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Construct a grid computing environment for bioinformatics

Construct a grid computing environment for bioinformatics

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international symposium on parallel Architectures, Algorithms and Networks (ISPAN)

作者： Yu-Lun Kuo Chao-Tung Yang Chuan-Lin Lai Tsai-Ming Tseng High-Performance Computing Laboratory Department of Computer Science and Information Engineering Tunghai University Taichung Taiwan

ISBN: (纸本)0769521355

Internet computing and grid technologies promise to change the way we tackle complex problems. They will enable large-scale aggregation and sharing of computational, data and other resources across institutional boundaries. And harnessing these new technologies effectively will transform scientific disciplines ranging from high-energy physics to the life sciences. The computational analysis of biological sequences is a kind of computation driven science. Cause the biology data growing quickly and these databases are heterogeneous. We can use the grid system sharing and integrating the heterogeneous biology database. As we know, bioinformatics tools can speed up analysis the large-scale sequence data, especially about sequence alignment. The FASTA is a tool for aligning multiple protein or nucleotide sequences. FASTA which we used is a distributed and parallel version. The software uses a message-passing library called MPl (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers. A grid computing environment is proposed and constructed on multiple Linux PC clusters by using Globus Toolkit (GT) and SUN Grid Engine (SGE). The experimental results and performances of the bioinformatics tool using on grid system are also presented in this paper.

关键词： Grid computing Bioinformatics Sequences Biology computing Large-scale systems databases Internet Physics Proteins Software libraries

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LessLog: a logless file replication algorithm for peer-to-peer distributed systems

LessLog: a logless file replication algorithm for peer-to-pe...

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international symposium on parallel and distributed Processing (IPDPS)

作者： Kuang-Li Huang Tai-Yi Huang J.C.Y. Chou Department of Computer Science National Tsing Hua University Hsinchu Taiwan

Summary form only given. The technique of replicating frequently-accessed files to other nodes has been widely used in a high-performance distributed system to reduce the load of the nodes hosting these files. Traditional file replication algorithms rely on the analysis of client-access logs to determine the location of the replicated nodes. We present LessLog, a loglessfile replication algorithm, developed for a peer-to-peer distributed system. We first construct a lookup tree for each node. LessLog uses bitwise operations to determine the location of the replicated node without any client-access history. In addition, each replication is guaranteed to reduce the workload of the replicating node by half. A fault-tolerant LessLog model is also presented. The experimental results show that LessLog successfully and efficiently reduces the load of overloaded nodes.

关键词： Peer to peer computing Fault tolerant systems System performance Algorithm design and analysis Delay Computer science History Protocols Centralized control Scalability

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Adaptive cache-driven request distribution in clustered EJB systems

Adaptive cache-driven request distribution in clustered EJB ...

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international Conference on parallel and distributed systems (ICPADS)

作者： H. Elmeleegy N. Adly M. Nagi Mubarak City for Scientific Research Egypt Computer Science Department Alexandria University Egypt

This paper presents an algorithm for request distribution in clustered EJB systems. A classification for EJB requests is first introduced, on which request distribution is based. The objective is to achieve load balancing and to enhance the caching performance in the EJB containers. The algorithm is based on periodically collecting traffic statistics from the EJB containers, and then solving a constrained optimization problem that finds the best distribution strategies for each request type. An event-driven simulator is built for the performance evaluation, where the TPC-W benchmark is used as the workload. Simulation results show that for relatively small sizes of the containers' caches, the algorithm outperforms the random and round robin algorithms, currently used in clustered EJB systems. In addition, it scales better with the cluster size and can adapt to the varying load patterns.

关键词： Containers Round robin Clustering algorithms Load management Computer science Internet Web server Logic databases Adaptive systems

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Heuristic resource allocation algorithms for maximizing allowable workload in dynamic, distributed real-time systems

Heuristic resource allocation algorithms for maximizing allo...

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international symposium on parallel and distributed Processing (IPDPS)

作者： D. Juedes F. Drews L. Welch D. Fleeman Center for Intelligent Distributed and Dependable Systems School of Electrical Engineering and Computer Science Ohio University Athens OH USA

Summary form only given. We examine several heuristic algorithms for the maximum allowable workload (MAW) problem for real-time systems with tasks having variable workloads. Briefly, the problem concerns the allocation of tasks to m processors, where each task t is characterized by a function t.r(w) that gives the running time of the task in terms of its workload (or input size) w. The objective of the maximum allowable workload problem is to find an allocation of tasks to processors so that the allocation is feasible (no task misses its deadline) when each task is given a workload of w or smaller and w is maximized. This optimization problem uses a robustness measure that is closely related to the MAIL (maximum allowable increase in load) metric recently proposed by Gertphol et al. The main contribution of this paper is the comparison of several heuristic algorithms for the MAW-RMS problem. Hillclimbing, random search, simulated annealing, and first-fit heuristics are presented and evaluated via simulation. As we show here, the first-fit greedy heuristic produces solutions of a reasonable quality compared to the other algorithms. In addition, we demonstrate the applicability of our model in air defense systems.

关键词： Resource management Heuristic algorithms Real time systems Upper bound Simulated annealing Scheduling algorithm Computer science Robustness Postal services Robots

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On modeling wireless sensor networks

On modeling wireless sensor networks

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international symposium on parallel and distributed Processing (IPDPS)

作者： D. Gracanin M. Eltoweissy S. Olariu A. Wadaa Department of Computer Science Virginia Technology Falls Church VA USA Department of Computer Science Old Dominion University Norfolk VA USA

Summary form only given. Most of the current research in wireless sensor networks (WSN, for short) is constraint driven and focuses on optimizing the use of limited resources (for example, power) at each sensor. While such constraints are important, there is a need for more general performance metrics describing the effectiveness of WSNs. There is also a need for a unified model that would enable comparison of different types of WSNs. We propose a new service-centric model that focuses on services provided by a WSN and their corresponding performance metrics. A WSN is modeled at different levels of abstraction. For each level, a set of services and a set of metrics are defined. A mapping between metrics at different levels relates high-level, mission-oriented metrics to low-level capability-oriented metrics. The proposed model consists of mission, network, region, sensor, and capability layers. Within each layer, four planes are identified, namely, communications, management, application, and generation learning. The proposed model provides a flexible, open framework for expressing and evaluating capabilities, functionalities, management, behavior, and evolution of a WSN. In addition, the proposed model provides a holistic approach to comparing WSNs and to measuring their effectiveness. The generation learning plane is unique in that it serves to extend the longevity of the network and to enhance the network effectiveness over time.

关键词： Wireless sensor networks Web services Measurement Sensor systems Computer science Quality of service Constraint optimization Operating systems Eyes distributed databases

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Towards efficient load balancing in structured P2P systems

Towards efficient load balancing in structured P2P systems

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international symposium on parallel and distributed Processing (IPDPS)

作者： Y. Zhu Y. Hu Department of ECECS University of Cincinnati USA

Summary form only given. Many solutions have been proposed to tackle the problem of load balancing in structured P2P systems. However, all these solutions either ignore the heterogeneity nature of the system, or reassign loads among nodes without considering proximity relationships, or both. We propose an efficient scheme to ensure fair load distribution in such P2P systems by utilizing proximity information. To our knowledge, this is the first work to utilize the proximity information to guide load balancing. In particular, our main contributions are: (1) A self-organized, fully distributed K-nary tree structure is constructed on top of a distributed hash table (DHT) for load balancing information collection/dissemination and load reassignment. (2) Load balancing is achieved by aligning those two skews in load distribution and node capacity inhere in P2P systems - that is, have higher capacity nodes carry more loads. (3) Proximity information is utilized to guide load balancing such that loads are assigned and transferred between physically close heavy nodes and light nodes, thereby minimizing the load transferring overhead and allowing load balancing to perform more efficiently.

关键词： Load management Peer to peer computing Bandwidth Intrusion detection Tree data structures distributed processing

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System-level fault-tolerance in large-scale parallel machines with buffered coscheduling

System-level fault-tolerance in large-scale parallel machine...

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international symposium on parallel and distributed Processing (IPDPS)

作者： F. Petrini K. Davis J.C. Sancho Performance and Architecture Laboratory (PAL) Computer and Computational Sciences (CCS) Division Los Alamos National Laboratory NM USA

Summary form only given. As the number of processors for multiteraflop systems grows to tens of thousands, with proposed petaflops systems likely to contain hundreds of thousands of processors, the assumption of fully reliable hardware has been abandoned. Although the mean time between failures for the individual components can be very high, the large total component count will inevitably lead to frequent failures. It is therefore of paramount importance to develop new software solutions to deal with the unavoidable reality of hardware faults. We will first describe the nature of the failures of current large-scale machines, and extrapolate these results to future machines. Based on this preliminary analysis we will present a new technology that we are currently developing, buffered coscheduling, which seeks to implement fault tolerance at the operating system level. Major design goals include dynamic reallocation of resources to allow continuing execution in the presence of hardware failures, very high scalability, high efficiency (low overhead), and transparency - requiring no changes to user applications. Preliminary results show that this is attainable with current hardware.

关键词： Fault tolerant systems Large-scale systems parallel machines Hardware Laboratories Supercomputers Operating systems Application software Concurrent computing Computer aided manufacturing

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Specification and architecture supports for component adaptations on distributed environments

Specification and architecture supports for component adapta...

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international symposium on parallel and distributed Processing (IPDPS)

作者： Chung-Kai Chen Cheng-Wei Chen Jenq-Kuen Lee Department of Computer Science National Tsing Hua University Hsinchu Taiwan

ISBN: (纸本)0769521320

Summary form only given. 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 is how one can have component models adapt and respond to environment changes autonomously. We argue that additional annotation specifications for components are needed to advance this process. 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.

关键词： Computer architecture Service oriented architecture Collision mitigation Component architectures Application software Embedded software Software reusability Assembly Computer science distributed computing

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Models for scheduling on large scale platforms: which policy for which application?

Models for scheduling on large scale platforms: which policy...

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international symposium on parallel and distributed Processing (IPDPS)

作者： P.-F. Dutot L. Eyraud G. Mounie D. Trystram ID-IMAG Montbonnot Saint Martin France

Summary form only given. In recent years, there was a huge development of low cost large scale parallel systems. The design of efficient parallel algorithms has to be reconsidered to take into account new parameters of such execution platforms which are characterized by a larger number of heterogeneous processors, often organized as hierarchical subsystems. Alternative computational models have been designed to take into account these new characteristics. parallel tasks model /spl times/ PT in short - is a promising alternative for scheduling parallel applications. Another way of looking at the problem (which is somehow a dual view) is the divisible load model (DL) where an application is considered as a collection of a large number of elementary - sequential - computing units. These two new views of the problem allow us to consider communications implicitly or to mask them, leading to more tractable problems. This paper, first, presents some approximation algorithms for the PT model with a special emphasis on new execution platforms. We show how to mix these results with the DL model to manage the resources of an actual computational grid of 600 processors.

关键词： Large-scale systems Costs Algorithm design and analysis parallel algorithms Computational modeling Processor scheduling Load modeling Approximation algorithms Resource management Grid computing

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Utilizing home node prediction to improve the performance of software distributed shared memory

Utilizing home node prediction to improve the performance of...

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international symposium on parallel and distributed Processing (IPDPS)

作者： S. Peng Computer Systems Laboratory Cornell University Ithaca NY

Summary form only given. Many researchers use a home-based lazy release consistent protocol (HLRC) to provide a simple, effective, and scalable way to build software distributed shared memory (DSM) systems. However, the performance of HLRC is notoriously sensitive to the initial page distribution among home nodes. We propose an adaptive HLRC protocol in which the home page designation is able to change according to the observed application sharing pattern. Our system differs from HLRC and other adaptive derivatives in the following respects. first, the number of home nodes for each shared page can be varied, as opposed to having only a single home node. Second, we use prediction in a novel way to dynamically change the the location of home nodes according to different memory access patterns. The home node of each shared page is able to propagate, perish, and migrate. An online home predictor determine whether or not the current node should remain a home node or drop from the current set of home nodes for a given page. Finally, all decisions concerning home node group membership are made locally, eliminating the costly global decision-making communication present in many other systems. Performance evaluations using six well-known DSM benchmarks show that our adaptive protocol outperforms conventional HLRC by up to 60%.

关键词： Software performance System performance Access protocols Coherence distributed computing Home computing Laboratories Application software Decision making Workstations

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