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Parallel Tools for Simulating the Depolarization Block on a Neural Model

Procedia Computer Science 2015年 51卷 745-754页

作者： Salvatore Cuomo Pasquale De Michele Ardelio Galletti Giovanni Ponti University of Naples Federico II Naples Italy ENEA Research Center Portici Naples Italy University of Naples Parthenope Naples Italy

The prototyping and the development of computational codes for biological models, in terms of reliability, efficient and portable building blocks allow to simulate real cerebral behaviours and to validate theories and experiments. A critical issue is the tuning of a model by means of several numerical simulations with the aim to reproduce real scenarios. This requires a huge amount of computational resources to assess the impact of parameters that influence the neuronal response. In this paper, we describe how parallel tools are adopted to simulate the so- called depolarization block of a CA1 pyramidal cell of hippocampus. Here, the high performance computing techniques are adopted in order to achieve a more efficient model simulation. Finally, we analyse the performance of this neural model, investigating the scalability and benefits on multi-core and on parallel and distributed architectures.

关键词： Parallel computing Computational Neuroscience multi-core computing

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multi-core computing: A novel accelerating method for chemometrics calculation

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CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS 2009年第1期96卷 94-97页

作者： Zhang, Zhi-Min Liang, Yi-Zeng Xu, Qing-Song Cent S Univ Res Ctr Modernizat Chinese Med Coll Chem & Chem Engn Changsha 410083 Hunan Peoples R China Cent S Univ Sch Math Sci & Comp Technol Changsha 410083 Peoples R China

The higher speed is the eternal pursuit of any chemometric algorithm. In order to take full advantage of the multi-core processor's computing resources (the prevailing current of personal computer) and accelerate the time-consuming algorithms in chemometrics, a novel multi-core computing method is introduced. Leave-one-out cross-validation is taken as an example to show the powerful capability of the multi-core computing. The comparison results show that the execution time drops rapidly with the increasing number of computing cores, which demonstrates that the multi-core computing is a promising tool for solving computing-intensive and data-intensive problems in chemometrics. (C) 2008 Published by Elsevier B.V.

关键词： multi-core computing Cross-validation Parallel algorithm Message Passing Interface

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Streaming Progressive TIN Densification Filter for Airborne LiDAR Point Clouds Using multi-core Architectures

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REMOTE SENSING 2014年第8期6卷 7212-7232页

作者： Kang, Xiaochen Liu, Jiping Lin, Xiangguo Wuhan Univ Sch Resource & Environm Sci Wuhan 430079 Peoples R China Chinese Acad Surveying & Mapping Beijing 100830 Peoples R China

As one of the key steps in the processing of airborne light detection and ranging (LiDAR) data, filtering often consumes a huge amount of time and physical memory. Conventional sequential algorithms are often inefficient in filtering massive point clouds, due to their huge computational cost and Input/Output (I/O) bottlenecks. The progressive TIN (Triangulated Irregular Network) densification (PTD) filter is a commonly employed iterative method that mainly consists of the TIN generation and the judging functions. However, better quality from the progressive process comes at the cost of increasing computing time. Fortunately, it is possible to take advantage of state-of-the-art multi-core computing facilities to speed up this computationally intensive task. A streaming framework for filtering point clouds by encapsulating the PTD filter into independent computing units is proposed in this paper. Through overlapping multiple computing units and the I/O events, the efficiency of the proposed method is improved greatly. More importantly, this framework is adaptive to many filters. Experiments suggest that the proposed streaming PTD (SPTD) is able to improve the performance of massive point clouds processing and alleviate the I/O bottlenecks. The experiments also demonstrate that this SPTD allows the quick processing of massive point clouds with better adaptability. In a 12-core environment, the SPTD gains a speedup of 7.0 for filtering 249 million points.

关键词： airborne LiDAR multi-core computing stream computing progressive TIN densification filtering

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DEXSim: an experimental environment for distributed execution of replicated simulators using a concept of single simulation multiple scenarios

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SIMULATION-TRANSACTIONS OF THE SOCIETY FOR MODELING AND SIMULATION INTERNATIONAL 2014年第4期90卷 355-376页

作者： Choi, Changbeom Seo, Kyung-Min Kim, Tag Gon Korea Adv Inst Sci & Technol Dept Elect Engn Taejon 305701 South Korea

This paper presents an efficient and scalable experimental environment for distributed execution of replicated simulators. By taking a performance-centered approach, the proposed technique makes the best use of distributed hardware resources for faster data collection. Accordingly, the primary contribution of this work is to describe how the environment improves scalability and utilizes distributed hardware resources efficiently. To do this, we suggest a new concept of single simulation multiple scenarios and propose a distributed execution simulation framework regarding the following three aspects: (1) layered architecture model design;(2) protocol definitions interacting with them;and (3) framework implementation. The proposed model architecture and protocol definitions guarantee a straightforward structural scalability and an efficient load-balanced utilization between hardware resources. Moreover, the framework operates simulation execution automatically without users' extra work. In order to prove the efficiency of the proposed framework, we performed three extensive experiments with different models, that is, different systems. The experimental results show that simulation performance increases proportionally with the number of hardware resources, minimizing the overhead of the proposed framework's utilization.

关键词： Faster data collection experimental frame distributed simulation multi-core computing

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Performance modeling and analysis of parallel Gaussian elimination on multi-core computers

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JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES 2014年第1期26卷 41-54页

作者： Sibai, Fadi N. Ctr Saudi Aramco P & CSD Dept Dhahran 31311 Saudi Arabia

Gaussian elimination is used in many applications and in particular in the solution of systems of linear equations. This paper presents mathematical performance models and analysis of four parallel Gaussian Elimination methods ( precisely the Original method and the new Meet in the Middle -MiM- algorithms and their variants with SIMD vectorization) on multi-core systems. Analytical performance models of the four methods are formulated and presented followed by evaluations of these models with modern multi-core systems' operation latencies. Our results reveal that the four methods generally exhibit good performance scaling with increasing matrix size and number of cores. SIMD vectorization only makes a large difference in performance for low number of cores. For a large matrix size ( n >= 16 K), the performance difference between the MiM and Original methods falls from 16 k with four cores to 4x with 16 K cores. The efficiencies of all four methods are low with 1 K cores or more stressing a major problem of multi-core systems where the network-on-chip and memory latencies are too high in relation to basic arithmetic operations. Thus Gaussian Elimination can greatly benefit from the resources of multi-core systems, but higher performance gains can be achieved if multi-core systems can be designed with lower memory operation, synchronization, and interconnect communication latencies, requirements of utmost importance and challenge in the exascale computing age. (C) 2013 Production and hosting by Elsevier B.V. on behalf of King Saud University.

关键词： Gaussian elimination multi-core computing Performance modeling and analysis

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An Approach to multi-core Functional Gate-level Simulation Minimizing Synchronization and Communication Overheads 14

An Approach to Multi-core Functional Gate-level Simulation M...

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14th International Workshop on Microprocessor Test and Verification (MTV) - Common Challenges and Solutions

作者： Ahmad, Tariq B. Ciesielski, Maciej UMASS Amherst ECE Dept Amherst MA 01003 USA

ISBN: (纸本)9781479932467

This paper addresses performance issues encountered in parallel functional gate-level simulation executed on multi-core machine. It demonstrates that a straightforward application of the multi-core simulation on a multi-core machine does not improve simulation performance. This is due to unbalanced partitioning, lack of sufficient concurrency in the design partitions, overhead due to communication between partitions, and synchronization overhead imposed by the simulator. We propose, implement and automate a generic (partitioning-independent) prediction-based solution to eliminate or minimize communication and synchronization overhead in an event-driven functional gate-level simulation on a multi-core machine. We demonstrate speedup obtained with this method on a set of real Opensource designs.

关键词： Gate-level simulation synchronization and communication overheads single-core simulation multi-core simulation multi-core computing RTL parallel simulation

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A Port-Configuration Assisted NIC IRQ Affinitization Scheme for multi-core Packet Forwarding Applications

A Port-Configuration Assisted NIC IRQ Affinitization Scheme ...

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IEEE Global Communications Conference (GLOBECOM)

作者： Tsai, Wen-Yen Huang, Nen-Fu Hung, Hsien-Wei Natl Tsing Hua Univ Inst Commun Engn Hsinchu Taiwan

ISBN: (纸本)9781467309219;9781467309202

Interrupt affinitization of network interface cards (NICs) is a fundamental composition that defines how packets are processed by which CPU-cores on multi-core platforms. In this paper, we propose a simple port-configuration assisted scheme to attain an optimal affinitization for packet forwarding applications. Experiments ranging from bridging, routing, flow tracking to deep packet inspection are conducted to show the performance impacts utilizing different affinitization approaches. As a result, our proposed scheme achieves the same performance level as the best fixed affinitization scheme. In addition, the effectiveness of interrupt balancing is demonstrated for our scheme to be superior to the widely-deployed irqbalance with varying network settings.

关键词： IRQ affinitization multi-core computing IRQ balancing

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二次特征值问题的并行精化Jacobi-Davidson方法及其多核并行实现

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高等学校计算数学学报 2012年第4期34卷 357-364页

作者：王顺绪淮海工学院理学院

1引言受功耗、散热和制造工艺等因素的影响,按Moore定律预测的CPU发展速度以每18个月增加一倍的指数级增长方式受到了极大的挑战,单核CPU的运行速度几乎已经达到极限,处理器的发展前景是多核CPU,拥有多核CPU的计算机是并行计算机,目前... 详细信息

1引言受功耗、散热和制造工艺等因素的影响,按Moore定律预测的CPU发展速度以每18个月增加一倍的指数级增长方式受到了极大的挑战,单核CPU的运行速度几乎已经达到极限,处理器的发展前景是多核CPU,拥有多核CPU的计算机是并行计算机,目前多核并行计算机已经普及到千家万户,这种并行计算机是未来发展的主流.由于多核和单核CPU设计理念的不同,软件的执行方式有着本质的不同,单核CPU上运行良好的

关键词： quadratic eigenvalue problems Jacobi-Davidson method refined method multi-core computing

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Implicit Parallel Time Integrators

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JOURNAL OF SCIENTIFIC computing 2011年第2期49卷 167-179页

作者： Christlieb, Andrew Ong, Benjamin Michigan State Univ Dept Math E Lansing MI 48823 USA

In this work, we discuss a family of parallel implicit time integrators for multi-core and potentially multi-node or multi-gpgpu systems. The method is an extension of Revisionist Integral Deferred Correction (RIDC) by Christlieb, Macdonald and Ong (SISC-2010) which constructed parallel explicit time integrators. The key idea is to re-write the defect correction framework so that, after initial startup costs, each correction loop can be lagged behind the previous correction loop in a manner that facilitates running the predictor and correctors in parallel. In this paper, we show that RIDC provides a framework to use p cores to generate a pth-order implicit solution to an initial value problem (IVP) in approximately the same wall clock time as a single core, backward Euler implementation (pa parts per thousand currency sign12). The construction, convergence and stability of the schemes are presented, along with supporting numerical evidence.

关键词： Initial value problems Integral deferred correction Parallel computation multi-core computing

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Modules in Community: Injecting More Parallelism Into Computer Science Curricula 11

Modules in Community: Injecting More Parallelism Into Comput...

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42nd ACM Technical Symposium on Computer Science Education

作者： Brown, Richard Shoop, Elizabeth St Olaf Coll Northfield MN 55057 USA

ISBN: (纸本)9781450305006

Given the recent emergence of multi-core and distributed computing that is transforming mainstream application areas in industry, demand is rising for teaching more parallelism and concurrency in CS curricula. We argue for teaching these topics incrementally in CS courses at all undergraduate levels, and propose a comprehensive approach involving flexible teaching modules with experiential programming exercises, technical and instructor supplementary materials, and an online community of educators to support adopters and module contributors. Progress on developing these materials and online resources is reported.

关键词： Parallelism multi-core computing

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