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2010 IEEE workshop on Principles of Advanced and distributed simulation, PADS 2010

2010 IEEE Workshop on Principles of Advanced and Distributed...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

ISBN: (纸本)9781424472918

The proceedings contain 18 papers. The topics discussed include: new approaches to protein functional inference and ligand screening with application to the human kinome;federate fault tolerance in HLA-based simulation;continuous matching algorithm for interest management in distributed virtual environments;a methodology to predict the performance of distributed simulations;optimizing a business process model by using simulation;selecting simulation algorithm portfolios by genetic algorithms;on validation of semantic composability in data-driven simulation;integrative models of the hepatitis C virus infection: modeling wicked problems;functional level hardware simulation with pull-model data flow;flow: a stream processing system simulator;reversible parallel discrete-event execution of large-scale epidemic outbreak models;validation of radio channel models using an anechoic chamber;and explicit spatial scattering for load balancing in conservatively synchronized parallel discrete-event simulations.

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P-GAS: parallelizing a cycle-accurate event-driven many-core processor simulator using parallel discrete event simulation 10

P-GAS: Parallelizing a cycle-accurate event-driven many-core...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Lv, Huiwei Cheng, Yuan Bai, Lu Chen, Mingyu Fan, Dongrui Sun, Ninghui Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Sciences China Graduate School Chinese Academy of Sciences China

ISBN: (纸本)9781424472918

Multi-core processors are commonly available now, but most traditional computer architectural simulators still use single-thread execution. In this paper we use parallel discrete event simulation (PDES) to speedup a cycle-accurate event-driven many-core processor simulator. Evaluation against the sequential version shows that the parallelized one achieves an average speedup of 10.9× (up to 13.6×) running SPLASH-2 kernel on a 16-core host machine, with cycle counter differences of less than 0.1%. Moreover, super-linear speedups are achieved between running 1 thread and 8 threads due to reduced overhead of insert-event-to-queue time and increased cache size in parallel processing. We conclude that PDES could be an attractive option for achieving fast cycle-accurate many-core processor simulations. © 2010 IEEE.

关键词： Simulators

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parallel particle-based reaction diffusion: A GPU implementation

Parallel particle-based reaction diffusion: A GPU implementa...

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9th International workshop on parallel and distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International workshop on High-Performance Computational Systems Biology, HiBi 2010

作者： Dematté, Lorenzo Microsoft Research University of Trento Center for Computational and Systems Biology Trento Italy

ISBN: (纸本)9780769542652

Space is a very important aspect in the simulation of biochemical models;recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and large models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localised fluctuations, transportation phenomena and diffusion. A common drawback of spatial models lies in their complexity: models could become very large, and their simulation could be time consuming, especially if we want to capture the systems behaviour in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to move from sequential to parallel simulation algorithms. In this paper we analyse Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of GPUs. The implementation offers good speedups (up to 130x) and real time, high quality graphics output at almost no performance penalties. © 2010 IEEE.

关键词： Graphics processing unit

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Explicit spatial scattering for load balancing in conservatively synchronized parallel discrete-event simulations 10

Explicit spatial scattering for load balancing in conservati...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Thulasidasan, Sunil Kasiviswanathan, Shiva Prasad Eidenbenz, Stephan Romero, Phillip Los Alamos National Laboratory United States

ISBN: (纸本)9781424472918

We re-examine the problem of load balancing in conservatively synchronized parallel, discrete-event simulations executed on high-performance computing clusters, focusing on simulations where computational and messaging load tend to be spatially clustered. Such domains are frequently characterized by the presence of geographic "hot-spots" - regions that generate significantly more simulation events than others. Examples of such domains include simulation of urban regions, transportation networks and networks where interaction between entities is often constrained by physical proximity. Noting that in conservatively synchronized parallel simulations, the speed of execution of the simulation is determined by the slowest ( i.e most heavily loaded) simulation process, we study different partitioning strategies in achieving equitable processor-load distribution in domains with spatially clustered load. In particular, we study the effectiveness of partitioning via spatial scattering to achieve optimal load balance. In this partitioning technique, nearby entities are explicitly assigned to different processors, thereby scattering the load across the cluster. This is motivated by two observations, namely, (i) since load is spatially clustered, spatial scattering should, intuitively, spread the load across the compute cluster, and (ii) in parallel simulations, equitable distribution of CPU load is a greater determinant of execution speed than message passing overhead. Through large-scale simulation experiments - both of abstracted and real simulation models - we observe that scatter partitioning, even with its greatly increased messaging overhead, significantly outperforms more conventional spatial partitioning techniques that seek to reduce messaging overhead. Further, even if hot-spots change over the course of the simulation, if the underlying feature of spatial clustering is retained, load continues to be balanced with spatial scattering leading us to the observation that

关键词： Message passing

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ON THE PERFORMANCE AND COST OF SOME PRAM MODELS ON CMP HARDWARE

ON THE PERFORMANCE AND COST OF SOME PRAM MODELS ON CMP HARDW...

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10th workshop on Advances in parallel and distributed Computational Models/22nd IEEE International parallel and distributed Processing Symposium

作者： Forsell, Martti VTT Tech Res Ctr Finland Platform Architectures Team FI-90571 Oulu Finland

ISBN: (纸本)9781424416943

The parallel Random Access Machine is a very strong model of parallel computing that has resisted cost-efficient implementation attempts for decades. Recently, the development of VLSI technology has provided means for indirect on-chip implementation, but there are different variants of the PRAM model that provide different performance, area and power figures and it is not known how their implementations compare to each others. In this paper we measure the performance and estimate the cost of practical implementations of four PRAM models including EREW, Limited Arbitrary CRCW, Full Arbitrary CRCW, Full Arbitrary Multioperation CRCW on our Eclipse chip multiprocessor framework. Interestingly, the most powerful model shows the lowest simulation cost and highest performance/area and performance/power figures.

关键词： parallel computing PRAM performance silicon area power consumption

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Federate fault tolerance in HLA-based simulation 10

Federate fault tolerance in HLA-based simulation

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Li, Zengxiang Cai, Wentong Turner, Stephen John Pan, Ke Parallel and Distributed Computing Center School of Computing Engineering Nanyang Technological University Singapore 639798 Singapore

ISBN: (纸本)9781424472918

A large scale HLA-based simulation (federation) is composed of a large number of simulation components (federates), which may be developed by different participants and executed at different locations. These federates are subject to failures due to various reasons. What is worse, the risk of federation failure increases with the number of federates in the federation. In this paper, a fault tolerance mechanism is proposed to tolerate the crash-stop failures of federates. By exploiting the decoupled federate architecture, federate failures can be masked from the federation and recovery can take place without interrupting the executions of other federates. A basic state recovery protocol is first proposed to recover the state of the failed federate relying on the checkpoint and message logging taken before the failure. Then, an optimized protocol is further developed to accelerate the state recovery procedure. Experiments are carried out to verify that the proposed mechanism provides correct failure recovery. The experimental results also indicate that the optimized protocol can outperform the basic one considerably. © 2010 IEEE.

关键词： Fault tolerance

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Efficient gigabit ethernet switch models for large-scale simulation 10

Efficient gigabit ethernet switch models for large-scale sim...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Jin, Dong Nicol, David M. Caesar, Matthew University of Illinois at Urbana-Champaign United States

ISBN: (纸本)9781424472918

Ethernet is the most widely implemented low-level networking technology used today, with Gigabit Ethernet seen as the emerging standard implementation. The backbones of many large scale networks (e.g., data centers, metro-area deployments) are increasingly made up of Gigabit Ethernet as the underlying technology, and Ethernet is seeing increasing use in dynamic and failure-prone settings (e.g., wireless backhaul, developing regions) with high rates of churn. Correspondingly, when using simulation to study such networks and applications that run on them, the switching makes up a significant fraction of the model, and can make up a significant amount of the simulation activity. This paper describes a unique testbed that gathers highly accurate measurements of loss and latency through a switch, experiments that reveal the behavior of three commercial switches, and then proposes simulation models that explain the observed data. The models vary in their computational complexity and in their accuracy with respect to frame loss patterns, and latency through the switch. In particular, the simplest model predicts a frame's loss and latency immediately at the time of its arrival, which keeps the computational cost close to one event per frame per switch, provides excellent temporal separation between switches (useful for parallel simulation), while providing excellent accuracy for loss and adequate accuracy for latency. © 2010 IEEE.

关键词： Ethernet

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Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis

Predicting the effects of parameters changes in stochastic m...

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9th International workshop on parallel and distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International workshop on High-Performance Computational Systems Biology, HiBi 2010

作者： Forlin, Michele Mazza, Tommaso Prandi, Davide Microsoft Research University of Trento Centre for Computational and Systems Biology Trento Italy

ISBN: (纸本)9780769542652

Usually researchers require many experiments to verify how biological systems respond to stimuli. However, the high cost of reagents and facilities as well as the time required to carry out experiments are sometimes the main cause of failure. In this regards, Information Technology offers a valuable help: modeling and simulation are mathematical tools to execute virtual experiments on computing devices. Through synthetic experimentation, researchers can sample the parameters space of a biological system and obtain hundreds of potential results, ready to be reused to design and conduct more targeted wet-lab experiments. A non negligible achievement of this is the enormous saving of resources and time. In this paper, we present a plug-in-based software prototype that combines high performance computing and statistics. Our framework relies on parallel computing to run large numbers of synthetic experiments. Multivariate analysis is then used to interpret and validate results. The software is tested on two well-known oscillatory models: Predator-Prey (Lotka-Volterra) and Repressilator. © 2010 IEEE.

关键词： Stochastic models

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Proceeding of the 2nd workshop on Bio-Inspired Algorithms for distributed Systems, BADS '10

Proceeding of the 2nd Workshop on Bio-Inspired Algorithms fo...

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2nd workshop on Bio-Inspired Algorithms for distributed Systems, BADS 2010

ISBN: (纸本)9781450300865

The proceedings contain 6 papers. The topics discussed include: GPU-accelerated differential evolutionary Markov chain Monte Carlo method for multi-objective optimization over continuous space;a study of parallel and distributed particle swarm optimization methods;ant system for service deployment in private and public clouds;an evolutionary game theoretic approach to adaptive and stable application deployment in clouds;GUMP: adapting client/server messaging protocols into peer-to-peer serverless environments;and simulation experiences with an ecological approach for pervasive service systems.

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Towards efficient distributed simulation in modelica using transmission line modeling

Towards efficient distributed simulation in modelica using t...

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3rd International workshop on Equation-Based Object-Oriented Modeling Languages and Tools, EOOLT 2010 - In Conjunction with the MODELS 2010 Conference

作者： Sjölund, Martin Braun, Robert Fritzson, Peter Krus, Petter Dept. of Computer and Information Science Linköping University Sweden Dept. of Management and Engineering Linköping University Sweden

The current development towards multiple processor cores in personal computers is making distribution and parallelization of simulation software increasingly important. The possible speedups from parallelism are however often limited with the current centralized solver algorithms, which are commonly used in today's simulation environments. An alternative method investigated in this work utilizes distributed solver algorithms using the transmission line modeling (TLM) method. Creation of models using TLM elements to separate model components makes them very suitable for computation in parallel because larger models can be partitioned into smaller independent submodels. The computation time can also be decreased by using small numerical solver step sizes only on those few submodels that need this for numerical stability. This is especially relevant for large and demanding models. In this paper we present work in how to combine TLM and solver inlining techniques in the Modelica equation-based language, giving the potential for efficient distributed simulation of model components over several processors.

关键词： Electric lines

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