Distributed BLAST in a grid computing context

The Basic Local Alignment Search Tool (BLAST) is one of the best known sequence comparison programs available in bioinformatics. It is used to compare query sequences to a set of target sequences, with the intention of finding similar sequences in the target set. Here, we present a distributed BLAST service which operates over a set of heterogeneous Grid resources and is made available through a Globus toolkit v.3 Grid service. This work has been carried out in the context of the BRIDGES project, a UK e-Science project aimed at providing a Grid based environment for biomedical research. Input consisting of multiple query sequences is partitioned into sub-jobs on the basis of the number of idle compute nodes available and then processed on these in batches. To achieve this, we have implemented our own Java-based scheduler which distributes sub-jobs across an array of resources utilizing a variety of local job scheduling systems

Tarmo: A Framework for Parallelized Bounded Model Checking

This paper investigates approaches to parallelizing Bounded Model Checking (BMC) for shared memory environments as well as for clusters of workstations. We present a generic framework for parallelized BMC named Tarmo. Our framework can be used with any incremental SAT encoding for BMC but for the results in this paper we use only the current state-of-the-art encoding for full PLTL. Using this encoding allows us to check both safety and liveness properties, contrary to an earlier work on distributing BMC that is limited to safety properties only. Despite our focus on BMC after it has been translated to SAT, existing distributed SAT solvers are not well suited for our application. This is because solving a BMC problem is not solving a set of independent SAT instances but rather involves solving multiple related SAT instances, encoded incrementally, where the satisfiability of each instance corresponds to the existence of a counterexample of a specific length. Our framework includes a generic architecture for a shared clause database that allows easy clause sharing between SAT solver threads solving various such instances. We present extensive experimental results obtained with multiple variants of our Tarmo implementation. Our shared memory variants have a significantly better performance than conventional single threaded approaches, which is a result that many users can benefit from as multi-core and multi-processor technology is widely available. Furthermore we demonstrate that our framework can be deployed in a typical cluster of workstations, where several multi-core machines are connected by a network

A Review Of Design And Control Of Automated Guided Vehicle Systems

This paper presents a review on design and control of automated guided vehicle systems. We address most key related issues including guide-path design, estimating the number of vehicles, vehicle scheduling, idle-vehicle positioning, battery management, vehicle routing, and conflict resolution. We discuss and classify important models and results from key publications in literature on automated guided vehicle systems, including often-neglected areas, such as idle-vehicle positioning and battery management. In addition, we propose a decision framework for design and implementation of automated guided vehicle systems, and suggest some fruitful research directions

An Approach to Line Balancing on Virtual Supervisor Induction Method and Intelligent Agents

This approach develops a method for solving the line-balancing problem, which is based on two stages. The works in a first stage is to identify the task of workstation, the assignment of the tasks to stations on the line and the recognized balance delay. In this stage we propose the induction VS method, which allows further identify the exact position between pieces, machine into a workstation and also between extern workstation, as well as intracellular and intercellular part. This way each task is identified and measured. In the second stage is to carry out a macro-approach to choose the resource to perform each of them. The hybrid intelligent agent architecture is proposed for this second stage, which has consideration of machining sequence. The integration between both technologies allows us to develop new hybrid architecture capable to reduce the computational time in the deliberative layers fundamentally. Finally, a reconfigurable testbed has been proposed for future experiments and results to evaluate this new balancing method. Some previous computational experiments provide that the proposed approach is efficient to solve practical transfer line design for balancing problem

Best matching processes in distributed systems

The growing complexity and dynamic behavior of modern manufacturing and service industries along with competitive and globalized markets have gradually transformed traditional centralized systems into distributed networks of e- (electronic) Systems. Emerging examples include e-Factories, virtual enterprises, smart farms, automated warehouses, and intelligent transportation systems. These (and similar) distributed systems, regardless of context and application, have a property in common: They all involve certain types of interactions (collaborative, competitive, or both) among their distributed individuals—from clusters of passive sensors and machines to complex networks of computers, intelligent robots, humans, and enterprises. Having this common property, such systems may encounter common challenges in terms of suboptimal interactions and thus poor performance, caused by potential mismatch between individuals. For example, mismatched subassembly parts, vehicles—routes, suppliers—retailers, employees—departments, and products—automated guided vehicles—storage locations may lead to low-quality products, congested roads, unstable supply networks, conflicts, and low service level, respectively. This research refers to this problem as best matching, and investigates it as a major design principle of CCT, the Collaborative Control Theory. The original contribution of this research is to elaborate on the fundamentals of best matching in distributed and collaborative systems, by providing general frameworks for (1) Systematic analysis, inclusive taxonomy, analogical and structural comparison between different matching processes; (2) Specification and formulation of problems, and development of algorithms and protocols for best matching; (3) Validation of the models, algorithms, and protocols through extensive numerical experiments and case studies. The first goal is addressed by investigating matching problems in distributed production, manufacturing, supply, and service systems based on a recently developed reference model, the PRISM Taxonomy of Best Matching. Following the second goal, the identified problems are then formulated as mixed-integer programs. Due to the computational complexity of matching problems, various optimization algorithms are developed for solving different problem instances, including modified genetic algorithms, tabu search, and neighbourhood search heuristics. The dynamic and collaborative/competitive behaviors of matching processes in distributed settings are also formulated and examined through various collaboration, best matching, and task administration protocols. In line with the third goal, four case studies are conducted on various manufacturing, supply, and service systems to highlight the impact of best matching on their operational performance, including service level, utilization, stability, and cost-effectiveness, and validate the computational merits of the developed solution methodologies

Application of lean scheduling and production control in non-repetitive manufacturing systems using intelligent agent decision support

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Lean Manufacturing (LM) is widely accepted as a world-class manufacturing paradigm, its currency and superiority are manifested in numerous recent success stories. Most lean tools including Just-in-Time (JIT) were designed for repetitive serial production systems. This resulted in a substantial stream of research which dismissed a priori the suitability of LM for non-repetitive non-serial job-shops. The extension of LM into non-repetitive production systems is opposed on the basis of the sheer complexity of applying JIT pull production control in non-repetitive systems fabricating a high variety of products. However, the application of LM in job-shops is not unexplored. Studies proposing the extension of leanness into non-repetitive production systems have promoted the modification of pull control mechanisms or reconfiguration of job-shops into cellular manufacturing systems. This thesis sought to address the shortcomings of the aforementioned approaches. The contribution of this thesis to knowledge in the field of production and operations management is threefold: Firstly, a Multi-Agent System (MAS) is designed to directly apply pull production control to a good approximation of a real-life job-shop. The scale and complexity of the developed MAS prove that the application of pull production control in non-repetitive manufacturing systems is challenging, perplex and laborious. Secondly, the thesis examines three pull production control mechanisms namely, Kanban, Base Stock and Constant Work-in-Process (CONWIP) which it enhances so as to prevent system deadlocks, an issue largely unaddressed in the relevant literature. Having successfully tested the transferability of pull production control to non-repetitive manufacturing, the third contribution of this thesis is that it uses experimental and empirical data to examine the impact of pull production control on job-shop performance. The thesis identifies issues resulting from the application of pull control in job-shops which have implications for industry practice and concludes by outlining further research that can be undertaken in this direction

Grid-enabling FIRST: Speeding up simulation applications using WinGrid

The vision of grid computing is to make computational power, storage capacity, data and applications available to users as readily as electricity and other utilities. Grid infrastructures and applications have traditionally been geared towards dedicated, centralized, high performance clusters running on UNIX flavour operating systems (commonly referred to as cluster-based grid computing). This can be contrasted with desktop-based grid computing which refers to the aggregation of non-dedicated, de-centralized, commodity PCs connected through a network and running (mostly) the Microsoft Windowstrade operating system. Large scale adoption of such Windowstrade-based grid infrastructure may be facilitated via grid-enabling existing Windows applications. This paper presents the WinGridtrade approach to grid enabling existing Windowstrade based commercial-off-the-shelf (COTS) simulation packages (CSPs). Through the use of a case study developed in conjunction with Ford Motor Company, the paper demonstrates how experimentation with the CSP Witnesstrade and FIRST can achieve a linear speedup when WinGridtrade is used to harness idle PC computing resources. This, combined with the lessons learned from the case study, has encouraged us to develop the Web service extensions to WinGridtrade. It is hoped that this would facilitate wider acceptance of WinGridtrade among enterprises having stringent security policies in place

Spider: An overview of an object-oriented distributed computing system

The Spider Project is an object-oriented distributed system which provides a testbed for researchers in the Department of Computer Science, CSUSB, to conduct research on distributed systems

Introduction to Production: Philosophies, Flow, and Analysis

Production is a fundamental societal and economic activity. Production has to do with the transformation of raw materials into useful objects and includes the knowledge to complete the transformation effectively. Thus, production is a board topic ranging from philosophies about how to approach production such as lean and quick response manufacturing, how to organize production facilities, how to analyze production operations, how to control the flow of materials during production, the devices used to move materials within a facility, and strategies for coordinating multiple production facilities. An integrated introduction to production is presented in a set of learning modules. In significant part, these learning modules are based on over 20 years of interactions with the professional production community in the West Michigan region where Grand Rapids and Holland are the principal cities. This community consists almost exclusively of small and medium size companies engaged primarily in high mix, low volume manufacturing. Students in the Bachelor of Science in Engineering and Master of Science in Engineering programs at Grand Valley State University often work in production for these companies. Thus, interactions are facilitated particularly though master’s degree capstone projects, several of which are referenced in the learning modules. The learning modules are well-grounded in established production concepts. Emphasis is placed on proven procedures such as systematic layout planning, factory physics, various production flow control techniques such as kanban and POLCA, and discrete event simulation. Professional practice is a focus of the learning modules. Material from processional groups such as the Lean Enterprise Institute and the Material Handling Institute (MHI) is integrated. The opportunity to read and discuss professional publications presenting production improvement projects is provided. Students are referred to professional videos and web sites throughout the learning modules. All materials provided are referenced are open access and free of charge. When downloading the main file, it is important to also download and use the Main File Support as it contains supplemental materials.https://scholarworks.gvsu.edu/books/1022/thumbnail.jp