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3rd International workshop on Science Gateways for Life Sciences 2011, IWSG-Life 2011

作者： Gesing, Sandra Grunzke, Richard Balaskó, Ákos Birkenheuer, Georg Blunk, Dirk Breuers, Sebastian Brinkmann, André Fels, Gregor Herres-Pawlis, Sonja Kacsuk, Peter Kozlovszky, Miklos Krüger, Jens Packschies, Lars Schäfer, Patrick Schuller, Bernd Schuster, Johannes Steinke, Thomas Szikszay Fabri, Anna Wewior, Martin Müller-Pfefferkorn, Ralph Kohlbacher, Oliver Zentrum Für Bioinformatik Eberhard-Karls-Universität Tübingen Germany Zentrum Für Informationsdienste und Hochleistungsrechnen Technische Universität Dresden Germany MTA SZTAKI Computer and Automation Research Institute Hungarian Academy of Sciences Budapest Hungary Paderborn Center for Parallel Computing Universität Paderborn Germany Department Für Chemie Universität zu Köln Germany Department Chemie Universität Paderborn Germany Fakultät Chemie TU Dortmund Germany Regionales Rechenzentrum Universität zu Köln Germany Konrad-Zuse-Institut Für Informationstechnik Berlin Germany Forschungszentrum Jülich Germany

Structural Bioinformatics is concerned with computational methods for the analysis and modeling of three-dimensional molecular structures. There is a plethora of computational tools available to work with structural data on a large scale. Using these tools on distributed computing infrastructures (DCI), however, is often hampered by a lack of suitable interfaces. The MoSGrid (Molecular simulation Grid) science gateway provides an intuitive user interface to several widelyused tools in structural bioinformatics. It ensures the confidentiality, integrity and availability of data via a granular security concept which covers all layers of the infrastructure. The concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled grid portal WS-PGRADE, the gUSE (grid User Support Environment) DCI services, and the cloud file system XtreemFS. The security infrastructure presented here allows single sign-on and thus lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics. Copyright © 2011 for the individual papers by the papers authors.

关键词： User interfaces

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proceedings of the 16th international workshop on high-level parallel programming models and supportive environments

IEEE International Symposium on Parallel and Distributed Pro...

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IEEE International Symposium on parallel and distributed Processing workshops and Phd Forum 2011年 1139-1140页

作者： Hoefler, Torsten Eigenmann, Rudolf Gerndt, Michael Müller, Frank Rasmussen, Craig Schulz, Martin Alam, Sadaf Balaji, Pavan Barrett, Richard Bode, Brett Bosilca, George Bronevetsky, Greg Danalis, Anthony De Supinski, Bronis Ding, Chen Fahringer, Thomas Ishikawa, Yutaka Knüpfer, Andreas Mohr, Bernd Scholz, Sven-Bodo Skjellum, Tony Snir, Marc Tillier, Fabian Larsson, Jesper Willcock, Jeremiah Wolf, Felix Blue Waters Directorate NCSA University of Illinois Urbana-Champaign United States Purdue University United States Technische Universität München Germany North Carolina State University United States Los Alamos National Laboratory United States Lawrence Livermore National Laboratory United States Swiss National Supercomputing Centre Switzerland Argonne National Laboratory United States Sandia National Laboratories United States National Center for Supercomputing Applications United States University of Tennessee Knoxville United States University of Rochester United States University of Innsbruck Austria University of Tokyo Japan Technische Universität Dresden Germany Forschungszentrum Jülich Germany University of Herfordshire United Kingdom University of Alabama Birmingham United States University of Illinois Urbana-Champaign United States Microsoft United States Träff University of Vienna Austria Indiana University United States German Research School for Simulation Sciences Germany

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Reversible parallel discrete-event execution of large-scale epidemic outbreak models 10

Reversible parallel discrete-event execution of large-scale ...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Perumalla, Kalyan S. Seal, Sudip K. Oak Ridge National Laboratory Oak Ridge TN United States

ISBN: (纸本)9781424472918

The spatial scale, runtime speed and behavioral detail of epidemic outbreak simulations together require the use of large-scale parallel processing. In this paper, an optimistic parallel discrete event execution of a reaction-diffusion simulation model of epidemic outbreaks is presented, with an implementation over the μsik simulator. Rollback support is achieved with the development of a novel reversible model that combines reverse computation with a small amount of incremental state saving. parallel speedup and other runtime performance metrics of the simulation are tested on a small (8,192-core) Blue Gene / P system, while scalability is demonstrated on 65,536 cores of a large Cray XT5 system. Scenarios representing large population sizes (up to several hundred million individuals in the largest case) are exercised. © 2010 IEEE.

关键词： Population statistics

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Exploring multi-grained parallelism in compute-intensive DEVS simulations 10

Exploring multi-grained parallelism in compute-intensive DEV...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Liu, Qi Wainer, Gabriel Department of Systems and Computer Engineering Carleton University Ottawa ON Canada

ISBN: (纸本)9781424472918

We propose a computing technique for efficient parallel simulation of compute-intensive DEVS models on the IBM Cell processor, combining multi-grained parallelism and various optimizations to speed up the event execution. Unlike most existing parallelization strategies, our approach explicitly exploits the massive fine-grained event-level parallelism inherent in the simulation process, while most of the logical processes are virtualized, making the achievable parallelism more deterministic and predictable. Together, the parallelization and optimization strategies produced promising experimental results, accelerating the simulation of a 3D environmental model by a factor of up to 33.06. The proposed methods can also be applied to other multicore and shared-memory architectures. © 2010 IEEE.

关键词： parallel processing systems

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2010 IEEE workshop on Principles of Advanced and distributed simulation, PADS 2010

2010 IEEE Workshop on Principles of Advanced and Distributed...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

ISBN: (纸本)9781424472918

The proceedings contain 18 papers. The topics discussed include: new approaches to protein functional inference and ligand screening with application to the human kinome;federate fault tolerance in HLA-based simulation;continuous matching algorithm for interest management in distributed virtual environments;a methodology to predict the performance of distributed simulations;optimizing a business process model by using simulation;selecting simulation algorithm portfolios by genetic algorithms;on validation of semantic composability in data-driven simulation;integrative models of the hepatitis C virus infection: modeling wicked problems;functional level hardware simulation with pull-model data flow;flow: a stream processing system simulator;reversible parallel discrete-event execution of large-scale epidemic outbreak models;validation of radio channel models using an anechoic chamber;and explicit spatial scattering for load balancing in conservatively synchronized parallel discrete-event simulations.

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P-GAS: parallelizing a cycle-accurate event-driven many-core processor simulator using parallel discrete event simulation 10

P-GAS: Parallelizing a cycle-accurate event-driven many-core...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Lv, Huiwei Cheng, Yuan Bai, Lu Chen, Mingyu Fan, Dongrui Sun, Ninghui Key Laboratory of Computer System and Architecture Institute of Computing Technology Chinese Academy of Sciences China Graduate School Chinese Academy of Sciences China

ISBN: (纸本)9781424472918

Multi-core processors are commonly available now, but most traditional computer architectural simulators still use single-thread execution. In this paper we use parallel discrete event simulation (PDES) to speedup a cycle-accurate event-driven many-core processor simulator. Evaluation against the sequential version shows that the parallelized one achieves an average speedup of 10.9× (up to 13.6×) running SPLASH-2 kernel on a 16-core host machine, with cycle counter differences of less than 0.1%. Moreover, super-linear speedups are achieved between running 1 thread and 8 threads due to reduced overhead of insert-event-to-queue time and increased cache size in parallel processing. We conclude that PDES could be an attractive option for achieving fast cycle-accurate many-core processor simulations. © 2010 IEEE.

关键词： Simulators

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parallel particle-based reaction diffusion: A GPU implementation

Parallel particle-based reaction diffusion: A GPU implementa...

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9th International workshop on parallel and distributed Methods in Verification, PDMC 2010 - Joint with the 2nd International workshop on High-Performance Computational Systems Biology, HiBi 2010

作者： Dematté, Lorenzo Microsoft Research University of Trento Center for Computational and Systems Biology Trento Italy

ISBN: (纸本)9780769542652

Space is a very important aspect in the simulation of biochemical models;recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and large models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localised fluctuations, transportation phenomena and diffusion. A common drawback of spatial models lies in their complexity: models could become very large, and their simulation could be time consuming, especially if we want to capture the systems behaviour in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to move from sequential to parallel simulation algorithms. In this paper we analyse Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of GPUs. The implementation offers good speedups (up to 130x) and real time, high quality graphics output at almost no performance penalties. © 2010 IEEE.

关键词： Graphics processing unit

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Explicit spatial scattering for load balancing in conservatively synchronized parallel discrete-event simulations 10

Explicit spatial scattering for load balancing in conservati...

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Thulasidasan, Sunil Kasiviswanathan, Shiva Prasad Eidenbenz, Stephan Romero, Phillip Los Alamos National Laboratory United States

ISBN: (纸本)9781424472918

We re-examine the problem of load balancing in conservatively synchronized parallel, discrete-event simulations executed on high-performance computing clusters, focusing on simulations where computational and messaging load tend to be spatially clustered. Such domains are frequently characterized by the presence of geographic "hot-spots" - regions that generate significantly more simulation events than others. Examples of such domains include simulation of urban regions, transportation networks and networks where interaction between entities is often constrained by physical proximity. Noting that in conservatively synchronized parallel simulations, the speed of execution of the simulation is determined by the slowest ( i.e most heavily loaded) simulation process, we study different partitioning strategies in achieving equitable processor-load distribution in domains with spatially clustered load. In particular, we study the effectiveness of partitioning via spatial scattering to achieve optimal load balance. In this partitioning technique, nearby entities are explicitly assigned to different processors, thereby scattering the load across the cluster. This is motivated by two observations, namely, (i) since load is spatially clustered, spatial scattering should, intuitively, spread the load across the compute cluster, and (ii) in parallel simulations, equitable distribution of CPU load is a greater determinant of execution speed than message passing overhead. Through large-scale simulation experiments - both of abstracted and real simulation models - we observe that scatter partitioning, even with its greatly increased messaging overhead, significantly outperforms more conventional spatial partitioning techniques that seek to reduce messaging overhead. Further, even if hot-spots change over the course of the simulation, if the underlying feature of spatial clustering is retained, load continues to be balanced with spatial scattering leading us to the observation that

关键词： Message passing

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ON THE PERFORMANCE AND COST OF SOME PRAM MODELS ON CMP HARDWARE

ON THE PERFORMANCE AND COST OF SOME PRAM MODELS ON CMP HARDW...

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10th workshop on Advances in parallel and distributed Computational Models/22nd IEEE International parallel and distributed Processing Symposium

作者： Forsell, Martti VTT Tech Res Ctr Finland Platform Architectures Team FI-90571 Oulu Finland

ISBN: (纸本)9781424416943

The parallel Random Access Machine is a very strong model of parallel computing that has resisted cost-efficient implementation attempts for decades. Recently, the development of VLSI technology has provided means for indirect on-chip implementation, but there are different variants of the PRAM model that provide different performance, area and power figures and it is not known how their implementations compare to each others. In this paper we measure the performance and estimate the cost of practical implementations of four PRAM models including EREW, Limited Arbitrary CRCW, Full Arbitrary CRCW, Full Arbitrary Multioperation CRCW on our Eclipse chip multiprocessor framework. Interestingly, the most powerful model shows the lowest simulation cost and highest performance/area and performance/power figures.

关键词： parallel computing PRAM performance silicon area power consumption

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Federate fault tolerance in HLA-based simulation 10

Federate fault tolerance in HLA-based simulation

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24th Annual workshop on Principles of Advanced and distributed simulation, PADS 2010

作者： Li, Zengxiang Cai, Wentong Turner, Stephen John Pan, Ke Parallel and Distributed Computing Center School of Computing Engineering Nanyang Technological University Singapore 639798 Singapore

ISBN: (纸本)9781424472918

A large scale HLA-based simulation (federation) is composed of a large number of simulation components (federates), which may be developed by different participants and executed at different locations. These federates are subject to failures due to various reasons. What is worse, the risk of federation failure increases with the number of federates in the federation. In this paper, a fault tolerance mechanism is proposed to tolerate the crash-stop failures of federates. By exploiting the decoupled federate architecture, federate failures can be masked from the federation and recovery can take place without interrupting the executions of other federates. A basic state recovery protocol is first proposed to recover the state of the failed federate relying on the checkpoint and message logging taken before the failure. Then, an optimized protocol is further developed to accelerate the state recovery procedure. Experiments are carried out to verify that the proposed mechanism provides correct failure recovery. The experimental results also indicate that the optimized protocol can outperform the basic one considerably. © 2010 IEEE.

关键词： Fault tolerance

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