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On parallelization of a spatially-explicit structured ecological model for integrated ecosystem simulation

international JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2006年第4期20卷 571-581页

作者： Wang, Dali Berry, Michael W. Gross, Louis J. Univ Tennessee Dept Comp Sci Knoxville TN 37996 USA Univ Tennessee Dept Ecol & Evolutionary Biol Knoxville TN 37996 USA Univ Tennessee Dept Math Knoxville TN 37996 USA

Spatially explicit landscape population models are widely used to analyze the dynamics of an ecological species over a realistic landscape. These models may be data intensive applications when they include the age and size structure of the species in conjunction with spatial information coming from a geographic information system (GIS). We report on parallelization of a spatially explicit landscape model (PALFISH), in a component-based simulation framework, utilizing different parallel architectures. A multithreaded programming language (Pthread) is used to deliver high scalability on a symmetric multiprocessor (SMP), and a message-passing library is deployed for parallel implementation on both an SMP and a commodity cluster. The PALFISH model delivers essentially identical results as a sequential version but with high scalability: yielding a speedup factor of 12 as the runtime is reduced from 35 hours (sequential ALFISH) to 2.5 hours on a 14-processor SMP. Hardware performance data were collected to better characterize the parallel execution of the model on the different architectures. This is the first documentation of a high performance application in natural resource management that uses different parallel computing libraries and platforms. Due to the diverse needs for computationally intensive multimodels in scientific applications, our conclusions arising from a practical application which brings the software component paradigm to high-performance scientific computing, can provide guidance for appropriate parallelization approaches incorporating multiple temporal and spatial scales.

关键词： component-based parallel computing integrated ecological simulation spatially-explicit model performance evaluation computational ecology

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12th international Conference on parallel and distributed systems

12th International Conference on Parallel and Distributed Sy...

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international Conference on parallel and distributed systems (ICPADS)

The following topics are dealt with: heterogeneous scheduling; stabilization algorithms; availability and security; MPI & shared memory; scheduling and resource management; parallel and distributed algorithms; Web performance; data dissemination in sensor networks; QoS in interconnection networks; streaming; sensor network deployment; power-aware protocols; grids; multiprocessor scheduling; multicore scheduling; P2P networks; switch design; parallel programming tools; communication networks; fault tolerance; resource monitoring; and ad hoc and wireless networks.

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Proceedings of the 7th IEEE/ACM international Conference on Grid Computing, GRID 2006

Proceedings of the 7th IEEE/ACM International Conference on ...

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7th IEEE/ACM international Conference on Grid Computing, GRID 2006

ISBN: (纸本)1424403448

The proceedings contain 49 papers. The topics discussed include: QoS-constrained stochastic workflow scheduling in enterprise and scientific grids;resource discovery techniques in distributed desktop grid environments;overhead analysis of grid workflow applications;workflow global computing with YML;run-time optimization of grid workflow applications;a gridFTP overlay network service;YA: fast and scalable discovery of idle CPUs in a P2P network;fault-aware scheduling for bag-of-tasks applications on desktop grids;QoS support for workflows in a volatile grid;using workflow for dynamic security context management in grid-based applications;flexible and secure logging of grid data access;multi-replication with intelligent staging in data-intensive grid applications;a QoS-aware heuristic algorithm for replica replacement;and operating system support for space application in grid storage systems.

关键词： Semantics

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On parallelization of a spatially-explicit structured ecological model for integrated ecosystem simulation

On parallelization of a spatially-explicit structured ecolog...

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workshop on scheduling for Large-Scale distributed Platforms

关键词： component-based parallel computing integrated ecological simulation spatially-explicit model performance evaluation computational ecology

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Enabling parallel scientific applications with workflow tools

Enabling parallel scientific applications with workflow tool...

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4th international workshop on Challenges of Large Applications in distributed Environments (CLADE 2006)

作者： Lathers, Adam Su, Mei-Hui Kulungowski, Alex Lin, Abel W. Mehta, Gaurang Peltier, Steven T. Deelman, Ewa Ellisman, Mark H. Univ Calif San Diego Natl Ctr Microscopy & Imaging Res La Jolla CA 92093 USA Univ So Calif Inst Informat Sci Marina Del Rey CA 90292 USA

ISBN: (纸本)1424404207

Electron tomography is a powerful too] for deriving three-dimensional (3D) structural information about biological systems within the spatial scale spanning 1 nm(3) and 10 mm(3). With this technique, it is possible to derive detailed models of sub-cellular components such as organelles and synaptic complexes and to resolve the 3D distribution of their protein constituents in situ. Due in part to exponentially growing raw data-sizes, there continues to be a need for the increased integration of High-Performance Computing (HPC) and Grid technologies with traditional electron tomography processes to provide faster data processing throughput. This is increasingly relevant because emerging mathematical algorithms that provide better data fidelity are more computationally intensive for larger raw data sizes. Progress has been made towards the transparent use of HPC and Grid tools for launching scientific applications without passing on the necessary administrative overhead and complexity (resource administration, authentication, scheduling, data delivery) to the non-computer scientist end-user. There is still a need, however, to simplify the use of these tools for applications developers who are developing novel algorithms for computation. Here we describe the architecture of the Telescience Project (http://***), specifically the use of layered workflow technologies to parallelize and execute scientific codes across a distributed and heterogeneous computational resource pool (including resources from the TeraGrid and OptIPuter projects) without the need for the application developer to understand the intricacies of the Grid.

关键词： grid computing pegasus telescience workflow

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Flexible, low-overhead event logging to support resource scheduling

Flexible, low-overhead event logging to support resource sch...

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international Conference on parallel and distributed systems (ICPADS)

作者： J. Stoess V. Uhlig University of Karlsruhe Germany IBM Thomas J. Watson Research Center New York USA

Flexible resource management and scheduling policies require detailed system-state information. Traditional, monolithic operating systems with a centralized kernel derive the required information directly, by inspection of internal data structures or maintaining additional accounting data. In systems with distributed or multi-level resource managers that reside in different subsystems and protection domains, direct inspection is unfeasible. In this paper, we present how system event logging - a mechanism usually used in the context of performance analysis and debugging - can also be used for resource scheduling. Event logs provide accumulated, pre-processed, and structured state information independent of the internal structure of individual system components or applications. We describe methods of low-overhead data collection and data analysis and present a prototypical application to multiprocessor scheduling of virtual machines

关键词： resource management Inspection Operating systems Kernel Data structures Protection Performance analysis Debugging Data analysis Virtual prototyping

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The GHS grid scheduling system: implementation and performance comparison 06

The GHS grid scheduling system: implementation and performan...

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international Symposium on parallel and distributed Processing (IPDPS)

作者： Ming Wu Xian-He Sun Department of Computer Science Illinois Institute of Technology Chicago IL USA

ISBN: (纸本)9781424400546

Effective task scheduling and deployment is hard to achieve in a grid environment, where computing resources are heterogamous and shared between local and grid users without a central control. Current scheduling systems, such as AppLeS, use NWS (network weather service) for short-term estimation of resource availability and do not address the influence of the variation of resource availability in task scheduling. These inherent limitations prevent existing scheduling systems from working effectively to solve large-scale tasks in a grid environment. Adopting APST (AppLeS parameter sweep template) as the deployment environment, we have developed a task scheduling system for large-scale applications based on our recent results in performance prediction and task scheduling. Preliminary experimental results show that the newly developed system works well and is significantly more appropriate for large applications than existing systems

关键词： Processor scheduling Availability Grid computing Large-scale systems Sun resource management Costs Monitoring Middleware Computer science

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An economy-driven mapping heuristic for hierarchical master-slave applications in grid systems 06

An economy-driven mapping heuristic for hierarchical master-...

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international Symposium on parallel and distributed Processing (IPDPS)

作者： N. Ranaldo E. Zimeo Department of Engineering University of Sannio Benevento Italy Research Centre on Software Technology University of Sannio Benevento Italy

ISBN: (纸本)9781424400546

In heterogeneous distributed systems, such as grids, a resource broker is responsible of automatically selecting resources, and mapping application tasks to them. A crucial aspect of resource broker design, especially in a next commercial exploitation of grid systems, in which economy theories for resource management will be applied, is the support to task mapping based on the fulfillment of quality of service (QoS) constraints. The paper presents an economy-driven mapping heuristic, called time minimization, for mapping and scheduling the tasks assigned to the slaves of a master-slave application in a hierarchical and heterogeneous distributed system. The validity and accuracy of such heuristic are tested by implementing it in a resource broker of a hierarchical grid middleware used for running a real world application.

关键词： Master-slave resource management Grid computing Quality of service scheduling Application software distributed computing Middleware Environmental economics Costs

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Multisite co-allocation algorithms for computational grid 06

Multisite co-allocation algorithms for computational grid

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international Symposium on parallel and distributed Processing (IPDPS)

作者： Weizhe Zhang A.M.K. Cheng Mingzeng Hu School of Computer Science and Technology Harbin Institute of Technology P.R. China Real-Time Systems Laboratory University of Houston Houston TX USA

ISBN: (纸本)9781424400546

Efficient multisite job scheduling facilitates the cooperation of multi-domain massively parallel processor systems in a computing grid environment. However, co-allocation, heterogeneity, adaptability, and scalability emerge as tough challenges for the design of multisite job scheduling models and algorithms. This paper presents a new multisite job scheduling schema based on the multisite job scheduling model and the performance model for a heterogeneous grid environment. There are three key components: resource selection, reservation, and backfilling. The optimal and greedy-heuristic adaptive resource selection strategies are introduced. The conservative and easy backfilling are incorporated into the backfilling procedure. Experiments indicate that the scheduler and the algorithm are effective and perform better than a non-adaptive algorithm

关键词： Grid computing Processor scheduling Concurrent computing scheduling algorithm Delay Computer science Scalability Power systems Power engineering computing resource management

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IMAGE: an approach to building standards-based enterprise grids 06

IMAGE: an approach to building standards-based enterprise gr...

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international Symposium on parallel and distributed Processing (IPDPS)

作者： G. Mateescu M. Sosonkina Research Computing Support Group National Research Council Canada Ottawa ONT Canada Scalable Computing Laboratory USDOE Ames Laboratory Ames IA USA

ISBN: (纸本)9781424400546

We describe a system for aggregating heterogeneous resources from distinct administrative domains into an enterprise-wide compute grid, such that the aggregated resource provides the services of reliable and flexible queuing, scheduling, execution, and monitoring of batch applications. The system provides scheduling across multiple cluster grids, user account mapping across domains, and file staging, thereby enabling the consolidation of organization-wide distributed resources into a virtual resource, while preserving local control of resources. The concept of abstract queue, as the unit of aggregating heterogeneous resources, is introduced and instantiated for distributed resource scheduling. The proposed system is an open source, standards-based alternative to similar commercial systems

关键词： Grid computing resource management Processor scheduling Control systems Laboratories Open source software Authorization Councils Open source hardware Humans

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