Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice Kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. The algorithms can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). The proposed parallel algorithms are controlled-error approximations of kinetic Monte Carlo algorithms, departing from the predominant paradigm of creating parallel KMC algorithms with exactly the same master equation as the serial one. Our methodology relies on a spatial decomposition of the Markov operator underlying the KMC algorithm into a hierarchy of operators corresponding to the processors' structure in the parallel architecture. Based on this operator decomposition, we formulate Fractional Step Approximation schemes by employing the Trotter Theorem and its random variants; these schemes, (a) determine the communication schedule} between processors, and (b) are run independently on each processor through a serial KMC simulation, called a kernel, on each fractional step time-window. Furthermore, the proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules.Comment: 34 pages, 9 figure

Asymptotic Approximations for TCP Compound

In this paper, we derive an approximation for throughput of TCP Compound connections under random losses. Throughput expressions for TCP Compound under a deterministic loss model exist in the literature. These are obtained assuming the window sizes are continuous, i.e., a fluid behaviour is assumed. We validate this model theoretically. We show that under the deterministic loss model, the TCP window evolution for TCP Compound is periodic and is independent of the initial window size. We then consider the case when packets are lost randomly and independently of each other. We discuss Markov chain models to analyze performance of TCP in this scenario. We use insights from the deterministic loss model to get an appropriate scaling for the window size process and show that these scaled processes, indexed by p, the packet error rate, converge to a limit Markov chain process as p goes to 0. We show the existence and uniqueness of the stationary distribution for this limit process. Using the stationary distribution for the limit process, we obtain approximations for throughput, under random losses, for TCP Compound when packet error rates are small. We compare our results with ns2 simulations which show a good match.Comment: Longer version for NCC 201

Error bounds for last-column-block-augmented truncations of block-structured Markov chains

This paper discusses the error estimation of the last-column-block-augmented northwest-corner truncation (LC-block-augmented truncation, for short) of block-structured Markov chains (BSMCs) in continuous time. We first derive upper bounds for the absolute difference between the time-averaged functionals of a BSMC and its LC-block-augmented truncation, under the assumption that the BSMC satisfies the general $f$-modulated drift condition. We then establish computable bounds for a special case where the BSMC is exponentially ergodic. To derive such computable bounds for the general case, we propose a method that reduces BSMCs to be exponentially ergodic. We also apply the obtained bounds to level-dependent quasi-birth-and-death processes (LD-QBDs), and discuss the properties of the bounds through the numerical results on an M/M/$s$ retrial queue, which is a representative example of LD-QBDs. Finally, we present computable perturbation bounds for the stationary distribution vectors of BSMCs.Comment: This version has fixed the bugs for the positions of Figures 1 through

Applying Mean-field Approximation to Continuous Time Markov Chains

The mean-field analysis technique is used to perform analysis of a systems with a large number of components to determine the emergent deterministic behaviour and how this behaviour modifies when its parameters are perturbed. The computer science performance modelling and analysis community has found the mean-field method useful for modelling large-scale computer and communication networks. Applying mean-field analysis from the computer science perspective requires the following major steps: (1) describing how the agents populations evolve by means of a system of differential equations, (2) finding the emergent deterministic behaviour of the system by solving such differential equations, and (3) analysing properties of this behaviour either by relying on simulation or by using logics. Depending on the system under analysis, performing these steps may become challenging. Often, modifications of the general idea are needed. In this tutorial we consider illustrating examples to discuss how the mean-field method is used in different application areas. Starting from the application of the classical technique, moving to cases where additional steps have to be used, such as systems with local communication. Finally we illustrate the application of the simulation and uid model checking analysis techniques