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parallel EST clustering 16

Parallel EST clustering

引用

16th international parallel and distributed processing symposium, ipdps 2002

作者： Kalyanaraman, A. Aluru, S. Kothari, S. Dept. of CS Iowa State University AmesIA50011 United States Dept. of ECpE Iowa State University AmesIA50011 United States

ISBN: (纸本)0769515738

Expressed sequence tags, abbreviated ESTs, are DNA fragments experimentally derived from expressed portions of genes. Clustering of ESTs is essential for gene recognition and understanding important genetic variations such as those resulting in diseases. In this paper, we present the design and development of a parallel software system for EST clustering. the novel features of our approach include 1) space efficient algorithms to keep the space requirement linear in the size of the input data set, 2) a combination of algorithmic techniques to reduce the total work without sacrificing the quality of EST clustering, and 3) use of parallel processing to reduce the run-time and facilitate the clustering of large data sets. Using a combination of these techniques, we report the clustering of 50,000 maize ESTs in 16 minutes on a 32-processor IBM SP. To our knowledge, this is the first effort in building a parallel software system for EST clustering. © 2002 IEEE.

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Mobile active objects for highly dynamic distributed computing 16

Mobile active objects for highly dynamic distributed computi...

引用

16th international parallel and distributed processing symposium, ipdps 2002

作者： Fortino, G. Frattolillo, F. Russo, W. Zimeo, E. DEIS University of Calabria RendeCS87030 Italy School of Engineering University of Sannio Benevento82100 Italy

ISBN: (纸本)0769515738

the pervasiveness of Internet-based communication technologies is fostering new forms of distributed computing, namely, large-scale, highly decentralized computing and mobile computing. In this context, new application domains such as M-commerce, mobile multimedia, and cooperative information systems, demand for adaptive and flexible middlewares and frameworks which fully exploit logical mobility and support programmable coordination infrastructures. In this paper, we present a distributed computational model which extends an active object model by introducing the mobile active object concept in order to support a multi paradigm design approach. Mobile active objects are autonomous network-aware entities or mobile agents which coordinate to one another through on-demand installable interaction spaces featured by events. the model is embedded in ActiWare - our customizable Java-based framework for the development of highly dynamic distributed applications. © 2002 IEEE.

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parallel and distributed computing with coevolutionary algorithms 16

Parallel and distributed computing with coevolutionary algor...

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Seredynski, F. Zomaya, A.Y. Department of Computer Science Institute of Insurance Wesola 52 Kielce25-353 Poland Parallel Computing Research Laboratory Department of Electrical and Electronic Engineering University of Western Australia Nedlands PerthWA6907 Australia

ISBN: (纸本)0769515738

the problem of parallel and distributed function optimization is considered. Two coevolutionary algorithms with different degrees of parallelism and different levels of a global coordination are used for this purpose and compared with sequential genetic algorithm (GA). the first coevolutionary algorithm called a loosely coupled genetic algorithm (LCGA) represents a competitive coevolutionary approach to problem solving and is compared with another coevolutionary algoritm called cooperative coevolutionary genetic algorithm (CCGA). the algorithms are applied for parallel and distributed optimization of a number of test functions known in the area of evolutionary computation. We show that both coevolutionary algorithms outperform a sequential GA. While both LCGA and CCGA algorithms offer high quality solutions, they may compete to outperform each other in some specific test optimization problems. the LCGA may be recommended to be used in optimization systems when high degree of parallelism is possible and non global coordination is expected while the CCGA algorithm is useful when low degree of parallelism and global coordination is acceptable. © 2002 IEEE.

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A new model for static mapping of parallel applications with task and data parallelism 16

A new model for static mapping of parallel applications with...

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Roig, C. Ripoll, A. Senar, M.A. Guirado, F. Luque, E. Universitat de Lleida Dept. of CS Jaume II 69 Lleida25001 Spain Universitat Autònoma de Barcelona Dept. of CS BellaterraBarcelona08193 Spain

ISBN: (纸本)0769515738

the efficient mapping of parallel tasks is essential in order to exploit the gain from parallelisation. In this work, we focus on modelling and mapping message-passing applications that are defined by the programmer with an arbitrary interaction pattern among tasks. A new model is proposed, known as TTIG (Temporal Task Interaction Graph), which captures not only computation and communication costs, but also the percentages of concurrency between tasks. From this model, a mapping strategy is developed that minimises expected execution time by properly exploiting task parallelism. the effectiveness of this approach has been proven for a real image-processing application on a cluster of PCs. © 2002 IEEE.

关键词： mapping algorithms mapping of image-processing application modelling message-passing applications static mapping task and data parallelism

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Architecture of the Entropia distributed computing system 16

Architecture of the Entropia distributed computing system

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Chien, A.A. Entropia Inc. 10145 Pacific Heights Suite 800 San DiegoCA92121 United States University of California San Diego 9500 Gilman Drive San DiegoCA92093 United States

ISBN: (纸本)0769515738

distributed computing, the exploitation of idle cycles on pervasive desktop PC systems, offers the opportunity to increase the available computing power by orders of magnitude (10-1,000 times). However, for desktop PC distributed computing to be widely accepted within enterprises, the systems much achieve high levels of robustness, security, scalability, unobtrusiveness and manageability. We describe the Entropia distributed computing system as a case study, detailing its internal architecture and philosophy in attacking these key problems. In particular, key aspects of the Entropia system include the use of (1) scalable Web/database technology for system management, (2) network tunneling and application name-spaces for logical connectivity, (3) binary sand-boxing technology for security and unobtrusiveness, and (4) an open integration model to allow applications from many sources to be incorporated. these technologies are combined to produce a robust, flexible, high-performance system which is now in use in numerous enterprises, supporting a wide range of applications. © 2002 IEEE.

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Massively parallel solutions for molecular sequence analysis 16

Massively parallel solutions for molecular sequence analysis

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Schmidt, B. Schröder, H. Schimmler, M. Nanyang Technological University School of Computer Engineering Singapore639798 Singapore Technische Universität Braunschweig Institut für Datentechnik und Kommunikationsnetze Hans-Sommer-Str. 66 Braunschweig38106 Germany

ISBN: (纸本)0769515738

In this paper we present new approaches to high performance protein database scanning on two novel massively parallel architectures to gain supercomputer power at low cost. the first architecture is built around a Beowulf PC-cluster linked by a high-speed network and fine-grained parallel Systola 1024 processor boards connected to each node. the second architecture is the Fuzion 150, a new parallel computer with a linear SIMD array of 1536 processing elements on a single chip. We present the design of a database scanning application based on the Smith-Waterman algorithm in order to derive efficient mappings onto these architectures. the implementations lead to significant runtime savings for large-scale database scanning. this result shows that both architectures provide high-throughput sequence similarity analysis solutions at a good price/performance ratio. © 2002 IEEE.

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Efficient parallel algorithms for 2-dimensional ising spin models 16

Efficient parallel algorithms for 2-dimensional ising spin m...

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Santos, E.E. Feng, Shuangtong Rickman, J.M. Department of Computer Science Virginia Polytechnic Institute and State University BlacksburgVA United States Department of Material Science and Engineering Lehigh University BethlehemPA United States

ISBN: (纸本)0769515738

In this paper, we design and implement a variety of parallel algorithms for both sweep spin selection and random spin selection. We analyze our parallel algorithms on LogP, a portable and general parallel machine model. We then obtain rigorous theoretical run-time results on LogP for all the parallel algorithms. Moreover, a guiding equation is derived for choosing data layouts (blocked vs. stripped) for sweep spin selection. In regards to random spin selection, we are able to develop parallel algorithms with efficient communication schemes. We introduce two novel schemes, namely the FML scheme and the α-scheme. We analyze randomness of our schemes using statistical methods and provided comparisons between the different schemes. © 2002 IEEE.

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Fault tolerant distributed coloring algorithms that stabilize in linear time 16

Fault tolerant distributed coloring algorithms that stabiliz...

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Hedetniemi, S.T. Jacobs, D.P. Srimani, P.K. Department of Computer Science Clemson University ClemsonSC29634-0974 United States

ISBN: (纸本)0769515738

We propose two new self-stabilizing distributed algorithms for proper Δ+1 (Δ is the maximum degree of a node in the graph) coloring of arbitrary system graphs. Both algorithms are capable of working with multiple types of demons (schedulers) as is the most recent algorithm in [1]. the first algorithm converges in O(m) moves while the second converges in at most n moves (n is the number of nodes and m is the number of edges in the graph) as opposed to the O(Δ x n) moves required by the algorithm [1]. the second improvement is that neither of the proposed algorithms requires each node to have knowledge of Δ, as is required in [1]. Further, the coloring produced by our first algorithm provides an interesting special case of coloring, e.g., Grundy Coloring [2]. © 2002 IEEE.

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Resource-aware real-time CORBA in multi-server distributed environment 16

Resource-aware real-time CORBA in multi-server distributed e...

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Ravirala, M. Sivasubramanian, S. Kothari, S. Department of Electrical and Computer Engineering Iowa State University AmesIA50011 United States

ISBN: (纸本)0769515738

the emerging distributed applications require end-to-end support for various quality-of-service (QoS) aspects, including bandwidth, latency, jitter, and dependability. the Common Object Request Broker Architecture (CORBA) is an open distributed object computing infrastructure, standardized by the Object Management Group (OMG). Its goal is to minimize the effort required to develop high-quality systems by composing applications using reusable software components. However, CORBA is not sufficient to provide QoS guarantees in a distributed environment as it lacks capabilities to specify and enforce QoS constraints. For enforcing these constraints, OMG came up with Real-Time CORBA (RTCORBA) specification that can guarantee end-to-end predictability in a complex real-time system. Currently, RTCORBA specification addresses the location transparency, but does not address the resource monitoring and management issues critical for meeting the QoS constraints in a multi-server distributed processing environment. In this paper, we identify the functionalities that are required to ensure predictability in such an environment and propose a resource management framework for RTCORBA. We present its design, a prototype implementation using ORBit ORB, and an example to illustrate its use. © 2002 IEEE.

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Failure behavior analysis for reliable distributed embedded systems 16

Failure behavior analysis for reliable distributed embedded ...

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16th international parallel and distributed processing symposium, ipdps 2002

作者： Trapp, M. Schurmann, B. Tetteroo, T. Department of Computer Science University of Kaiserslautern Germany

ISBN: (纸本)0769515738

Failure behavior analysis is a very important phase in developing large distributed embedded systems with weak safety requirements which do graceful degradation in case of failures. Today, the analysis will usually be done by standard methods like FTA and FMEA considering the existence of faults, only. Gradations of errors are not regarded, although this is a very coarse system behavior approximation. In contrast to that, our advanced failure behavior analysis yields more sophisticated and graded results. We obtain comprehensive results by assigning a quality description to all the information in a system and extending the pure information flow to an information quality flow, that models system failure behavior, too. We model this information quality flow by object-oriented hierarchical petri nets. Large parts of these nets can automatically be generated from the existing behavioral system structure. A net simulator enables us to perform all the sophisticated analyses we need to examine the failure behavior. © 2002 IEEE.

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