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Investigating the speedup of systems biology simulation using the SZTAKI Desktop Grid 14

Investigating the speedup of systems biology simulation usin...

引用

Simulation Winter Conference

作者： Simon J. E. Taylor Mohammadmersad Ghorbani Navonil Mustafee Tamas Kiss Peter Borsody Annette Payne David Gilbert Modelling & Simulation Group Brunel University Uxbridge UK Centre for Innovation and Service Research University of Exeter Business School Exeter UK Centre for Parallel Computing University of Westminster London UK Centre for Systems and Synthetic Biology Brunel University Uxbridge UK

ISBN: (纸本)9781479974870

systems biology studies the complex interactions of biological and biochemical systems rather than their individual molecular components. System biology simulations can be embarrassingly parallel jobs that have no dependency among individual simulation instances, and thus lend themselves to parallel execution over distributed resources to reduce their overall execution time. One example of such distributed resources is a Desktop Grid for Volunteer computing that aims to use vast numbers of computers to support scientific applications. The SZTAKI Desktop Grid (SZDG) uses a modified form of the volunteer computing software BOINC to implement an institution-wide Desktop Grid. This paper reports on experiences of porting the SIMAP systems biology ODE simulator to SZDG. A case study using a simulation of the mammalian ErbB signaling pathway reports on significant speedup.

关键词： Biological system modeling Computational modeling Portals systems biology Mathematical model Numerical models Educational institutions

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Self-organized cooperation between agents that have to solve resource collection tasks

Self-organized cooperation between agents that have to solve...

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IEEE Swarm Intelligence Symposium, SIS

作者： Ruby L. V. Moritz Martin Middendorf Parallel Computing and Complex Systems Group Institute of Computer Science University Leipzig Germany

We analyze the behavior and efficiency of a task-force of heterogeneous agents, which have different skills to solve a resource collection task. The agents can move within an arena and are able to cooperate in order to accessing the skills of other agents. Cooperation between agents is only possible, when they form a group by moving to the same location. Yet the number of agents on the same location is restricted. Thus the agents can only cooperate with a limited number of other agents at a time. Different strategies for the agents to decide whether to cooperate or not and how to detect the most favorable partner for cooperation within their surrounding are are investigated. In the studied scenarios the amounts of the different resources that are available varies between different locations. The agents are forced to decide whether to follow the drive of their own efficiency, or rather to build a cooperation with close-by agents that might be located in a different direction.

关键词： Batteries Particle swarm optimization Materials Availability Turning Sensors Robots

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Wait-free Hyperobjects for Task-parallel Programming systems

Wait-free Hyperobjects for Task-Parallel Programming Systems

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International Symposium on parallel and Distributed Processing (IPDPS)

作者： Martin Wimmer Institute of Information Systems Research Group Parallel Computing Faculty of Informatics Vienna University of Technology Vienna Austria

ISBN: (纸本)9781467360661

Hyperobjects are efficient mechanisms to coordinate accesses to shared variables and data-structures in task-parallel programming models, where each thread can operate on its own coordinated local view of the shared data. Synchronization between local views is restricted to occur at well-defined points in the execution, and can be left to the hyperobject implementation. This paper provides a general model for hyperobjects that does not require programming language or runtime support and may therefore be used with any task-parallel programming system. We show that hyperobjects can be efficiently implemented in a wait-free manner, meaning that all concurrent accesses to a hyperobject are guaranteed to complete in a bounded number of steps. The novel finisher hyperobject presented in this paper provides transitive termination detection for task-parallel programs. It can be used to efficiently implement task synchronization primitives like finish. However, finishers can also be used to manage reference-counted resources, e.g. shared pointers and copy-on-write pointers. Finally, we provide a wait-free variant of the associative reducer hyperobject known from the Cilk++ programming language.

关键词： Synchronization Computational modeling Object oriented modeling Instruction sets Programming Computer languages Runtime

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mpicroscope: Towards an MPI benchmark tool for performance guideline verification

mpicroscope: Towards an MPI benchmark tool for performance g...

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19th European MPI Users' group Meeting on Recent Advances in the Message Passing Interface, EuroMPI 2012

作者： Träff, Jesper Larsson Vienna University of Technology Institute of Information Systems Research Group Parallel Computing Favoritenstrasse 16 1040 Wien Austria

ISBN: (纸本)9783642335174

We discuss a new, stand-alone MPI benchmark program (for now called mpicroscope) for assessing the performance of collective communication patterns, in particular of the standard MPI 2.2 collective operations. The benchmark is intended to facilitate comparisons between different ways of expressing the same functionality towards performing automatic detection of violations of self-consistent MPI performance guidelines. The benchmark can be used by MPI library developers for assessing the relative quality of new algorithms and implementations. It can also be used to make users aware of aspects of their MPI library where performance (portability) problems may lurk. The current version of the benchmark automatically detects, for any measured communication pattern, two universal, self-consistent guidelines that encourage monotone and split-robust performance. The benchmark aims to employ sound benchmarking procedures and is controlled via command-line options. It covers the MPI 2.2 collective operations, and a number of alternative patterns that express MPI collective functionality. In contrast to many other benchmarks data can be structured as described by an MPI derived datatype. We present results from a small InfiniBand cluster with a vendor MPI library, showing performance guideline violations that were detected and highlighted with mpicroscope. © 2012 Springer-Verlag.

关键词： Benchmarking

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An analysis of provisioning and allocation policies for infrastructure-as-a-service clouds 12

An analysis of provisioning and allocation policies for infr...

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12th IEEE/ACM International Symposium on Cluster, Cloud and Grid computing, CCGrid 2012

作者： Villegas, David Antoniou, Athanasios Sadjadi, Seyed Masoud Iosup, Alexandru School of Computing and Information Sciences Florida International University Miami FL United States Parallel and Distributed Systems Group Delft University of Technology Delft Netherlands

ISBN: (纸本)9780769546919

Today, many commercial and private cloud computing providers offer resources for leasing under the infrastructure as a service (IaaS) paradigm. Although an abundance of mechanisms already facilitate the lease and use of single infrastructure resources, to complete multi-job workloads IaaS users still need to select adequate provisioning and allocation policies to instantiate resources and map computational jobs to them. While such policies have been studied in the past, no experimental investigation in the context of clouds currently exists that considers them jointly. In this paper we present a comprehensive and empirical performance-cost analysis of provisioning and allocation policies in IaaS clouds. We first introduce a taxonomy of both types of policies, based on the type of information used in the decision process, and map to this taxonomy eight provisioning and four allocation policies. Then, we analyze the performance and cost of these policies through experimentation in three clouds, including Amazon EC2. We show that policies that dynamically provision and/or allocate resources can achieve better performance and cost. Finally, we also look at the interplay between provisioning and allocation, for which we show preliminary results. © 2012 IEEE.

关键词： Taxonomies

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Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes

Annotation guided local similarity search in multiple sequen...

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： Ruby L. V. Moritz Matthias Bernt Martin Middendorf Universitatsklinikum Leipzig Leipzig Sachsen DE Parallel Computing and Complex Systems Group University Leipzig Germany

Given a set of nucleotide sequences and corresponding gene annotations which might contain a moderate number of errors we consider the problem to identify common substrings occurring in homologous genes and to identify putative errors in the given annotations. The problem is solved by identifying nodes in a suffix tree that contains all substrings occurring in the data set. Due to the large size of the targeted data set our approach employs a truncated version of suffix trees. The approach is successfully applied to the mitochondrial nucleotide sequences and the corresponding annotations available in RefSeq for more than 2000 metazoan species. We demonstrate that the approach finds appropriate subsequences despite of errors in the given annotations. Moreover, it identifies several hundred errors within the RefSeq annotations.

关键词： Indexes Genomics Encoding Proteins Vegetation Tree data structures Memory management

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Efficient MPI implementation of a parallel, stable merge algorithm

Efficient MPI implementation of a parallel, stable merge alg...

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19th European MPI Users' group Meeting on Recent Advances in the Message Passing Interface, EuroMPI 2012

作者： Siebert, Christian Träff, Jesper Larsson RWTH Aachen University German Research School for Simulation Sciences GmbH Schinkelstrasse 2a 52062 Aachen Germany Vienna University of Technology Institute of Information Systems Research Group Parallel Computing Favoritenstrasse 16 1040 Wien Austria

ISBN: (纸本)9783642335174

We study different approaches to implement an optimal, stable two-way merge algorithm for distributed-memory parallel architectures. The algorithm takes as input two ordered sequences, which are distributed blockwise across all available processes such that each process owns a block of elements of each sequence. The task for each process is to produce an ordered block of elements from the stable merge of the input sequences. We present an optimal, perfectly load-balanced, stable parallel algorithm that accomplishes this task. We describe three different implementation alternatives using one-sided communication of the Message-Passing Interface (MPI). Further, we discuss problematic issues with the current MPI 2.2 one-sided interface and enabling features that may be found in future versions of the MPI standard. Experimental results on a large IBM Blue Gene/P supercomputer show perfect scalability of our implementation: with a fixed input size per process the running time remains (almost) constant with increasing number of processes, and with a fixed total problem size our implementation improves the time to solution for up to 32,768 MPI processes. © 2012 Springer-Verlag.

关键词： Message passing

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Investigating volunteer computing for simul8: A feasibility study

Investigating volunteer computing for simul8: A feasibility ...

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2012 Operational Research Society Simulation Workshop, SW 2012

作者： Taylor, Simon J.E. Ghorbani, Mohammadmersin Kiss, Tamas Elder, Mark ICT Innovation Group Dept. of Information Systems and Computing Brunel University Uxbridge MiddlesexUB8 3PH United Kingdom Centre for Parallel Computing University of Westminster New Cavendish Street LondonW1W 6UW United Kingdom Simul8 Corporation 141 St. James' Road GlasgowG4 0LT United Kingdom

ISBN: (纸本)0903440504

Simulation software such as Simul8 is used to study complex systems in many areas. Experimentation can be time consuming. If a study requires many experiments, and each experiment requires multiple replications, then even with short run times the overall time to perform the study can be large. If models take longer to run, then this time can be excessive. Many organisations have commodity PCs that often remain idle or run applications that do not demand the processing power of a typical contemporary PC. Volunteer computing is a form of Desktop Grid computing that aims to use vast numbers of home computers to support computing applications. The SZTAKI Desktop Grid (SZDG) uses a modified form of the volunteer computing software BOINC to implement an institution-wide Desktop Grid. To investigate the feasibility of using Volunteer computing with Simul8, this paper reports on experiences of porting Simul8 to a SZDG.

关键词： Discrete event simulation

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Towards an effective unified programming model for many-cores

Towards an effective unified programming model for many-core...

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25th IEEE International parallel and Distributed Processing Symposium, Workshops and Phd Forum, IPDPSW 2011

作者： Varbanescu, Ana Lucia Hijma, Pieter Van Nieuwpoort, Rob Bal, Henri Computing Systems Group Vrije Universiteit Amsterdam Netherlands Parallel and Distributed Systems Group Delft University of Technology Netherlands ASTRON Dwingeloo Netherlands

ISBN: (纸本)9780769543857

Building an effective programming model for many-core processors is challenging. On the one hand, the increasing variety of platforms and their specific programming models force users to take a hardware-centric approach not only for implementing parallel applications, but also for designing them. This approach diminishes portability and, eventually, limits performance. On the other hand, to effectively cope with the increased number of large-scale workloads that require parallelization, a portable, application-centric programming model is desirable. Such a model enables programmers to focus first on extracting and exploiting parallelism from their applications, as opposed to generating parallelism for specific hardware, and only second on platform-specific implementation and optimizations. In this paper, we first present a survey of programming models designed for programming three families of many-cores: general purpose many-cores (GPMCs), graphics processing units (GPUs), and the Cell/B.E. We analyze the usability of these models, their ability to improve platform programmability, and the specific features that contribute to this improvement. Next, we also discuss two types of generic models: parallelism-centric and application-centric. We also analyze their features and impact on platform programmability. Based on this analysis, we recommend two application-centric models (OmpSs and OpenCL) as promising candidates for a unified programming model for many-cores and we discuss potential enhancements for them. © 2011 IEEE.

关键词： Computer graphics

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Towards an Effective Unified Programming Model for Many-Cores

Towards an Effective Unified Programming Model for Many-Core...

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IEEE International Symposium on parallel and Distributed Processing Workshops and Phd Forum (IPDPSW)

作者： Ana Lucia Varbanescu Pieter Hijma Rob van Nieuwpoort Henri Bal Parallel and Distributed Systems Group Delft University of Technnology Netherlands Computing Systems Group Vrije Universiteit Amsterdam Netherlands ASTRON Dwingeloo Netherlands

Building an effective programming model for many-core processors is challenging. On the one hand, the increasing variety of platforms and their specific programming models force users to take a hardware-centric approach not only for implementing parallel applications, but also for designing them. This approach diminishes portability and, eventually, limits performance. On the other hand, to effectively cope with the increased number of large-scale workloads that require parallelization, a portable, application-centric programming model is desirable. Such a model enables programmers to focus first on extracting and exploiting parallelism from their applications, as opposed to generating parallelism for specific hardware, and only second on platform-specific implementation and optimizations. In this paper, we first present a survey of programming models designed for programming three families of many-cores: general purpose many-cores (GPMCs), graphics processing units (GPUs), and the Cell/B.E.. We analyze the usability of these models, their ability to improve platform programmability, and the specific features that contribute to this improvement. Next, we also discuss two types of generic models: parallelism-centric and application-centric. We also analyze their features and impact on platform programmability. Based on this analysis, we recommend two application-centric models (OmpSs and OpenCL) as promising candidates for a unified programming model for many-cores and we discuss potential enhancements for them.

关键词： Programming parallel processing Computer architecture Data models Concurrent computing Computational modeling Productivity

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