A growing trend in developing large and complex applications on today's Teraflop computers is to integrate stand-alone and/or semi-independent program components into a comprehensive simulation package. One exampl...
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ISBN:
(纸本)0769521320
A growing trend in developing large and complex applications on today's Teraflop computers is to integrate stand-alone and/or semi-independent program components into a comprehensive simulation package. One example is the climate system model which consists of atmosphere, ocean, land-surface and sea-ice. Each component is semi-independent and has been developed at different institutions. We study how this multi-component multi-executable application can run effectively on distributed memory architectures. We identify five effective execution modes and develop the MPH library to support application developments utilizing these modes. MPH performs component-name registration, resource allocation and initial component hand-shaking in a flexible way.
In this paper, we treat the linkage disequilibrium, used to discover haplotypes, candidate to explain multi-factorial diseases such as diabetes or obesity, as an optimization problem where a given objective function h...
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ISBN:
(纸本)0769521320
In this paper, we treat the linkage disequilibrium, used to discover haplotypes, candidate to explain multi-factorial diseases such as diabetes or obesity, as an optimization problem where a given objective function has to be optimized. In order to determine what kind of algorithm will be able to solve this problem, we first study the specificities and the structure of the problem. Results of this study show that exact algorithms are not adapted to this specific problem and lead us to the development of a parallel dedicated adaptive multipopulation genetic algorithm that is able to find several haplotypes of different sizes. After describing the biological problem, we present the dedicated genetic algorithm, its specificities, such as the use of several populations and its advanced mechanisms such as the adaptive choice of operators, random immigrants, and its parallel implementation. We give results on a real dataset.
With the growing number of known RNA genes efficient and accurate computational analysis of RNA sequences is becoming increasingly important. Stochastic context-free grammars (SCFGs) are used as a popular tool to mode...
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ISBN:
(纸本)0769521320
With the growing number of known RNA genes efficient and accurate computational analysis of RNA sequences is becoming increasingly important. Stochastic context-free grammars (SCFGs) are used as a popular tool to model RNA secondary structures. However, algorithms for aligning an RNA sequence to an SCFG are highly compute-intensive. This has so far limited applications of SCFGs to relatively small problem sizes. In this paper we present the design of a parallel RNA sequence-structure alignment algorithm. Its implementation on a PC cluster leads to significant runtime savings. This makes it possible to compute sequence-structure alignments of even the largest RNAs such as SSU rRNAs and LSU rRNAs in reasonable time.
In this paper, we consider steady-state scheduling techniques for mapping a collection of task graphs onto heterogeneous systems, such as clusters and grids. We advocate the use of steady-state scheduling to solve thi...
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ISBN:
(纸本)0769522106
In this paper, we consider steady-state scheduling techniques for mapping a collection of task graphs onto heterogeneous systems, such as clusters and grids. We advocate the use of steady-state scheduling to solve this difficult problem. Due to space limitations, we concentrate on complexity results. We show that the problem of optimizing the steady-state throughput is NP-Complete in the general case. We formulate a compact version of the problem that belongs to the NP complexity class but which does not restrict the optimality of the solution. We provide many positive results in the extended version [5]. Indeed, we show how to determine in polynomial time the best steady-state scheduling strategy for a large class of application graphs and for an arbitrary platform graphs, using a linear programming approach.
In this paper a fast algorithm for solving a large system with an essentially Toeplitz five-band coefficient matrix is presented. The first two and last two rows are influenced by boundary conditions. The five band co...
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ISBN:
(纸本)0769521320
In this paper a fast algorithm for solving a large system with an essentially Toeplitz five-band coefficient matrix is presented. The first two and last two rows are influenced by boundary conditions. The five band core of this matrix is factored as the product of tridiagonal matri-ces for the purpose of obtaining a solution of a linear system more efficiently. An error term for the approximate solution is presented following the work by Yan and Chung [12]. An algorithm is developed for solving the two systems and is tested using two multiprocessor machines with different architectures.
Since the introduction of the Java language less then a decade ago, there have been several attempts to create a runtime system for distributed execution of multithreaded Java applications. The goal of these attempts ...
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ISBN:
(纸本)0769521320
Since the introduction of the Java language less then a decade ago, there have been several attempts to create a runtime system for distributed execution of multithreaded Java applications. The goal of these attempts was to gain increased computational power while preserving Java's convenient parallel programming paradigm. This paper gives a detailed overview of the existing distributed runtime systems for Java and presents a new approach, implemented in a system called JavaSplit. Unlike previous works, which either forfeit Java's portability or introduce unconventional programming constructs, JavaSplit is able to execute standard multithreaded Java while preserving portability. JavaSplit works by rewriting the bytecodes of a given parallel application, transforming it into a distributed application that incorporates all the runtime logic. Each runtime node carries out its part of the resulting distributed computation using nothing but its local standard (unmodified) Java Virtual Machine (JVM).
Clustering of several storage servers is a common way to build fast and fault tolerant storage systems. One application can be found in the context of parallel programs that already run on clustered systems and need t...
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ISBN:
(纸本)0769521320
Clustering of several storage servers is a common way to build fast and fault tolerant storage systems. One application can be found in the context of parallel programs that already run on clustered systems and need to write and read a huge amount of data from and to disks. Another application field are web and video streaming server that cause intense data transfer from and to disks. In this paper a distributed storage system is reviewed under the aspect of fault tolerance and reconfiguration of the data layout after faults. Data objects are stored in a data layout according to RAID level 3 among disk subsystems of different computers. Concurrent up- and down-streaming of data is provided by a technique that ensures data consistency. This consistency has been found to be beneficial for concurrent access and reconfiguration. Beyond, the system does not need a meta-data server, which often represents a bottleneck for distributed storage systems.
Within the trend of object-based distributed computing, we present the design and implementation of a numerical simulation for electromagnetic waves propagation. A sequential Java design and implementation is first pr...
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ISBN:
(纸本)0769521320
Within the trend of object-based distributed computing, we present the design and implementation of a numerical simulation for electromagnetic waves propagation. A sequential Java design and implementation is first presented. Further, a distributed and parallel version is derived from the first, using an active object pattern. In addition, benchmarks are presented on this non embarrassingly parallel application. A first contribution of this paper resides in the sequential object-oriented design that proved to be very modular and extensible;the classes and abstractions are designed to allow both element and volume type methods, furthermore, valid on structured, unstructured, or hybrid meshes. Compared to a Fortran version, the performance of this highly modular version proved to be in the same range. It is also shown how smoothly the sequential version can be distributed, keeping the same structuring and object abstractions, allowing to deal with larger data size. Finally, benchmarks on up to 64 processors compare the performances with respect to sequential and parallel versions, putting that in perspective with a comparable Fortran version.
Two of the main threads in distributed computing that recently show noticeable progress are Grid Computing and the development of Web-based services. It is our opinion that the adoption of the standards fostered by th...
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ISBN:
(纸本)0769521320
Two of the main threads in distributed computing that recently show noticeable progress are Grid Computing and the development of Web-based services. It is our opinion that the adoption of the standards fostered by the web-service community could improve the level of usability and interoperability of grid systems and lead to the development of meta-computing systems based on reusable, interoperable components. Up to now the adoption of Web Services in Grid projects has never penetrated the core computational model. This is mainly due to the fact that Web Services use by default the SOAP protocol which is extremely ill suited to computational science applications. In this paper we show how we leveraged the Web Service Invocation Framework (WSIF) to develop a new high performance binding based on XDR coding and how we improved the general WSIF performance by developing an extension based on a fully static service invocation.
With the arrival of the new computing paradigm in addressing autonomous systems for heterogeneous distributed architectures, distributed component technologies face challenges ahead. One of the key issues will be how ...
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ISBN:
(纸本)0769521320
With the arrival of the new computing paradigm in addressing autonomous systems for heterogeneous distributed architectures, distributed component technologies face challenges ahead. One of the key issues will be how one can have component models adapt and respond to environment changes autonomously. In our research work, we argue that additional annotation specifications for components are needed to advance this process. In this paper, we first present additional annotation specifications for components. This information can then be retrieved by Java introspection and represented in DAML+OIL language, which is based on the RDF schema and the XML syntax. Based on the specifications, we then present a Component Management Service (CMS) model and architecture to address the specification and composition issues of components on heterogeneous distributed architectures. Experimental results show significant performance improvements with our support of component adaptations in all cases. Our work presents a major advance for areas related to specifications and compositions of distributed components.
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