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International Conference on Parallel Processing Workshops (ICPPW)

作者： Daniel Becker John C. Linford Rolf Rabenseifner Felix Wolf Forschungszentrum Jülich Institute for Advanced Simulation Julich Germany Department of Computer Science RWTH Aachen University Aachen Germany High-Performance Computing-Center University of Stuttgart Stuttgart Germany Department of Computer Science Virginia Technology Blacksburg VA USA

Event traces are helpful in understanding the performance behavior of message-passing applications since they allow in-depth analyses of communication and synchronization patterns. However, the absence of synchronized hardware clocks may render the analysis ineffective because inaccurate relative event timings can misrepresent the logical event order and lead to errors when quantifying the impact of certain behaviors. Although linear offset interpolation can restore consistency to some degree, inaccuracies and time-dependent drifts may still disarrange the original succession of events - especially during longer runs. In our earlier work, we have presented an algorithm that removes the remaining violations of the logical event order postmortem and, in addition, have outlined the initial design of a parallel version. Here, we complete the parallel design and describe its implementation within the SCALASCA trace-analysis framework. We demonstrate its suitability for large-scale applications running on more than a thousand application processes and show how the correction can improve the trace analysis of a real-world application example.

关键词： Clocks Synchronization Algorithm design and analysis Interpolation Program processors Accuracy Servers

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simulations of 3D flow and sediment transport in a fishway

Simulations of 3D flow and sediment transport in a fishway

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19th IASTED International Conference on Modelling and simulation, MS 2008

作者： Chang, Wen-Yi Lien, Ho-Cheng Lee, Lung-Cheng Tsai, Whey-Fong Lai, Jihn-Sung Tan, Yih-Chi Guo, Wen-Dar National Center for High-Performance Computing Hsinchu Science Park No. 7 R and D Rd. VI Hsinchu 30076 Taiwan Department of Bioenvironmental Systems Eng. National Taiwan University Taipei City 106 Taiwan WG-ENV ICID. SG Chinese Taipei Committee China Hydrotech Research Institute Taiwan Dept. of Bioenvironmental System Eng. National Taiwan University Taipei City 106 Taiwan Hydrotech Research Institute National Taiwan University Taipei City 106 Taiwan

ISBN: (纸本)9780889867420

A 3D two-phase flow numerical model based on the large eddy simulation is developed to deal with the free surface problems by using the surface capturing method. In addition, the advection-diffusion equation is incorporated into the model to deal with the sediment transport problems. For validations, the analytical solutions of re-suspended sediment concentration distributions by Hjemfelt and Lenau (1970), and the measured data of deposited sediment concentration distributions by Jobson and Sayre (1970) are employed for comparisons. Then, this numerical model is used for simulation of 3D flow and sediment transport in a fish-bone-type fishway. The flow patterns and sediment transport processes in a fishbone-type fishway are illustrated.

关键词： Sediment transport

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Flood inundation simulations in the lowlands of the Changhua County, Taiwan

Flood inundation simulations in the lowlands of the Changhua...

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19th IASTED International Conference on Modelling and simulation, MS 2008

作者： Lien, Ho-Cheng Chang, Wen-Yi Tsai, Whey-Fong Lai, Jihn-Sung Chang, Shiang-Kuan Pan, Tsung-Yi Tan, Yih-Chi National Center for High-Performance Computing Hsinchu Science Park No. 7 R and D Rd. VI Hsinchu 30076 Taiwan Department of Bioenvironmental Systems Eng. National Taiwan University Taipei City 106 Taiwan Department of Bioenvironmental System Engineering National Taiwan University Taipei City 106 Taiwan Disaster Research Center National Taiwan University Taipei City 106 Taiwan WG-ENV ICID. SG Chinese Taipei Committee China Hydrotech Research Institute Taiwan Dept. of Bioenvironmental Systems Eng. National Taiwan University Taipei City 106 Taiwan

ISBN: (纸本)9780889867420

A two-dimensional (2D) inundation model is applied to simulate flood inundation due to typhoon storm rainfall in the Changhua county located in the lowlands of western Taiwan. Using collected data in the Changhua county, the inundation-prone areas and depths are simulated to calibrate parameters of the 2D inundation model. The calibrated parameters are used to simulate 5-year and 200-year return-period potential inundation. With different precision of Digital Elevation Model (DEM) data for land surface topography, in a local drainage system inundation depths are simulated to analyze the effects of grid size related to DEM accuracy. The potential inundation-prone areas can be simulated and analyzed in advance to provide the disaster prevention information for planning of emergency response and design of flood protection.

关键词： Floods

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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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Virtual storage image implementation in a SAN system to improve storage capacity, fault tolerance and bandwidth

Virtual storage image implementation in a SAN system to impr...

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INTERMAG 2006 - IEEE International Magnetics Conference

作者： Deng, Y. Wang, F. Zhou, K. Wu, S. Center for Grid Computing Cambridge-Cranfteld High Performance Computing Facilities Cranfield University Campus Bedfordshire MK430AL United Kingdom Key Laboratory of Data Storage System Ministry of Education Huazhong University of Science and Technology Wuhan 430074 China

No abstract available

ISBN: (纸本)1424414792

No abstract available

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Energy Principle of Atomic and Molecular systems

Energy Principle of Atomic and Molecular Systems

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IEEE International Nanoelectronics Conference (INEC)

作者： J.Y. Hsu National Center of High-performance Computing Hsinchu Taiwan Department of Engineering and System Science National Tsing Hua University Hsinchu Taiwan

The fundamental equation to describe condensed matter physics, quantum chemistry, or molecular biology is well known, which is no other than the Schrodinger equation, but it is in general too complicated to solve. The difficulty is often suggested as due to Coulomb interactions, leading to ingenious methods, for example, the density functional theory to model the electron-electron interaction, and the pseudopotential theory to model the electron-ion interaction. However, the electron-ion interaction relies on the one-body electron distribution, and the electron-electron interaction the two-body. It is shown that the electron kinetic energy cannot be reduced to few-body interactions from the many-body without incurring an error, since a particle in the many-body environment encounters more spatial bumpiness due to collisions with neighboring particles to thus jack up its kinetic energy. The correlation and coherence effect, the Slater's determinant, the virial theorem, effective and pseudo potentials, and their applications to simple atoms and molecules are discussed.

关键词： Charge carrier processes Electrons Kinetic energy Distribution functions Density functional theory Physics Schrodinger equation Coherence high performance computing Quantum computing

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Storage management mechanism for a scalable streaming media system

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WSEAS Transactions on Computers 2006年第4期5卷 746-752页

作者： Deng, Yuhui Wang, Frank Feng, Dan Helian, Na Milward, Dave Thompson, Steve Center for Grid Computing Cambridge-Cranfield High Performance Computing Facilities Cranfield University Campus Bedfordshire MK43 0AL United Kingdom Key Laboratory of Data Storage System Ministry of Education Huazhong University of Science and Technology Wuhan 430074 China London Metropolitan University London United Kingdom Xyratex United Kingdom

Streaming media is pervasive on the Internet now and continues to grow rapidly. A large scale streaming media system may demand thousands of disks to satisfy both the bandwidth and storage capacity requirements imposed by thousands of concurrent clients. While performance has long been the focus of large scale storage systems research, manageability has become the dominant criterion in evaluating storage solutions, as the cost of storage management outweighs the cost of the storage devices themselves by a factor of three to eight. This paper designs and implements a highly reliable and available distributed media data oriented innovative Storage Management Mechanism (SMM) in a scalable streaming media system. All heterogeneous storage resources across the system are aggregated as a single logical view which strikes a good balance between a distributed data storage and centralized storage management. The centralized SMM dramatically simplifies the storage administration as the size and complexity of the streaming media system grows. Fault tolerance and dynamic load balance at the disk level and system level are achieved to provide high reliability and availability due to the SMM.

关键词： Multimedia systems

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Noise reduction from genotyping microarrays using probe level information

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In Silico Biology 2006年第1-2期6卷 79-92页

作者： Komura, Daisuke Nishimura, Kunihiro Ishikawa, Shumpei Panda, Binaya Huang, Jing Nakamura, Hiroshi Ihara, Sigeo Hirose, Michitaka Jones, Keith W. Aburatani, Hiroyuki Department of Dependable and High-performance Computing Research Center for Advanced Science and Technology University of Tokyo Meguro-ku Tokyo 153-8904 4-6-1 Komaba Japan Department of Intelligent and Cooperative System Research Center for Advanced Science and Technology University of Tokyo Meguro-ku Tokyo 153-8904 4-6-1 Komaba Japan Genome Science Division Research Center for Advanced Science and Technology University of Tokyo Meguro-ku Tokyo 153-8904 4-6-1 Komaba Japan Affymetrix Inc. Santa Clara CA 95051 3380 Central Expressway United States CREST Japan Science and Technology Agency Kawaguchi Saitama 4-1-8 Honchou Japan

Genomic copy number change is one of the important phenomenon observed in cancer and other genetic disorders. Recently oligonucleotide microarrays have been used to analyze changes in the copy number. Although high density microarrays provide genome wide useful data on copy number, they are often associated with substantial amount of experimental noise that could affect the performance of the analyses. We used the high density oligonucleotide genotyping microarrays in our experiments that uses redundant probe tiling approach for individual SNPs. We found that the noise in the genotyping microarray data is associated with several experimental steps during target preparation and devised an algorithm that takes into account those experimental parameters. Additionally, defective probes that do not hybridize well to the target and therefore could not be modified inherently were detected and omitted automatically by using the algorithm. When we applied the algorithm to actual datasets, we could reduce the noise substantially without compressing the dynamic range. Additionally, combinatorial use of our noise reduction algorithm and conventional breakpoint detection algorithm successfully detected a microamplification of c-myc which was overlooked in the raw data. The algorithm described here is freely available with the software upon request to all non-profit researchers. © 2006 IOS Press. All rights reserved.

关键词： Gene dosage Genotyping microarray Noise reduction

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Virtual Storage Image Implementation in a SAN system to Improve Storage Capacity, Fault Tolerance and Bandwidth

Virtual Storage Image Implementation in a SAN System to Impr...

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Intermag 2006 (INTERMAG 2006), vol.2

作者： Y. Deng F. Wang K. Zhou S. Wu Center for Grid Computing Cambridge-Cranfield High Performance Computing Facility Cranfield Bedfordshire UK Key Laboratory of Data Storage System Ministry of Education School of Computer Huazhong University of Science and Technology Wuhan China

With a SAN (Storage Area Network), large-capacity storage can be shared among multiple hosts at high speed. The potential market for SAN is enormous, but the technology won't become ubiquitous overnight. The complex administration is indicated by many researches as a key barrier to adopt SAN solutions. This paper designs and implements a virtual storage image (VSI) that aggregates storage space located on heterogeneous storage nodes (see Fig.1)in a Fibre Channel point-to-point (FC-P2P) SAN.

关键词： Image storage Storage area networks Fault tolerant systems Bandwidth File systems Space technology Aggregates Linux Fault tolerance Load management

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Correlation and coherence in many-electron system

Correlation and coherence in many-electron system

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2005 5th IEEE Conference on Nanotechnology

作者： Hsu, JangYu Pogorelov, Eugeny Kao, YeeMou National Center for High Performance Computing Hsinchu Taiwan Department of Engineering and System Science National Tsing Hua University Hsinchu Taiwan Department of Mathematics National Chiao Tung University Hsinchu Taiwan

ISBN: (纸本)0780391993

The inclusion of the correlation effect in many electron system was shown in the self-consistent density functional theory to yield the virial theorem, an important relation between the kinetic and the potential energies. This provides a correspondence principle and an accuracy that could rule out mechanisms not begetting results within the error limit. The coherence effect of exchange antisymmetry for fermions can readily couple with the correlation effect to result in rich physics. We show from a Variational Quantum Monte Carlo code that in the excited states of helium atom, the triplet state of like spins tends to have less repulsive dispersion than the singlet state of opposite spins. ©2005 IEEE.

关键词： Quantum theory

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