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Managing ATLAS data on a petabyte-scale with DQ2

Journal of Physics: Conference Series 2008年第6期119卷

作者： M Branco D Cameron B Gaidioz V Garonne B Koblitz M Lassnig R Rocha P Salgado T Wenaus European Organization for Nuclear Research (CERN) CH-1211 Genève Switzerland Department of Physics University of Oslo P.b. 1048 Blindern N-0316 Oslo Norway Distributed and Parallel Systems University of Innsbruck A-6020 Innsbruck Austria Physics Application Software Brookhaven National Laboratory NY-11973 USA

The ATLAS detector at CERN's Large Hadron Collider presents data handling requirements on an unprecedented scale. From 2008 on the ATLAS distributed data management system, Don Quijote2 (DQ2), must manage tens of petabytes of experiment data per year, distributed globally via the LCG, OSG and NDGF computing grids, now commonly known as the WLCG. Since its inception in 2005 DQ2 has continuously managed all experiment data for the ATLAS collaboration, which now comprises over 3000 scientists participating from more than 150 universities and laboratories in 34 countries. Fulfilling its primary requirement of providing a highly distributed, fault-tolerant and scalable architecture DQ2 was successfully upgraded from managing data on a terabyte-scale to managing data on a petabyte-scale. We present improvements and enhancements to DQ2 based on the increasing demands for ATLAS data management. We describe performance issues, architectural changes and implementation decisions, the current state of deployment in test and production as well as anticipated future improvements. Test results presented here show that DQ2 is capable of handling data up to and beyond the requirements of full-scale data-taking.

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A 55 TFLOPS simulation of amyloid-forming peptides from yeast prion Sup35 with the special-purpose computer system MDGRAPE-3

A 55 TFLOPS simulation of amyloid-forming peptides from yeas...

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2006 ACM/IEEE Conference on Supercomputing, SC'06

作者： Narumi, Tetsu Ohno, Yousuke Okimoto, Noriaki Koishi, Takahiro Suenaga, Atsushi Futatsugi, Noriyuki Yanai, Ryoko Himeno, Ryutaro Fujikawa, Shigenori Taiji, Makoto Ikei, Mitsuru Intel K.K. High Performance Molecular Simulation Team Genomic Sciences Center Innovative Nanopatterning Laboratory Topochemical Design Laboratory Frontier Research System Advanced Center for Computing and Communication Software and Solutions Group Parallel and Distributed Solutions Group

ISBN: (纸本)0769527000

We have achieved a sustained performance of 55 TFLOPS for molecular dynamics simulations of the amyloid fibril formation of peptides from the yeast Sup35 in an aqueous solution. For performing the calculations, we used the MDGRAPE-3 system - -a special-purpose computer system for molecular dynamics simulations. Its nominal peak performance was 415 TFLOPS for Coulomb force calculations;this is the highest-ever performance reported for classical molecular dynamics simulations. Amyloid fibril formation is known to be related to the occurrence of severe diseases such as Alzheimer's, Parkinson's, and Creutzfeldt-Jakob diseases. The Sup35 protein is a "yeast prion protein," which forms mini-crystals due to aggregation;it forms an effective platform for studying the formation process of amyloid fibrils. In these simulations, we first elucidate that the amyloid-forming peptides GNNQQNY aggregate at a higher frequency than non-amyloid-forming peptides SQNGNQQRG;further, the GNNQQNY peptides tend to form parallel two-stranded -sheets that would grow into a cross- amyloid nucleus. The results are consistent with those obtained experimentally. Furthermore, we could observe an early elongation of the amyloid nucleus. This result is expected to contribute toward a deeper understanding of the amyloid growth mechanism. © 2006 IEEE.

关键词： Peptides

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Message from the program co-chairs

Proceedings - Fifth International Conference on Grid and Coo...

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Proceedings - Fifth International Conference on Grid and Cooperative Computing, GCC 2006 2006年 12-12页

作者： Xiao, Wong Buyya, Rajkumar Liu, Yunhao National Laboratory for Parallel and Distributed Processing Changsha China GRIDS Lab. Dept. of Computer Science and Software Engineering University of Melbourne Australia Dept. of Computer Science Hong Kong University of Science and Technology Hong Kong Hong Kong

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Message from the program co-chairs

Proceedings - Fifth International Conference on Grid and Coo...

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Proceedings - Fifth International Conference on Grid and Cooperative Computing, GCC 2006 - Workshops 2006年 12-12页

作者： Nong, Xiao Buyya, Rajkumar Liu, Yunhao National Laboratory for Parallel and Distributed Processing Changsha China GRIDS Lab. Dept. of Computer Science and Software Engineering University of Melbourne Australia Dept. of Computer Science Hong Kong University of Science and Technology Hong Kong Hong Kong

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Property-oriented testing of real-time systems

Property-oriented testing of real-time systems

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Proceedings - 11th Asia-Pacific software Engineering Conference, APSEC 2004

作者： Li, Shuhao Wang, Ji Dong, Wei Qi, Zhi-Chang National Laboratory for Parallel and Distributed Processing Changsha China State Key Laboratory for Software Engineering Wuhan University China

ISBN: (纸本)0769522459

Although Statecharts has gained widespread use as a formalism for modeling reactive real-time systems, testing these systems still confronts some difficulties, of which a major one is the existence of numerous and complex system behaviors. It is extremely difficult to conduct comprehensive and in-depth testing of such real-time systems. This paper presents an approach to property-oriented real-time testing. Necessary real-time extensions are proposed such that the time-enriched Statecharts can describe non-trivial timing constraints. The properties to be tested are characterized by a restricted real-time logic. Then the targeted test sequences are derived from the real-time models according to the user-specified properties. Using this approach, testing efforts can be focused on particular properties of the real-time systems and usually only a small portion of the total behaviors needs to be tested. © 2004 IEEE.

关键词： Real time systems

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Property-oriented testing of real-time systems

Property-oriented testing of real-time systems

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Asia-Pacific Conference on software Engineering

作者： Shuhao Li Ji Wang Wei Dong Zhi-Chang Qi National Laboratory for Parallel and Distributed Processing Changsha China State Key Laboratory for Software Engineering Wuhan University of China China

Although statecharts has gained widespread use as a formalism for modeling reactive real-time systems, testing these systems still confronts some difficulties, of which a major one is the existence of numerous and complex system behaviors. It is extremely difficult to conduct comprehensive and in-depth testing of such real-time systems. This paper presents an approach to property-oriented real-time testing. Necessary real-time extensions are proposed such that the time-enriched statecharts can describe nontrivial timing constraints. The properties to be tested are characterized by a restricted real-time logic. Then the targeted test sequences are derived from the real-time models according to the user-specified properties. Using this approach, testing efforts can be focused on particular properties of the real-time systems and usually only a small portion of the total behaviors needs to be tested.

关键词： System testing Real time systems software testing software engineering

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On the performance of Maestro2 high performance network equipment, using new improvement techniques

On the performance of Maestro2 high performance network equi...

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IEEE International Conference on Performance, Computing and Communications (IPCCC)

作者： S. Yamagiwa K. Ferreira L.M. Campos K. Aoki M. Ono K. Wada M. Fukuda L. Sousa PDM&FC Lisboa Portugal Parallel and Distributed Computing Laboratory University of Tsukuba Tsukuba Ibaraki Japan Computing and Software Systems UW1-331 University of Washington Bothell Bothell WA USA IST/INESC Lisboa Portugal

Cluster computers have become the vehicle of choice to build high performance computing environments. To fully exploit the computing power of these environments, one must utilize high performance network and protocol technologies, since the communication patterns of parallel applications running on clusters require low latency and high throughput, not achievable by using off-the-shell network technologies. We have developed a technology to build high performance network equipment, called MaestroS. This paper describes the novel techniques used by Maestro2 to extract maximum performance from the physical medium and studies the impact of software-level parameters. The results obtained clearly show that Maestro2 is a promising technology, presenting very good results both in terms of latency and throughput. The results also show the large impact of software overhead in the overall performance of the system and validate the need for optimized communication libraries for high performance computing.

关键词： High performance computing Delay Throughput Vehicles Computer networks Concurrent computing Protocols Communications technology Application software Communication system software

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Asynchronous parallelization of Guo's algorithm for function optimization

Asynchronous parallelization of Guo's algorithm for function...

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Congress on Evolutionary Computation

作者： Lishan Kang Zhuo Kang Yan Li Pu Liu Yuping Chen State Key Laboratory of Parallel and Distributed Processing State Key Laboratory of Software Engineering Wuhan University of China Wuhan China

Recently Tao Guo (1999) proposed a stochastic search algorithm in his PhD thesis for solving function optimization problems. He combined the subspace search method (a general multi-parent recombination strategy) with the population hill-climbing method. The former keeps a global search for the overall situation, and the latter maintains the convergence of the algorithm. Guo's algorithm has many advantages, such as the simplicity of its structure, the high accuracy of its results, the wide range of its applications, and the robustness of its use. In this paper a preliminary theoretical analysis of the algorithm is given and some numerical experiments are performed using Guo's algorithm to demonstrate the theoretical results. Three asynchronous parallel algorithms with different granularities for MIMD machines are designed by parallelizing Guo's algorithm.

关键词： Algorithm design and analysis parallel algorithms Constraint optimization software algorithms Optimization methods Laboratories Design optimization distributed processing software engineering Electronic mail

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Continuations for parallel logic programming 00

Continuations for parallel logic programming

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Proceedings of the 2nd International ACM SIGPLAN Conference on Principles and Practice of Declarative Programming (PPDP'00)

作者： Todoran, Eneia Papaspyrou, Nikolaos S. Technical University of Cluj-Napoca Dept. of Computer Science Parallel/Distributed Syst. Lab. Baritiu Str. 28 3400 Cluj-Napoca Romania Natl. Technical University of Athens Dept. of Elec./Computer Engineering Software Engineering Laboratory 15780 Zografou Greece

ISBN: (纸本)1581132654

This paper gives denotational models for three logic programming languages of progressive complexity, adopting the "logic programming without logic" approach. The first language is the control flow kernel of sequential Prolog, featuring sequential composition and backtracking. A committed-choice concurrent logic language with parallel composition (parallel AND) and don't care nondeterminism is studied next. The third language is the core of Warren's basic Andorra model, combining parallel composition and don't care nondeterminism with two forms of don't know nondeterminism (interpreted as sequential and parallel OR) and favoring deterministic over nondeterministic computation. We show that continuations are a valuable tool in the analysis and design of semantic models for both sequential and parallel logic programming. Instead of using mathematical notation, we use the functional programming language Haskell as a metalanguage for our denotational semantics, and employ monads in order to facilitate the transition from one language under study to another.

关键词： Logic programming

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Evolutionary Modeling of Systems of Ordinary Differential Equations with Genetic Programming

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Genetic Programming and Evolvable Machines 2000年第4期1卷 309-337页

作者： Cao, Hongqing Kang, Lishan Chen, Yuping Yu, Jingxian State Key Laboratory of Software Engineering Wuhan University Wuhan P. R. China State Key Laboratory of Parallel and Distributed Processing P. R. China Institute of Electrochemistry Department of Chemistry Wuhan University Wuhan P. R. China

This paper describes an approach to the evolutionary modeling problem of ordinary differential equations including systems of ordinary differential equations and higher-order differential equations. Hybrid evolutionary modeling algorithms are presented to implement the automatic modeling of one- and multi-dimensional dynamic systems respectively. The main idea of the method is to embed a genetic algorithm in genetic programming where the latter is employed to discover and optimize the structure of a model, while the former is employed to optimize its parameters. A number of practical examples are used to demonstrate the effectiveness of the approach. Experimental results show that the algorithm has some advantages over most available modeling methods.

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