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arXiv 2021年

作者： Abdelfattah, Ahmad Barra, Valeria Beams, Natalie Bleile, Ryan Brown, Jed Camier, Jean-Sylvain Carson, Robert Chalmers, Noel Dobrev, Veselin Dudouit, Yohann Fischer, Paul Karakus, Ali Kerkemeier, Stefan Kolev, Tzanio Lan, Yu-Hsiang Merzari, Elia Min, Misun Phillips, Malachi Rathnayake, Thilina Rieben, Robert Stitt, Thomas Tomboulides, Ananias Tomov, Stanimire Tomov, Vladimir Vargas, Arturo Warburton, Tim Weiss, Kenneth Center for Applied Scientific Computing Lawrence Livermore National Laboratory LivermoreCA94550 United States Mathematics and Computer Science Argonne National Laboratory LemontIL60439 United States Department of Computer Science University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Innovative Computing Laboratory University of Tennessee KnoxvilleTN37996 United States Department of Computer Science University of Colorado BoulderCO80309 United States Department of Mathematics Virginia Tech BlacksburgVA24061 United States AMD Research Advanced Micro Devices Inc. AustinTX78735 United States Weapons and Complex Integration Lawrence Livermore National Laboratory LivermoreCA94550 United States Computational Engineering Division Lawrence Livermore National Laboratory LivermoreCA94550 United States Department of Nuclear Engineering Penn State PA16802 United States Department of Mechanical Engineering Aristotle University of Thessaloniki 54124 Greece Mechanical Engineering Department Middle East Technical University Ankara06800 Turkey

In this paper we describe the research and development activities in the Center for Efficient Exascale Dis-cretization within the US Exascale computing Project, targeting state-of-the-art high-order finite-element algorithms for high-order applications on GPU-accelerated platforms. We discuss the GPU developments in several components of the CEED software stack, including the libCEED, MAGMA, MFEM, libParanumal, and Nek projects. We report performance and capability improvements in several CEED-enabled applications on both NVIDIA and AMD GPU systems. © 2021, CC BY-NC-ND.

关键词： Finite element method

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Efficient exascale discretizations: High-order finite element methods

arXiv

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arXiv 2021年

作者： Kolev, Tzanio Fischer, Paul Min, Misun Dongarra, Jack Brown, Jed Dobrev, Veselin Warburton, Tim Tomov, Stanimire Shephard, Mark S. Abdelfattah, Ahmad Barra, Valeria Beams, Natalie Camier, Jean-Sylvain Chalmers, Noel Dudouit, Yohann Karakus, Ali Karlin, Ian Kerkemeier, Stefan Lan, Yu-Hsiang Medina, David Merzari, Elia Obabko, Aleksandr Pazner, Will Rathnayake, Thilina Smith, Cameron W. Spies, Lukas Swirydowicz, Kasia Thompson, Jeremy Tomboulides, Ananias Tomov, Vladimir Center for Applied Scientific Computing Lawrence Livermore National Laboratory LivermoreCA94550 United States Mathematics and Computer Science Argonne National Laboratory LemontIL60439 United States Department of Computer Science University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Mechanical Science and Engineering University of Illinois at Urbana-Champaign UrbanaIL61801 United States Innovative Computing Laboratory University of Tennessee KnoxvilleTN37996 United States Department of Computer Science University of Colorado BoulderCO80309 United States Scientific Computation Research Center Rensselaer Polytechnic Institute TroyNY12180 United States Department of Mathematics Virginia Tech BlacksburgVA24061 United States AMD Research AustinTX78735 United States Mechanical Engineering Department Middle East Technical University Ankara06800 Turkey Occalytics LLC WeehawkenNJ07086 United States Department of Nuclear Engineering Penn StatePA16802 United States Pacific Northwest National Laboratory WA99352 United States

Efficient exploitation of exascale architectures requires rethinking of the numerical algorithms used in many large-scale applications. These architectures favor algorithms that expose ultra fine-grain parallelism and maximize the ratio of floating point operations to energy intensive data movement. One of the few viable approaches to achieve high efficiency in the area of PDE discretizations on unstructured grids is to use matrix-free/partially-assembled high-order finite element methods, since these methods can increase the accuracy and/or lower the computational time due to reduced data motion. In this paper we provide an overview of the research and development activities in the Center for Efficient Exascale Discretizations (CEED), a co-design center in the Exascale computing Project that is focused on the development of next-generation discretization software and algorithms to enable a wide range of finite element applications to run efficiently on future hardware. CEED is a research partnership involving more than 30 computational scientists from two US national labs and five universities, including members of the Nek5000, MFEM, MAGMA and PETSc projects. We discuss the CEED co-design activities based on targeted benchmarks, miniapps and discretization libraries and our work on performance optimizations for large-scale GPU architectures. We also provide a broad overview of research and development activities in areas such as unstructured adaptive mesh refinement algorithms, matrix-free linear solvers, high-order data visualization, and list examples of collaborations with several ECP and external applications. Copyright © 2021, The Authors. All rights reserved.

关键词： Data visualization

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Lethe-DEM: An open-source parallel discrete element solver with load balancing

arXiv

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arXiv 2021年

作者： Golshan, Shahab Munch, Peter Gassmöller, Rene Kronbichler, Martin Blaisa, Bruno Department of Chemical Engineering École Polytechique de Montréal PO Box 6079 Stn Centre-Ville MontréalQCH3C 3A7 Canada Continuum Simulations Institute of Material Systems Modeling Helmholtz-Zentrum Hereon GmbH Germany Max-Planck-Str. 1 Geesthacht21502 Germany Institute for Computational Mechanics Technical University of Munich Boltzmannstr. 15 Garching85748 Germany Department of Geological Sciences University of Florida GainesvilleFL United States Division of Scientific Computing Department of Information Technology Uppsala University Box 337 Uppsala75105 Sweden

Approximately 75% of the raw material and 50% of the products in the chemical industry are granular materials. The Discrete Element Method (DEM) provides detailed insights of phenomena at particle scale and it is therefore often used for modeling granular materials. However, because DEM tracks the motion and contact of individual particles separately, its computational cost increases non-linearly O(np log(np)) - O(n2p) depending on the algorithm) with the number of particles (np). In this article, we introduce a new open-source parallel DEM software with load balancing: Lethe-DEM. Lethe-DEM, a module of Lethe, consists of solvers for two-dimensional and three-dimensional DEM simulations. Load-balancing allows Lethe-DEM to significantly increase the parallel efficiency by ≈ 25 − 70% depending on the granular simulation. We explain the fundamental modules of Lethe-DEM, its software architecture, and the governing equations. Furthermore, we verify Lethe-DEM with several tests including analytical solutions and comparison with other software. Comparisons with experiments in a flat-bottomed silo, wedge-shaped silo, and rotating drum validate Lethe-DEM. We investigate the strong and weak scaling of Lethe-DEM with 1 ≤ nc ≤ 192 and 32 ≤ nc ≤ 320 processes, respectively, with and without load-balancing. The strong-scaling analysis is performed on the wedge-shaped silo and rotating drum simulations, while for the weak-scaling analysis, we use a dam break simulation. The best scalability of Lethe-DEM is obtained in the range of 5000 ≤ np/nc ≤ 15 000. Finally, we demonstrate that large scale simulations can be carried out with Lethe-DEM using the simulation of a three-dimensional cylindrical silo with np = 4.3 × 106 on 320 cores. Copyright © 2021, The Authors. All rights reserved.

关键词： Finite difference method

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High-order partitioned spectral deferred correction solvers for multiphysics problems

arXiv

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arXiv 2019年

作者： Huang, Daniel Z. Pazner, Will Persson, Per-Olof Zahr, Matthew J. Institute for Computational and Mathematical Engineering Stanford University United States Center for Applied Scientific Computing Lawrence Livermore National Laboratory United States Department of Mathematics University of California Berkeley United States Department of Aerospace and Mechanical Engineering University of Notre Dame United States

We present an arbitrarily high-order, conditionally stable, partitioned spectral deferred correction (SDC) method for solving multiphysics problems using a sequence of pre-existing single-physics solvers. This method extends the work in [1, 2], which used implicit-explicit Runge-Kutta methods (IMEX) to build high-order, partitioned multiphysics solvers. We consider a generic multiphysics problem modeled as a system of coupled ordinary differential equations (ODEs), coupled through coupling terms that can depend on the state of each subsystem;therefore the method applies to both a semi-discretized system of partial differential equations (PDEs) or problems naturally modeled as coupled systems of ODEs. The sufficient conditions to build arbitrarily high-order partitioned SDC schemes are derived. Based on these conditions, various of partitioned SDC schemes are designed. The stability of the first-order partitioned SDC scheme is analyzed in detail on a coupled, linear model problem. We show that the scheme is conditionally stable, and under conditions on the coupling strength, the scheme can be unconditionally stable. We demonstrate the performance of the proposed partitioned solvers on several classes of multiphysics problems including a simple linear system of ODEs, advection-diffusion-reaction systems, and fluid-structure interaction problems with both incompressible and compressible flows, where we verify the design order of the SDC schemes and study various stability properties. We also directly compare the accuracy, stability, and cost of the proposed partitioned SDC solver with the partitioned IMEX method in [1, 2] on this suite of test problems. The results suggest that the high-order partitioned SDC solvers are more robust than the partitioned IMEX solvers for the numerical examples considered in this work, while the IMEX methods require fewer implicit solves. Copyright © 2019, The Authors. All rights reserved.

关键词： Stability

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Deep nitsche method: Deep ritz method with essential boundary conditions

arXiv

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arXiv 2019年

作者： Liao, Yulei Ming, Pingbing LSEC Institute of Computational Mathematics and Scientific/Engineering Computing AMSS Chinese Academy of Sciences No. 55 East Road Zhong-Guan-Cun Beijing100190 China School of Mathematical Sciences University of Chinese Academy of Sciences Beijing100049 China

We propose a new method to deal with the essential boundary conditions encountered in the deep learning-based numerical solvers for partial differential equations. The trial functions representing by deep neural networks are non-interpolatory, which makes the enforcement of the essential boundary conditions a nontrivial matter. Our method resorts to Nitsche's variational formulation to deal with this difficulty, which is consistent, and does not require significant extra computational costs. We prove the error estimate in the energy norm and illustrate the method on several representative problems posed in at most 100 dimension. Copyright © 2019, The Authors. All rights reserved.

关键词： Deep neural networks

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Global Sensitivity and Domain-Selective Testing for Functional-Valued Responses: An Application to Climate Economy Models

arXiv

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arXiv 2020年

作者： Fontana, Matteo Tavoni, Massimo Vantini, Simone Department of Management Economics and Industrial Engineering Politecnico di Milano Milan Italy RFF-CMCC European Institute on Economics and the Environment Centro Euro-Mediterraneo sui Cambiamenti Climatici Milan Italy MOX - Modelling and Scientific Computing Laboratory Department of Mathematics Politecnico di Milano Italy Royal Holloway University of London United Kingdom

Understanding the dynamics and evolution of climate change and associated uncertainties is key for designing robust policy actions. Computer models are key tools in this scientific effort, which have now reached a high level of sophistication and complexity. Model auditing is needed in order to better understand their results, and to deal with the fact that such models are increasingly opaque with respect to their inner workings. Current techniques such as Global Sensitivity Analysis (GSA) are limited to dealing either with multivariate outputs, stochastic ones, or finite-change inputs. This limits their applicability to time-varying variables such as future pathways of greenhouse gases. To provide additional semantics in the analysis of a model ensemble, we provide an extension of GSA methodologies tackling the case of stochastic functional outputs with finite change inputs. To deal with finite change inputs and functional outputs, we propose an extension of currently available GSA methodologies while we deal with the stochastic part by introducing a novel, domain-selective inferential technique for sensitivity indices. Our method is explored via a simulation study that shows its robustness and efficacy in detecting sensitivity patterns. We apply it to real world data, where its capabilities can provide to practitioners and policymakers additional information about the time dynamics of sensitivity patterns, as well as information about robustness. Copyright © 2020, The Authors. All rights reserved.

关键词： Greenhouse gases

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L-Sweeps: A scalable, parallel preconditioner for the high-frequency Helmholtz equation

arXiv

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arXiv 2019年

作者： Taus, Matthias Zepeda-Núñez, Leonardo Hewett, Russell J. Demanet, Laurent Institute of Analysis and Scientific Computing Vienna University of Technology Department of Mathematics Massachusetts Institute of Technology Computational Research Division Lawrence Berkeley National Laboratory Department of Mathematics University of California Berkeley Department of Mathematics University of Wisconsin-Madison Total E&P Research and Technology United States Department of Mathematics Virginia Tech

We present the first fast solver for the high-frequency Helmholtz equation that scales optimally in parallel, for a single right-hand side. The L-sweeps approach achieves this scalability by departing from the usual propagation pattern, in which information flows in a 180 degree cone from interfaces in a layered decomposition. Instead, with L-sweeps, information propagates in 90_ cones induced by a checkerboard domain decomposition (CDD). We extend the notion of accurate transmission conditions to CDDs and introduce a new sweeping strategy to efficiently track the wave fronts as they propagate through the CDD. The new approach decouples the subdomains at each wave front, so that they can be processed in parallel, resulting in better parallel scalability than previously demonstrated in the literature. The method has an overall O ((N/p) logω) empirical run-time for N = ndtotal degrees-of-freedom in a d-dimensional problem, frequency ω, and p = O(n) processors. We introduce the algorithm and provide a complexity analysis for our parallel implementation of the solver. We corroborate all claims in several two- and three-dimensional numerical examples involving constant, smooth, and discontinuous wave speeds. Copyright © 2019, The Authors. All rights reserved.

关键词： Helmholtz equation

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Drug3D-DTI: Improved Drug-target Interaction Prediction by Incorporating Spatial Information of Small Molecules

Drug3D-DTI: Improved Drug-target Interaction Prediction by I...

引用

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Zhirui Liao Xiaodi Huang Hiroshi Mamitsuka Shanfeng Zhu School of Computer Science Fudan University Shanghai China Institute of Artificial Intelligence Biomedicine Nanjing University Nanjing China School of Computing Mathematics and Engineering Charles Sturt University Albury NSW Australia Bioinformatics Center Institute for Chemical Research Kyoto University Uji Kyoto Japan Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai China Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University) Ministry of Education China MOE Frontiers Center for Brain Science Fudan University Shanghai China Zhangjiang Fudan International Innovation Center Shanghai China Shanghai Key Lab of Intelligent Information Processing Fudan University Shanghai China

ISBN: (纸本)9781665429825

A number of machine learning (ML) approaches for drug discovery have been available that rely only on sequential (1D) and planar (2D) information without effectively using the 3D information for generating features of drugs. However, 3D information of small molecules can reflect relative position of atoms more directly, which affects molecular properties. In this work, we present a new deep learning model called Drug3D-DTI for drug-target interaction prediction. Drug3D-DTI takes advantage of molecular spatial information, i.e., atom proximity in three-dimensional (3D) structures. We comprehensively evaluated the performance of Drug3D-DTI on two datasets with two tasks of regression and classification. In particular, we compared Drug3D-DTI with several existing methods including the two cutting-edge methods for compound-protein interaction prediction. From the experimental results, Drug3D-DTI clearly outperformed other methods under all settings. Further, this performance improvement was validated by ablation experiments and a case study. The implementation of Drug3D-DTI is available at (https://***/zhiruiliao/Drug3D-DTI).

关键词： Drugs Proteins Deep learning Solid modeling Three-dimensional displays Conferences Predictive models

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Sensor-based authentication in smartphone: A systematic review

Journal of Engineering Research (Kuwait)

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Journal of engineering Research (Kuwait) 2024年

作者： Shuwandy, Moceheb Lazam Jouda, A.S. Ahmed, M.A. Salih, Mahmood M. Al-qaysi, Z.T. Alamoodi, A.H. Garfan, Salem Albahri, O.S. Zaidan, B.B. Albahri, A.S. Computer Science Department College of Computer Science and Mathematics Tikrit University (TU) Tikrit Iraq Salahaddin Health Office Ministry of Health Tikrit Iraq MEU Research Unit Middle East University Amman Jordan Faculty of Computing and Meta-Technology (FKMT) Universiti Pendidikan Sultan Idris (UPSI) Perak Malaysia Hourani Center for Applied Scientific Research Al-Ahliyya Amman University Amman Jordan Victorian Institute of Technology Australia Computer Techniques Engineering Department Mazaya University College Nasiriyah Iraq Applied Science Research Center Applied Science Private University Amman Jordan SP Jain School of Global Management Lidcombe Sydney 2141 NSW Australia International Graduate School of Artificial Intelligence National Yunlin University of Science and Technology Douliu Taiwan Technical College Imam Ja'afar Al-Sadiq University Baghdad Iraq Iraqi Commission for Computers and Informatics (ICCI) Baghdad Iraq

With the widespread usage of smartphones, users not just using their smartphone for calls and messaging only, but they are using it for a variety of purposes such as banking transactions, e-mailing, chatting, online shopping, video conferencing, health monitoring, and many more. Most of these activities store personal and sensitive data of the user on the device, reaching this confidential information by unauthorized person may cause huge losses and bad consequences. Therefore, securing the smartphone's accessibility from unauthorized people became an extremely essential. With the advanced development in the area of sensor-based smartphone authentication methods, different methods were developed to be easily used by users through specific criteria. However, many aspects haven't been discovered yet in the area of sensor-based smartphone authentication methods. On the basis of that, this study aims to review the area of sensor-based smartphone authentication methods systematically to provide a comprehensive understanding of this new area and to discuss the current challenges and issues. To conduct this systematic review, four scientific digital databases were utilized;ScienceDirect, IEEE Xplore, Web of Science, and Scopus. The total number of studies found was n = 256 articles, only n = 46 articles were included based on our inclusion criteria. To provide a comprehensive understanding of the included studies, taxonomy was drawn. Also, this study provides a discussion on the current motivations, challenges and issues, and recommendations in sensor-based smartphone authentication methods. This review enlightens, encourage, and direct researchers to develop authentication solutions and reduce the current gaps in this area. © 2024 The Authors

关键词： Authentication MHealth Microphone Sensor Password Privacy Touch Sensor

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On the spectrum of mesons in quenched Sp(2N) gauge theories

arXiv

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arXiv 2023年

作者： Bennett, Ed Holligan, Jack Hong, Deog Ki Lee, Jong-Wan Lin, C.-J. David Lucini, Biagio Piai, Maurizio Vadacchino, Davide Swansea Academy of Advanced Computing Swansea University Fabian Way Swansea WalesSA1 8EN United Kingdom Biomedical and Physical Sciences Building Michigan State University East LansingMI48824 United States Department of Physics Pusan National University Busan46241 Korea Republic of Institute for Extreme Physics Pusan National University Busan46241 Korea Republic of Daejeon34126 Korea Republic of Institute of Physics National Yang Ming Chiao Tung University 1001 Ta-Hsueh Road Hsinchu30010 Taiwan Center for High Energy Physics Chung-Yuan Christian University Chung-Li32023 Taiwan Centre for Theoretical and Computational Physics National Yang Ming Chiao Tung University 1001 Ta-Hsueh Road Hsinchu30010 Taiwan Department of Mathematics Faculty of Science and Engineering Swansea University Fabian Way Swansea WalesSA1 8EN United Kingdom Department of Physics Faculty of Science and Engineering Swansea University Singleton Park Swansea WalesSA2 8PP United Kingdom Centre for Mathematical Sciences University of Plymouth PlymouthPL4 8AA United Kingdom

We report the findings of our extensive study of the spectra of flavoured mesons in lattice gauge theories with symplectic gauge group and fermion matter content treated in the quenched approximation. For the Sp(4), Sp(6), and Sp(8) gauge groups, the (Dirac) fermions transform in either the fundamental, or the 2-index, antisymmetric or symmetric, representations. This study sets the stage for future precision calculations with dynamical fermions in the low mass region of lattice parameter space. Our results have potential phenomenological applications ranging from composite Higgs models, to top (partial) compositeness, to dark matter models with composite, strong-coupling dynamical origin. Having adopted the Wilson flow as a scale-setting procedure, we apply Wilson chiral perturbation theory to extract the continuum and massless limits for the observables of interest. The resulting measurements are used to perform a simplified extrapolation to the large-N limit, hence drawing a preliminary connection with gauge theories with unitary groups. We conclude with a brief discussion of the Weinberg sum rules. © 2023, CC BY.

关键词： Perturbation techniques

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