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Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria 07

Large scale deployment of molecular docking application on c...

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7th IEEE international symposium on Cluster Computing and the Grid

作者： Kasam, Vinod Salzemann, Jean Jacq, Nicolas Mass, Astrid Breton, Vincent Phys Corpusculaire Lab Campus Cezeaux24 Av Landais F-63177 Aubiere France Sch Birlingoven Fraunho Inst Algorithms Sci Comp SCAI D-53754 St Augustin Germany

ISBN: (纸本)9780769528335

Computational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required. The WISDOM project successfully deployed virtual screening at large scale on EGEE grid infrastructures in the summer 2005 and achieved 46 million dockings in 45 days, which is equivalent to 80 CPU years. WISDOM is one good example of a successful deployment of an embarrassingly parallel application. In this paper, we describe the improvements in our deployment. We screened ZINC database against four targets implicated in malaria. During more than 2 months and a half, we have achieved 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tools.

关键词： Large-scale systems Computer applications Grid computing Diseases Chemical compounds databases Costs DNA Polymers Biology computing

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Models and Heuristics for Robust Resource Allocation in parallel and distributed Computing systems

Models and Heuristics for Robust Resource Allocation in Para...

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international symposium on parallel and distributed Processing (IPDPS)

作者： David L. Janovy Jay Smith Howard Jay Siegel Anthony A. Maciejewski Department of Electrical and Computer Engineering Colorado State University Fort Collins CO USA IBM Boulder CO USA Colorado State University Fort Collins CO US

This is an overview of the robust resource allocation research efforts that have been and continue to be conducted by the CSU robustness in computer systems group. parallel and distributed computing systems, consisting of a (usually heterogeneous) set of machines and networks, frequently operate in environments where delivered performance degrades due to unpredictable circumstances. Such unpredictability can be the result of sudden machine failures, increases in system load, or errors caused by inaccurate initial estimation. The research into developing models and heuristics for parallel and distributed computing systems that create robust resource allocations is presented.

关键词： Robustness Resource management distributed computing Stochastic processes Concurrent computing Uncertainty Actuators Computer science Road transportation Degradation

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A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multicore parallel Algorithms

A Graph-Theoretic Analysis of the Human Protein-Interaction ...

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international symposium on parallel and distributed Processing (IPDPS)

作者： David A. Bader Kamesh Madduri College of Computing Georgia Institute of Technology Atlanta GA USA

Protein-interaction network (PIN) analysis provides valuable insight into an organism's functional organization and evolutionary behavior. In this paper, we study a PIN formed by high-confidence human protein interactions obtained from various public interaction databases. This is the largest human PIN studied to date, comprising nearly 18,000 proteins and 44,000 interactions. A novel contribution of this paper is the computation of betweenness centrality, a graph-theoretic metric that is found to be positively correlated with the essentiality and evolutionary age of a protein. We observe that proteins with high betweenness centrality, but low connectivity are abundant in the human PIN. We have designed an efficient and portable parallel implementation for the calculation of this compute-intensive centrality metric. On the Sun Fire T2000 server with the UltraSparc T1 (Niagara) processor, we achieve a relative speedup of about 16 using 32 threads for a typical instance of betweenness centrality, reducing the running time from several minutes to 13 seconds.

关键词： Algorithm design and analysis Humans Proteins Multicore processing parallel algorithms databases Concurrent computing Portable computers Sun Fires

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On the Move to Meaningful Internet systems 2006: CoopIS, DOA, GADA, and ODBASE OTM Confederated international Conferences, CoopIS, DOA, GADA, and ODBASE ... Applications, incl. Internet/Web, and HCI)

引用

2007年

作者： Robert A Meersman Zahir Tari

ISBN: (纸本)9783540482871

This two-volume set LNCS 4275/4276 constitutes the refereed proceedings of the four confederated conferences CoopIS 2006, DOA 2006, GADA 2006, and ODBASE 2006 held as OTM 2006 in Montpellier, France in October/November 2006. The 106 revised full and 9 short papers presented together with 4 keynote speeches were carefully reviewed and selected from a total of 361 submissions. Corresponding with the four OTM 2006 main conferences CoopIS, ODBASE, GADA, and DOA, the papers are organized in topical sections on distributed information systems, workflow modelling, workflow management and discovery, dynamic and adaptable workflows, services metrics and pricing, formal approaches to services, trust and security in cooperative IS, P2P systems, collaborative systems design and development, collaborative systems development, cooperative IS applications, foundations, metadata, design, ontology mappings, information integration, agents, contexts, similarity and matching, resource selection and management, P2P-based systems, grid file transfer, parallel applications, scheduling in grid environments, autonomous and autonomic computing, grid infrastructures for data analysis, access control and security, programming aspects for developing scientific grid components, databases and data grids, distributed applications, evaluation, services, communications, searching techniques, types and notations, adaptivity, middleware, distribution support, and self-organisation.

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parallel on-chip ciphers development for the third generation mobile telecommunication system

Parallel on-chip ciphers development for the third generatio...

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3rd IASTED international Conference on Advances in Computer Science and Technology, ACST 2007

作者： Damaj, Issam W. Electrical and Computer Engineering Deparment Dhofar University P.O. Box 2509 211 Salalah Oman

ISBN: (纸本)9780889866560

The paper focuses on the synthesis of a highly parallel hardware implementation of the main cipher designed for the third generation mobile communication system. The investigated algorithm is the KASUMI block cipher. Currently, KASUMI is well known to be a strong encryption algorithm. The use of such an algorithm within critical applications, such as mobile communication, requires efficient, highly reliable and correct hardware implementation. We will investigate satisfying such requirements by proposing and adopting a step-wise refinement software engineering approach to develop correct hardware circuits. The method uses a formal functional programming notation for specifying algorithms. The parallel behavior is then obtained through the use of a combination of function decomposition strategies, besides, data and process refinement techniques. The refinements are inspired by the operators of Communicating Sequential Processes (CSP) and map easily to programs in Handel-C (a modern C-based high-level langauge with hardware output). In this paper, we obtain several hardware implementations with different performance characteristics by applying different refinements to the algorithm. The developed designs are compiled and tested under Celoxica's RC-1000 reconfigurable computer with its 2 million gates Virtex-E FPGA. Performance analysis and evaluation of these implementations are included.

关键词： C (programming language)

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DejaVu: Transparent User-Level Checkpointing, Migration, and Recovery for distributed systems

DejaVu: Transparent User-Level Checkpointing, Migration, and...

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international symposium on parallel and distributed Processing (IPDPS)

作者： Joseph F. Ruscio Michael A. Heffner Srinidhi Varadarajan Department of Computer Science Computing Systems Research Laboratory Virginia Polytechnic Institute and State University VA USA Evergrid VA USA

In this paper, we present a new fault tolerance system called DejaVu for transparent and automatic checkpointing, migration, and recovery of parallel and distributed applications. DejaVu provides a transparent parallel checkpointing and recovery mechanism that recovers from any combination of systems failures without any modification to parallel applications or the OS. It uses a new runtime mechanism for transparent incremental checkpointing that captures the least amount of state needed to maintain global consistency and provides a novel communication architecture that enables transparent migration of existing MPI codes, without source-code modifications. Performance results from the production-ready implementation show less than 5% overhead in real-world parallel applications with large memory footprints.

关键词： Checkpointing Application software Concurrent computing Runtime Stability Computer networks distributed computing Laboratories Computer science Fault tolerant systems

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parallel and distributed databases: Introduction

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2007年 4641 LNCS卷 293-293页

作者： Patiño-Martinez, Marta Vargas-Solar, Genoveva Baralis, Elena Kemme, Bettina

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A Scalable Approach for the Secure and Authorized Tracking of the Availability of Entities in distributed systems

A Scalable Approach for the Secure and Authorized Tracking o...

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international symposium on parallel and distributed Processing (IPDPS)

作者： Shrideep Pallickara Jaliya Ekanayake Geoffrey Fox Community Grids Lab Indiana University Bloomington IN USA

As the scale and proliferation of distributed applications continues to increase a need often arises to track the availability of entities that comprise the distributed system. An entity that is part of such a distributed system could be a resource, a service that provides a set of exposed capabilities, an application or a user. In this paper we present a transport-independent scheme for tracking the availability of entities in distributed systems. The scheme enforces the authorized generation and consumption of traces (encapsulating entity availability). The scheme also facilitates the secure distribution of traces while coping with some classes of denial of service attacks.

关键词： Availability Computer crime Authorization Probes Costs Transport protocols Control systems Information security Cryptography

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High Performance Computing in the Multi-core Area

High Performance Computing in the Multi-core Area

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international symposium on parallel and distributed Computing

作者： Arndt Bode Lehrstuhl für Rechnertechnik und Rechnerorganisation Technische Universität München Garching Germany

Summary form only given. Multi-core technologies, application specific accelerators and fault tolerance requirements are defining a new hardware basis for high performance computing systems. Multi-core will make evolve parallelism from a niche product in HPC to the standard programming model and, therefore, trigger new developments in languages, environments and tools. Accelerators and dynamic system behaviour from fault tolerance will make virtualization techniques necessary to support programmability. Energy efficiency as a new optimization target for HPCN systems will force future systems to bring all of these techniques together.

关键词： High performance computing Fault tolerant systems Hardware parallel processing Standards development parallel programming Energy efficiency distributed computing

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SLOSL--A Modelling Language for Topologies and Routing in Overlay Networks

SLOSL--A Modelling Language for Topologies and Routing in Ov...

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Euromicro Conference on parallel, distributed and Network-Based Processing

作者： Stefan Behnel Databases and Distributed Systems Group Darmstadt University of Technology Germany

Overlay networks are a fascinating field in the area of distributed systems. They combine challenges from self-organisation to extreme scalability and provide an interesting middleware layer for server-free Internet applications. The design aspects of their implementations, however, remained largely at the prototype level, which renders their integration and deployment in real applications hard. This paper describes an integrative, platform independent design approach for overlay networks that models topologies as data management systems. Local decisions about neighbours and message forwarding are expressed in an SQL-like language. The mapping to runnable implementations follows the model driven architecture approach

关键词： Network topology Routing Protocols Programming profession Internet Domain specific languages distributed databases Scalability Middleware Prototypes

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