260704
An implementation of parallel dynamic load balancing for adaptive computing in VLSI device simulation
A new parallel semiconductor device simulation using the dynamic load balancing approach is presented. This semiconductor device simulation based on adaptive finite volume error estimation, and monotone iterative methods has been developed and implemented on a Linux-cluster with MPI library. Two different parallel versions of the algorithm to perform a complete device simulation are proposed. The first one is a dynamic parallel domain decomposition approach. The second version is a parallel current-voltage characteristic points simulation. The implementation shows that a well-designed load balancing simulation can reduce the execution time up to an order of magnitude. Compared with the measured data, numerical simulations on P-N diode, N-MOSFET, and DTMOS devices are presented to show the accuracy and efficiency of the method.
12948988
Parallelization of Multiple Genome Alignment
In this work, we implement a genome alignment system which applies parallelization schemes to the ClustalW algorithm and the interface of database querying. Parallel construction of the distance matrices and parallelization of progressive alignment in the ClustalW algorithm are performed on PC-based Linux cluster with message-passing interface libraries. Achieved experiments show good speedup and significant parallel performance.
21349955
A unified optimization framework for microelectronics industry
In this paper, an object-oriented unified optimization framework (UOF) for general problem optimization is proposed. Based on evolutionary algorithms, numerical deterministic methods, and C++ objective design, the UOF possesses real-world applications for various optimization problems. The UOF is with interface between defining a general problem and generic solver; hence the two areas are bridged. The UOF's components are categorized into problem and solver parts, and they work independently. Therefore, the reusable high level code allows the adaptation to new problem and solver quickly. Practical applications in microelectronics industry confirm the functionality of the developed unified optimization framework.
18159266
A Distributed Simulation-Based Computational Intelligence Algorithm for Nanoscale Semiconductor Device Inverse Problem
In this paper, a distributed simulation-based computational intelligence algorithm for inverse problem of nanoscale semiconductor device is presented. This approach features a simulation-based optimization strategy, and mainly integrates the semiconductor process simulation, semiconductor device simulation, evolutionary strategy, and empirical knowledge on a distributed computing environment. For a set of given target current-voltage (I-V) curves of metal-oxide-semiconductor field effect transistors (MOSFETs) devices, the developed prototype executes evolutionary tasks to solve an inverse doping profile problem, and therefore optimize fabrication recipes. In the evolutionary loop, the established management server allocates the jobs of process simulation and device simulation on a PC-based Linux cluster with message passing interface (MPI) libraries. Good benchmark results including the speed-up, the load balancing, and the parallel efficiency are presented. Computed results, compared with the realistic measured data of 65 nm n-type MOSFET, show the accuracy and robustness of the method.
9048744
Web-based simulation experiments
The use of the World Wide Web and Java-based mobile code provides new opportunities for distributed simulation. First, the infrastructure provided by the Internet eliminates the need for multiprocessor hardware, making it feasible to distribute simulation models over different hardware platforms through the Internet. Second, "Internet-aware" mobile Java code makes the applications fully portable and reusable. These enabling technologies are already exploited for distributed simulation modeling. This paper reports on the preliminary results of an on-going effort to construct a parallel discrete event simulation support system to distribute simulation experiments over the Internet with a view on simulation optimization. A research prototype for ranking and selection problems is described. The overall project goals are discussed.
35624108
Optimal Parallel Routing in Star Graphs
Star graphs have been recently proposed as attractive alternatives to the popular hypercube for interconnecting processors on a parallel computer. In this paper, we present an efficient algorithm that constructs an optimal parallel routing in star graphs. Our result improves previous results for the problem.
6671949
Identification of critical genes in microarray experiments by a Neuro-Fuzzy approach
Gene expression profiling by microarray technology is usually difficult to interpret into a simpler pattern. One approach to resolve the complexity of gene expression profiles is the application of artificial neural networks (ANNs). A potential difficulty in this strategy, however, is that the non-linear nature of ANN makes it essentially a 'black-box' computation process. Addition of a fuzzy logic approach is useful because it can complement ANN by explicitly specifying membership function during computation. We employed a hybrid approach of neural network and fuzzy logic to further analyze a published microarray study of gene responses to eight bacteria in human macrophages. The original analysis by hierarchical clustering found common gene responses to all bacteria but did not address individual responses. Our method allowed exploration of the gene response of the host to individual bacterium. We implemented a two-layer, feed-forward neural network containing the principle of 'competitive learning' (i.e. 'winner-take-all'). The weights of the trained neural network were fed into a fuzzy logic inference system. A new measurement, called the impact rating (IR) was also introduced to explore the degree of importance of each gene. To assess the reliability of the IR value, a bootstrap re-sampling method was applied to the dataset and a confidence level for each IR was obtained. Our approach has successfully uncovered the unique features of host response to individual bacterium. Further, application of gene ontology (GO) annotation to the genes of high IR values in each response has suggested new biological pathways for individual host-pathogen interactions.
2154628
Distributed web-based simulation experiments for optimization
Abstract The web has grown tremendously over the past decade – with applications in education, marketing, financial services, and supply chain management. Web technology also has a significant impact on computer simulation. Most of the effort in web-based simulation is aimed at modeling, particularly at building simulation languages and at creating model libraries that can be assembled and executed over the web. This paper focuses on efficiency of simulation experimentation for optimization. We introduce a framework for combining the statistical efficiency of simulation optimization techniques with the effectiveness of parallel execution algorithms. In particular, a novel simulation sampling procedure, the Optimal Computing Budget Allocation (OCBA) algorithm, is implemented in a web-based environment for low-cost parallel and distributed simulation experimentation. A prototype implementation with some experimental results is presented to show the viability of web-enabled simulation environments.
6134463
Visualizing latent domain knowledge
Knowledge discovery and data mining commonly rely on finding salient patterns of association from a vast amount of data. Traditional citation analysis of scientific literature draws insights from strong citation patterns. Latent domain knowledge, in contrast to the mainstream domain knowledge, often consists of highly relevant but relatively infrequently cited scientific works. Visualizing latent domain knowledge presents a significant challenge to knowledge discovery and quantitative studies of science. We build upon a citation-based knowledge visualization procedure and develop an approach that not only captures knowledge structures from prominent and highly cited works, but also traces latent domain knowledge through low-frequency citation chains. We apply this approach to two cases: (1) identifying cross-domain applications of Pathfinder networks (PFNETs) and (2) clarifying the current status of scientific inquiry of a possible link between Bovine spongiform encephalopathy (BSE), also known as mad cow disease, and a new variant Creutzfeldt-Jakob disease (vCJD), a type of brain disease in humans.