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Large-scale branch contingency analysis through master/slave parallel computing

Journal of Modern Power Systems and Clean Energy 2013年第2期1卷 159-166页

作者： Xi YANG Cong LIU Jianhui WANG Decision and Information Sciences Division of Argonne National Laboratory ArgonneIL 60439USA

Contingency analysis(CA)requires fast execution time for real-time power system *** CA problems can naturally be divided into separate subtasks,parallel computing helps to speed up the computation *** paper proposes a master/slave parallel computing architecture and studies the computation of CA in a large-scale power system through high performance computing,adopting a message passing interface for *** particular,although the execution time of CA varies,there is a tradeoff between having an imbalanced workload and"paying"a synchronization penalty for parallel computing:either factor blocks the progress of *** proposed layered dynamic scheduling method is effective to tackle the challenge of high synchronization cost and workload imbalance and have the potential to further scale for the N-2 contingency analysis.

关键词： massive parallel computing Power system Contingency analysis

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A review of electrical impedance tomography in lung applications: Theory and algorithms for absolute images

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ANNUAL REVIEWS IN CONTROL 2019年 48卷 442-471页

作者： Martins, Thiago de Castro Sato, Andre Kubagawa de Moura, Fernando Silva Leon Bueno de Camargo, Erick Dario Silva, Olavo Luppi Rattis Santos, Talles Batista Zhao, Zhanqi Moeller, Knut Passos Amato, Marcelo Brito Mueller, Jennifer L. Lima, Raul Gonzalez Guerra Tsuzuki, Marcos de Sales Univ Sao Paulo Escola Politecn Computat Geometry Lab Sao Paulo SP Brazil Univ Fed ABC Ctr Engn Modeling & Appl Social Sci Santo Andre SP Brazil Univ Sao Paulo Escola Politecn Dept Mech Engn Sao Paulo SP Brazil Furtwangen Univ Inst Tech Med Furtwangen Germany Fourth Mil Med Univ Dept Biomed Engn Xian Shaanxi Peoples R China Univ Sao Paulo Hosp Clin Div Pulm Resp Intens Care Unit Sao Paulo SP Brazil Colorado State Univ Dept Math Ft Collins CO 80523 USA Colorado State Univ Sch Biomed Engn Ft Collins CO 80523 USA

Electrical Impedance Tomography (EIT) is under fast development. The present paper is a review of some procedures that have contributed to improve spatial resolution and material properties accuracy, admitivity or impeditivity accuracy. A review of EIT medical applications is presented and they were classified into three broad categories: ARDS patients, obstructive lung diseases and perioperative patients. The use of absolute EIT image may enable the assessment of absolute lung volume, which may significantly improve clinical acceptance of EIT. The Control Theory, State Observers more specifically, have a developed theory that can be used for designing and operating EIT devices. Electrode placement, current injection strategy and electrode electric potential measurements strategy should maximize the number of observable and controllable directions of the state vector space. A non-linear stochastic state observer, the Unscented Kalman Filter, is used directly for reconstructing absolute EIT images. Historically, difference images were explored first since they are more stable in the presence of modelling errors. Absolute images require more detailed models of contact impedance, stray capacitance and properly refined finite element mesh, where the electric potential gradient is high. parallelization of the forward program computation is necessary since the solution of the inverse problem often requires frequent solutions of the forward problem. Several reconstruction algorithms benefit from the Bayesian inverse problem approach and the concept of prior information. Anatomic and physiological information are used to form the prior information. An already tested methodology is presented to build the prior probability density function using an ensemble of CT scans and in vivo impedance measurements. Eight absolute EIT image algorithms are presented. (C) 2019 Elsevier Ltd. All rights reserved.

关键词： Electrical impedance tomography Anatomical atlas Bayesian inference massive parallel computing Approximation error ARDS Lung diseases

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parallel SPH modeling using dynamic domain decomposition and load balancing displacement of Voronoi subdomains

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COMPUTER PHYSICS COMMUNICATIONS 2019年 234卷 112-125页

作者： Egorova, M. S. Dyachkov, S. A. Parshikov, A. N. Zhakhovsky, V. V. Dukhov Res Inst Automat VNIIA Moscow Russia Moscow Inst Phys & Technol Dolgoprudnyi Moscow Region Russia Russian Acad Sci Joint Inst High Temp Moscow Russia Landau Inst Theoret Phys Chernogolovka Russia

A highly adaptive load balancing algorithm for parallel simulations using particle methods, such as molecular dynamics and smoothed particle hydrodynamics (SPH), is developed. Our algorithm is based on the dynamic spatial decomposition of simulated material samples between Voronoi subdomains, where each subdomain with all its particles is handled by a single computational process which is typically run on a single CPU core of a multiprocessor computing cluster. The algorithm displaces the positions of neighbor Voronoi subdomains in accordance with the local load imbalance between the corresponding processes. It results in particle transfers from heavy loaded processes to less-loaded ones. Iteration of the algorithm puts into alignment the processor loads. Convergence to a well-balanced decomposition from imbalanced one is improved by the usage of multi body terms in the balancing displacements. The high adaptability of the balancing algorithm to simulation conditions is illustrated by SPH modeling of the dynamic behavior of materials under extreme conditions, which are characterized by large pressure and velocity gradients, as a result of which the spatial distribution of particles varies greatly in time. The higher parallel efficiency of our algorithm in such conditions is demonstrated by comparison with the corresponding static decomposition of the computational domain. Our algorithm shows almost perfect strong scalability in tests using from tens to several thousand processes. (C) 2018 Elsevier B.V. All rights reserved.

关键词： Voronoi dynamic domain decomposition Load balancing Particle methods massive parallel computing

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A benchmark for the parallel code used in FMS and MOM-4

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OCEAN MODELLING 2007年第1期17卷 49-67页

作者： Schmidt, Martin Leibniz Inst Balt Sea Res Warnemunde D-18119 Rostock Germany

The numerical performance of the parallel code implemented in the Modular Ocean Model MOM-4 is investigated by numerical experiments. Several model configurations with different horizontal grid size are integrated in parallel with a varying number of MPI-tasks. The measured computation rates can be understood in terms of a generalized Amdahl's law. Advantages and limits of parallel integration of MOM-4 are discussed. An optimum task number and a maximum task number are given for each model configuration. MOM-4 is found to be suitable for parallel processing on high performance hardware. Distributing the numerical work over up to 512 tasks also projects with a high horizontal grid size of 1024 times 1024 grid points can be integrated with a sufficient computation rate. (c) 2006 Elsevier Ltd. All rights reserved.

关键词： ocean model massive parallel computing domain decomposition

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massively parallel computing of shortest raypath and traveltime in 2-D and 3-D models

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Terrestrial, Atmospheric and Oceanic Sciences 1996年第3期7卷 299-315页

作者： Kao, Jason C. Chen, How-Wei Cray Research Inc. Earth Sciences Aplication Division Eagan MN United States Institute of Seismology Institute of Applied Geophysics National Chung Cheng University Chiayi Taiwan

Based on Huygens' principle, the authors present an accurate and computationally efficient method to compute the shortest raypath and traveltime in a two-and three-dimensional (2-D and 3-D) space of a discrete block model. The efficiency of the method is achieved through approximation, while the accuracy of the calculated traveltime solely depends on machine precession. The accuracy of the raypath is realized by the small increment in the orientation of the ray incidence. Whether the computational efficiency and accuracy can be justified depends on the model's complexity and requirements in its own application. In addition, the feasibility of implementing the algorithm on the Cray T3D massively parallel Processors (MPP) is proposed. The velocity distribution in a 2-D space is discretized into homogeneous polygonal cells. The search for the shortest traveltime and path between two given points can be reduced to a discrete graph searching. In the general 3D case, the velocity model is characterized by discrete convex blocks bounded by polyhedral surfaces. Although the 3-D algorithm is a straight-forward extension of the 2-D case, the computing operations in 3-D are much more CPU intensive. The method is demonstrated with examples showing raypaths and wavefronts in 2D and 3D block models. On the basis of these examples, the proposed algorithm is capable of solving the optimal raypaths from different source points in parallel on the MPP system.

关键词： 2-D 3-D massive parallel computing MPP Raypath Traveltime

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Design and Implementation for GPU-based Seamless Rate Adaptive Decoder 9

Design and Implementation for GPU-based Seamless Rate Adapti...

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9th International Conference on Communications and Networking in China (CHINACOM 2014)

作者： Qiu, Lu Wang, Min Wu, Jun Zhang, Zhifeng Huang, Xinlin Tongji Univ Coll Elect & Informat Engn Shanghai Peoples R China Gannan Normal Univ Sch Math & Comp Sci Ganzhou Peoples R China

ISBN: (纸本)9781479959709

Recently, the research on rate adaption at receiver has caused widespread concern. Seamless rate adaptive (SRA) is one of the promising rate adaptation schemes for wireless communication system. However, the high complexity of decoding hinders its application. The graphics processor unit (GPU) is able to provide a low-cost and flexible software-based multicore architecture for high performance computing. This paper proposes a GPU design and implementation for SRA decoder. Firstly, we discuss the parallelism of SRA decoding algorithm. In order to improve the throughput of the GPU-based SRA decoder, a massive parallel architecture is used in SRA decoder, which consists of N x L parallel threads. Given fully consideration of the hardware architecture of GPU, we partition the block and select the appropriate number of threads within an individual block to further improve the throughput of GPU-based SRA decoder. In addition, we propose an efficient memory-usage mechanism in GPU-based SRA decoder which takes fully advantage of the shared memory in one block. Finally, We implement the SRA decoder on the Compute Unified Device Architecture (CUDA) platform. The GPU-based SRA decoder is flexible for different measurement matrix, and achieves a 60x speedup compared by its single-threaded counterpart performed on central processing unit (CPU).

关键词： GPU seamless rate adaptation massive parallel computing CUDA

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Development of an affinity evaluation and prediction system by using the shape complementary characteristic between proteins

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Journal of Bioinformatics and Computational Biology 2008年第6期6卷 1133-1156页

作者： Tsukamoto, Koki Yoshikawa, Tatsuya Hourai, Yuichiro Fukui, Kazuhiko Akiyama, Yutaka Computational Biology Research Center (CBRC) National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku Tokyo 135-0064 2-42 Aomi Japan Department of Bioinformatic Engineering Graduate School of Information Science and Technology Osaka University Toyonaka Osaka 560-8531 1-3 Machikaneyama Japan

A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. This system, which we call the affinity evaluation and prediction (AEP) system, was used to evaluate the interaction between 20 protein pairs. The system first executes a "round robin" shape complementarity search of the target protein group, and evaluates the interaction of the complex structures obtained by shape complementarity search. These complex structures are selected by using a statistical procedure that we developed called "grouping". At a low prevalence of 5.0%, our AEP system predicted protein-protein interaction with 65.0% recall, 15.1% precision, 80.0% accuracy, and had an area under the curve (AUC) of 0.74. By optimizing the grouping process, our AEP system successfully predicted 13 protein pairs (among 20 pairs) that were biologically significant combinations. Our ultimate goal is to construct an affinity database that will provide crucial information obtained using our AEP system to cell biologists and drug designers. © 2008 Imperial College Press.

关键词： Affinity analysis FFT massive parallel computing Prediction system Protein-protein docking Protein-protein interaction

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The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning

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Advances and Applications in Bioinformatics and Chemistry 2009年第1期2卷 1-15页

作者： Tsukamoto, Koki Yoshikawa, Tatsuya Yokota, Kiyonobu Hourai, Yuichiro Fukui, Kazuhiko Computational Biology Research Center (CBRC) National Institute of Advanced Industrial Science and Technology (AIST) Koto-ku Tokyo Japan Department of Bioinformatic Engineering Graduate School of Information Science and Technology Osaka University Toyonaka Osaka Japan

A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between the proteins. We used this system, which we call the affinity evaluation and prediction (AEP) system, to evaluate the interaction between 20 protein pairs. The system first executes a "round robin" shape complementarity search of the target protein group, and evaluates the interaction between the complex structures obtained by the search. These complex structures are selected by using a statistical procedure that we developed called 'grouping'. At a prevalence of 5.0%, our AEP system predicted protein-protein interactions with a 50.0% recall, 55.6% precision, 95.5% accuracy, and an F-measure of 0.526. By optimizing the grouping process, our AEP system successfully predicted 10 protein pairs (among 20 pairs) that were biologically relevant combinations. Our ultimate goal is to construct an affinity database that will provide cell biologists and drug designers with crucial information obtained using our AEP system. © 2009 Tsukamoto et al, publisher and licensee Dove Medical Press Ltd.

关键词： Affinity analysis FFT massive parallel computing Protein-protein docking Protein-protein interaction

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An approach to parallelization of sequential C code

An approach to parallelization of sequential C code

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2nd Eastern European Regional Conference on the Engineering of Computer Based Systems (ECBS-EERC)

作者： Vranic, Nikola Marinkovic, Vladimir Djukic, Miodrag Popovic, Miroslav RT RK Comp Based Syst LLC Novi Sad 2100 Serbia Univ Novi Sad Fac Tech Sci Novi Sad 21000 Serbia

ISBN: (纸本)9780769544182

massive parallel computing (MPC) originally appeared in the arena of multi-core processors and graphic processing units with parallel computing architecture. Nevertheless, most embedded software is still written in C, therefore C code parallelization is being subject of many ongoing R&D efforts. The most prominent approaches to parallelization of C code include Intel Cilk Plus, OpenCL, vfAnalyst, etc. The objective of this paper is to contribute to the automatic parallelization of existing sequential C code, without any source code modifications/annotations, by proposing two appropriate algorithms for parallelization, Block algorithm, and Operation based algorithm.

关键词： massive parallel computing multi-cores automatic code parallelization compilers

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Dynamic Algorithms for the massively parallel Computation Model 19

Dynamic Algorithms for the Massively Parallel Computation Mo...

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31st ACM Symposium on parallelism in Algorithms and Architecturess (SPAA)

作者： Italiano, Giuseppe F. Lattanzi, Silvio Mirrokni, Vahab S. Parotsidis, Nikos LUISS Univ Rome Italy Google Res New York NY USA Google Res Zurich Switzerland Univ Copenhagen Copenhagen Denmark

ISBN: (纸本)9781450361842

The massive parallel computing (MPC) model gained popularity during the last decade and it is now seen as the standard model for processing large scale data. One significant shortcoming of the model is that it assumes to work on static datasets while, in practice, real world datasets evolve continuously. To overcome this issue, in this paper we initiate the study of dynamic algorithms in the MPC model. We first discuss the main requirements for a dynamic parallel model and we show how to adapt the classic MPC model to capture them. Then we analyze the connection between classic dynamic algorithms and dynamic algorithms in the MPC model. Finally, we provide new efficient dynamic MPC algorithms for a variety of fundamental graph problems, including connectivity, minimum spanning tree and matching.

关键词： massive parallel computing dynamic algorithms mapreduce model

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