Parallelization of a Dynamic Monte Carlo Algorithm: a Partially Rejection-Free Conservative Approach

We experiment with a massively parallel implementation of an algorithm for simulating the dynamics of metastable decay in kinetic Ising models. The parallel scheme is directly applicable to a wide range of stochastic cellular automata where the discrete events (updates) are Poisson arrivals. For high performance, we utilize a continuous-time, asynchronous parallel version of the n-fold way rejection-free algorithm. Each processing element carries an lxl block of spins, and we employ the fast SHMEM-library routines on the Cray T3E distributed-memory parallel architecture. Different processing elements have different local simulated times. To ensure causality, the algorithm handles the asynchrony in a conservative fashion. Despite relatively low utilization and an intricate relationship between the average time increment and the size of the spin blocks, we find that for sufficiently large l the algorithm outperforms its corresponding parallel Metropolis (non-rejection-free) counterpart. As an example application, we present results for metastable decay in a model ferromagnetic or ferroelectric film, observed with a probe of area smaller than the total system.Comment: 17 pages, 7 figures, RevTex; submitted to the Journal of Computational Physic

An Interactive Problem Modeller and PDE Solver, Distributed on Large Scale Architectures

http://lifc.univ-fcomte.fr/dfma07/International audienceThis paper introduces a research project and a software environment to speed up and size up problem modeling with Partial Differential Equations (PDE). These PDE are defined from a \Mathematica interface, and are automatically solved by a devoted cellular automata program generated to be run on mainframes, clusters and Grids. Moreover, an interactive and graphic control of the cellular automata running allows to analyze the PDE model relevance. This environment improves large scale simulation usage in early stages of research projects

Astrobiological Complexity with Probabilistic Cellular Automata

Search for extraterrestrial life and intelligence constitutes one of the major endeavors in science, but has yet been quantitatively modeled only rarely and in a cursory and superficial fashion. We argue that probabilistic cellular automata (PCA) represent the best quantitative framework for modeling astrobiological history of the Milky Way and its Galactic Habitable Zone. The relevant astrobiological parameters are to be modeled as the elements of the input probability matrix for the PCA kernel. With the underlying simplicity of the cellular automata constructs, this approach enables a quick analysis of large and ambiguous input parameters' space. We perform a simple clustering analysis of typical astrobiological histories and discuss the relevant boundary conditions of practical importance for planning and guiding actual empirical astrobiological and SETI projects. In addition to showing how the present framework is adaptable to more complex situations and updated observational databases from current and near-future space missions, we demonstrate how numerical results could offer a cautious rationale for continuation of practical SETI searches.Comment: 37 pages, 11 figures, 2 tables; added journal reference belo

iC2mpi: A Platform for Parallel Execution of Graph-Structured Iterative Computations

Parallelization of sequential programs is often daunting because of the substantial development cost involved. Various solutions have been proposed to address this concern, including directive-based approaches and parallelization platforms. These solutions have not always been successful, in part because many try to address all types of applications. We propose a platform for parallelization of a class of applications that have similar computational structure, namely graph-structured iterative applications. iC2mpi is a unique proof-of-concept prototype platform that provides relatively easy parallelization of existing sequential programs and facilitates experimentation with static partitioning and dynamic load balancing schemes. We demonstrate with various generic application graph topologies and an existing application, namely a time-stepped battlefield management simulation, that our platform can produce good performance with very little effort

Facilitating arrhythmia simulation: the method of quantitative cellular automata modeling and parallel running

BACKGROUND: Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. METHODS: We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. RESULTS: We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. CONCLUSIONS: Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods described

Distributed Hybrid Simulation of the Internet of Things and Smart Territories

This paper deals with the use of hybrid simulation to build and compose heterogeneous simulation scenarios that can be proficiently exploited to model and represent the Internet of Things (IoT). Hybrid simulation is a methodology that combines multiple modalities of modeling/simulation. Complex scenarios are decomposed into simpler ones, each one being simulated through a specific simulation strategy. All these simulation building blocks are then synchronized and coordinated. This simulation methodology is an ideal one to represent IoT setups, which are usually very demanding, due to the heterogeneity of possible scenarios arising from the massive deployment of an enormous amount of sensors and devices. We present a use case concerned with the distributed simulation of smart territories, a novel view of decentralized geographical spaces that, thanks to the use of IoT, builds ICT services to manage resources in a way that is sustainable and not harmful to the environment. Three different simulation models are combined together, namely, an adaptive agent-based parallel and distributed simulator, an OMNeT++ based discrete event simulator and a script-language simulator based on MATLAB. Results from a performance analysis confirm the viability of using hybrid simulation to model complex IoT scenarios.Comment: arXiv admin note: substantial text overlap with arXiv:1605.0487