Parallel cellular programming skeleton

Cellular automata provide an abstract model of parallel com- putation that can be effectively used for modeling and simulation of com- plex phenomena and systems. The design and implementation of parallel programming languages based on skeletons simplify the design, test and code of parallel algorithms. We discuss here the main characteristics of cellular automata programming models and we show a cellular automata skeleton for the exploitation on the inherent parallelism of problems of this kind. As a practical example, we show how to solve the problem of heat equation through the skeleton.Presentado en el IX Workshop Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Parallel cellular programming skeleton

Cellular automata provide an abstract model of parallel com- putation that can be effectively used for modeling and simulation of com- plex phenomena and systems. The design and implementation of parallel programming languages based on skeletons simplify the design, test and code of parallel algorithms. We discuss here the main characteristics of cellular automata programming models and we show a cellular automata skeleton for the exploitation on the inherent parallelism of problems of this kind. As a practical example, we show how to solve the problem of heat equation through the skeleton.Presentado en el IX Workshop Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Studying Parallel Evolutionary Algorithms: The cellular Programming Case

Parallel evolutionary algorithms, studied to some extent over the past few years, have proven empirically worthwhile—though there seems to be lacking a better understanding of their workings. In this paper we concentrate on cellular (fine-grained) models, presenting a number of statistical measures, both at the genotypic and phenotypic levels. We demonstrate the application and utility of these measures on a specific example, that of the cellular programming evolutionary algorithm, when used to evolve solutions to a hard problem in the cellular-automata domain, known as synchronization

Speeding Up Tumor Growth Simulations Using Parallel Programming and Cellular Automata

The study of tumor growth biology with computer-based models is currently an area of active research. Different simulation techniques can be used to describe the complexity of any real tumor behavior, among these, "cellular automata"-based simulations provide an accurate tumor growth graphical representation while, at the same time, keep simpler the implementation of the automata as computer programs. Several authors have recently published relevant proposals, based on the latter approach, to solve tumor growth representation problem through the development of some strategies for accelerating the simulation model. These strategies achieve computational performance of cellular-models representation by the appropriate selection of data types, and the clever use of supporting data structures. However, as of today, multithreaded processing techniques and multicore processors have not been used to program cellular growth models with generality. This paper presents a new model that incorporates parallel programming for multi and manycore processors, and implements any synchronization requirement necessary to implement the solution. The proposed parallel model has been proved using Java and C++ program implementations on two different platforms: chipset Intel i5-4440 and one node of 16-processors cluster of our university. The improvement resulting from the introduction of parallelism into the model is analyzed in this paper, comparing it with the standard sequential simulation model currently used by researchers in mathematical oncology

Parallel Implementations of Cellular Automata for Traffic Models

The Biham-Middleton-Levine (BML) traffic model is a simple two-dimensional, discrete Cellular Automaton (CA) that has been used to study self-organization and phase transitions arising in traffic flows. From the computational point of view, the BML model exhibits the usual features of discrete CA, where the state of the automaton are updated according to simple rules that depend on the state of each cell and its neighbors. In this paper we study the impact of various optimizations for speeding up CA computations by using the BML model as a case study. In particular, we describe and analyze the impact of several parallel implementations that rely on CPU features, such as multiple cores or SIMD instructions, and on GPUs. Experimental evaluation provides quantitative measures of the payoff of each technique in terms of speedup with respect to a plain serial implementation. Our findings show that the performance gap between CPU and GPU implementations of the BML traffic model can be reduced by clever exploitation of all CPU features

An Architecture-Altering and Training Methodology for Neural Logic Networks: Application in the Banking Sector

Artificial neural networks have been universally acknowledged for their ability on constructing forecasting and classifying systems. Among their desirable features, it has always been the interpretation of their structure, aiming to provide further knowledge for the domain experts. A number of methodologies have been developed for this reason. One such paradigm is the neural logic networks concept. Neural logic networks have been especially designed in order to enable the interpretation of their structure into a number of simple logical rules and they can be seen as a network representation of a logical rule base. Although powerful by their definition in this context, neural logic networks have performed poorly when used in approaches that required training from data. Standard training methods, such as the back-propagation, require the network’s synapse weight altering, which destroys the network’s interpretability. The methodology in this paper overcomes these problems and proposes an architecture-altering technique, which enables the production of highly antagonistic solutions while preserving any weight-related information. The implementation involves genetic programming using a grammar-guided training approach, in order to provide arbitrarily large and connected neural logic networks. The methodology is tested in a problem from the banking sector with encouraging results

Developing Efficient Discrete Simulations on Multicore and GPU Architectures

In this paper we show how to efficiently implement parallel discrete simulations on multicoreandGPUarchitecturesthrougharealexampleofanapplication: acellularautomatamodel of laser dynamics. We describe the techniques employed to build and optimize the implementations using OpenMP and CUDA frameworks. We have evaluated the performance on two different hardware platforms that represent different target market segments: high-end platforms for scientific computing, using an Intel Xeon Platinum 8259CL server with 48 cores, and also an NVIDIA Tesla V100GPU,bothrunningonAmazonWebServer(AWS)Cloud;and on a consumer-oriented platform, using an Intel Core i9 9900k CPU and an NVIDIA GeForce GTX 1050 TI GPU. Performance results were compared and analyzed in detail. We show that excellent performance and scalability can be obtained in both platforms, and we extract some important issues that imply a performance degradation for them. We also found that current multicore CPUs with large core numbers can bring a performance very near to that of GPUs, and even identical in some cases.Ministerio de Economía, Industria y Competitividad, Gobierno de España (MINECO), and the Agencia Estatal de Investigación (AEI) of Spain, cofinanced by FEDER funds (EU) TIN2017-89842

Decision Making in the Medical Domain: Comparing the Effectiveness of GP-Generated Fuzzy Intelligent Structures

ABSTRACT: In this work, we examine the effectiveness of two intelligent models in medical domains. Namely, we apply grammar-guided genetic programming to produce fuzzy intelligent structures, such as fuzzy rule-based systems and fuzzy Petri nets, in medical data mining tasks. First, we use two context-free grammars to describe fuzzy rule-based systems and fuzzy Petri nets with genetic programming. Then, we apply cellular encoding in order to express the fuzzy Petri nets with arbitrary size and topology. The models are examined thoroughly in four real-world medical data sets. Results are presented in detail and the competitive advantages and drawbacks of the selected methodologies are discussed, in respect to the nature of each application domain. Conclusions are drawn on the effectiveness and efficiency of the presented approach

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