments to take advantage of SIMD and SIMT computing models. Launched in 2013, the GeantV project studies performance gains in propagating multiple particles in parallel, improving instruction throughput and data locality in HEP event simulation on modern parallel hardware architecture. Due to the complexity of geometry description and physics algorithms of a typical HEP application, performance analysis is indispensable in identifying factors limiting parallel execution. In this report, we will present design considerations and preliminary computing performance of GeantV physics models on coprocessors (Intel Xeon Phi and NVidia GPUs) as well as on mainstream CPUs.

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Cograph editing: Merging modules is equivalent to editing P4s

arXiv

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arXiv 2017年

作者： Fritz, Adrian Hellmuth, Marc Wieseke, Nicolas Stadler, Peter F. Computational Biology of Infection Research Helmholtz Centre for Infection Research Inhoffenstraße 7 BraunschweigD-38124 Germany University of Greifswald Dpt. of Mathematics and Computer Science Walther- Rathenau-Strasse 47 GreifswaldD-17487 Germany Saarland University Center for Bioinformatics Building e 2.1 P.O. Box 151150 SaarbrückenD-66041 Germany Parallel Computing and Complex Systems Group Department of Computer Science University of Leipzig Augustusplatz 10 LeipzigD-04109 Germany Bioinformatics Group Department of Computer Science Interdisciplinary Center of Bioinformatics University of Leipzig Härtelstraße 16-18 LeipzigD-04107 Germany Max-Planck-Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Inst. F. Theoretical Chemistry University of Vienna Währingerstraße 17 WienA-1090 Austria Santa Fe Institute 1399 Hyde Park Rd. Santa FeNM87501 United States

The modular decomposition of a graph G = (V;E) does not contain prime modules if and only if G is a cograph, that is, if no quadruple of vertices induces a simple connected path P4. The cograph editing problem consists in inserting into and deleting from G a set F of edges so that H = (V,EΔF) is a cograph and |F| is minimum. This NP-hard combinatorial optimization problem has recently found applications, e.g., in the context of phylogenetics. Efficient heuristics are hence of practical importance. The simple characterization of cographs in terms of their modular decomposition suggests that instead of editing G one could operate directly on the modular decomposition. We show here that editing the induced P4s is equivalent to resolving prime modules by means of a suitable defined merge operation on the submodules. Moreover, we characterize so-called module-preserving edit sets and demonstrate that optimal pairwise sequences of module-preserving edit sets exist for every non-cograph. This eventually leads to an exact algorithm for the cograph editing problem. In addition, we provide two heuristics with time complexity O(|V|3), resp., O(|V|2). Copyright © 2017, The Authors. All rights reserved.

关键词： Graph theory

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Electromagnetic Physics Models for parallel computing Architectures

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Journal of Physics: Conference Series 2016年第1期762卷

作者： G Amadio A Ananya J Apostolakis A Aurora M Bandieramonte A Bhattacharyya C Bianchini R Brun P Canal F Carminati L Duhem D Elvira A Gheata M Gheata I Goulas R Iope S Y Jun G Lima A Mohanty T Nikitina M Novak W Pokorski A Ribon R Seghal O Shadura S Vallecorsa S Wenzel Y Zhang Parallel Computing Center at São Paulo State University (UNESP) São Paulo Brazil CERN EP Department Geneva Switzerland Bhabha Atomic Research Centre (BARC) Mumbai India Mackenzie Presbyterian University São Paulo Brazil Fermilab MS234 P.O. Box 500 Batavia IL 60510 USA Intel Corporation Santa Clara CA 95052 USA Institute of Space Sciences Bucharest-Magurele Romania

The recent emergence of hardware architectures characterized by many-core or accelerated processors has opened new opportunities for concurrent programming models taking advantage of both SIMD and SIMT architectures. GeantV, a next generation detector simulation, has been designed to exploit both the vector capability of mainstream CPUs and multi-threading capabilities of coprocessors including NVidia GPUs and Intel Xeon Phi. The characteristics of these architectures are very different in terms of the vectorization depth and type of parallelization needed to achieve optimal performance. In this paper we describe implementation of electromagnetic physics models developed for parallel computing architectures as a part of the GeantV project. Results of preliminary performance evaluation and physics validation are presented as well.

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Modular physical modeling synthesis environments on GPU 40

Modular physical modeling synthesis environments on GPU

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40th International Computer Music Conference, ICMC 2014, Joint with the 11th Sound and Music computing Conference, SMC 2014 - Music Technology Meets Philosophy: From Digital Echos to Virtual Ethos

作者： Bilbao, Stefan Torin, Alberto Graham, Paul Perry, James Delap, Gordon Acoustics and Audio Group University of Edinburgh United Kingdom Edinburgh Parallel Computing Centre University of Edinburgh United Kingdom Department of Music NUI Maynooth Ireland

ISBN: (纸本)9789604661374

Physical modeling synthesis is a powerful means of access to a wide variety of synthetic sounds of an acoustic character-one longstanding design principle underlying such methods has been, and continues to be modularity, or the decomposition of a complex instrument into simpler building blocks. In this paper, various modular physical modeling design environments, based on the use of time stepping methods such as finite difference time domain methods are described, with an emphasis on the underlying computational behaviour of such methods, both in the run-time loop and in precomputation. As such methods are computationally intensive, additional emphasis is placed on issues surrounding parallelisation, and implementation in highly parallel hardware such as graphics processing units. This paper is paired with a recently completed multichannel piece, and the composer's perspective on working with such environments is also addressed. Copyright: © 2014 Stefan Bilbao and Alberto Torin et al.

关键词： Graphics processing unit

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