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IEEE International Symposium on Parallel and Distributed Processing With Applications

作者： Wu, Chao Sun, Guang-Zhong Chen, Guo-Liang School of Computer Science and Technology University of Science and Technology of China Anhui Key Laboratory of High Performance Computing Hefei Anhui 230027 China

ISBN: (纸本)9780769541907

A key problem of relational database is to aggregate different values of the same object and find the first k objects with highest overall values. Many sequential algorithms have been proposed to solve this problem. In this paper, we propose a new parallel algorithm using symmetry breaking strategy. New algorithm is proved to be instance optimal. Experiment results on both synthetic and real data also show that new algorithm costs fewer accesses, compared to previous algorithms. © 2010 IEEE.

关键词： Computational efficiency

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computing methods and application development of longitudinal strength of damaged ships

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ASME 2010 29th International Conference on Ocean, Offshore and Arctic Engineering, OMAE2010

作者： Yan, Renjun Yao, Qi Luo, Bailu Lei, Jiajing Peng, Li State Key Laboratory of High Performance Vessel Wuhan University of Technology Wuhan Hubei China Wuhan University of Technology Wuhan Hubei China

ISBN: (纸本)9780791849101

In this paper, it starts by providing a description of the scenarios of damages that can be found in the various accidental events. Based on a traditional standardized approach for calculating longitudinal strength of ships, an improved method for longitudinal strength of damaged ships, which can be applied to any traditional type of ships, is presented in next section. The variation of loads in damaged ships is related to the effects of the ingress of water with the consequences of changing the ship displacement, a non-symmetric floating body, and the load case of compartments before damage, etc. The computing methods used in this paper allow for research on corresponding applications. Using this computer program, a few case studies are carried out and the results are discussed. © 2010 by ASME.

关键词： Arctic engineering

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Generating provably correct algorithmic programs from formal specifications

Generating provably correct algorithmic programs from formal...

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10th International Conference on Quality Software, QSIC 2010

作者： Shi, Haihe Xue, Jinyun Institute of Software Chinese Academy of Sciences Beijing China Provincial Key Laboratory for High-Performance Computing Technology Jiangxi Normal University Nanchang China Graduate University Chinese Academy of Sciences Beijing China

ISBN: (纸本)9780769541310

Software automation has been viewed as a revolutionary way to improve the dependability and productivity of software. The paper takes the sorting algorithms as study cases, employs PAR method and generic techniques, and derives two abstract generic sorting algorithmic programs, from which a class of concrete sorting algorithmic programs can be generated automatically through operation replacement. And further specialized programs can be produced in multiple languages from a single copy of the instantiated algorithmic program automatically by means of the PAR platform. © 2010 IEEE.

关键词： Algorithmic languages

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An EM method based on entropy LD block partition for haplotype inference

An EM method based on entropy LD block partition for haploty...

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2010 IEEE 5th International Conference on Bio-Inspired computing: Theories and Applications, BIC-TA 2010

作者： Xu, Yun Wang, Ying Yao, Xiaohui Zhao, Yuzhong Department of Computer Science University of Science and Technology of China Hefei Anhui 230026 China Anhui Province-MOST Co-Key Laboratory of High Performance Computing and Its Application Hefei Anhui 230027 China

ISBN: (纸本)9781424464388

Genetic diseases have attracted much attention to the genetic research which depends on the data named haplotypes. Because of most haplotypes are generated from genotypes, haplotype inference (HI) problem becomes very popular. To solve this problem, we propose a new method based on EM and partition-ligation (PL) strategy. Compared to the previous methods, our algorithm uses the PL strategy based on multilocus linkage disequilibrium (LD), which has an advantage over the uniform block partition and pairwise LD. Considering the scale of data and the missing alleles, we also change the ligation strategy to control the complexity of time and space. The experimental results on the real data and the simulated data show that the algorithm in this paper has better performance than previous ones. © 2010 IEEE.

关键词： Maximum principle

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Location-aware routing for delay tolerant networks

Location-aware routing for delay tolerant networks

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作者： Tian, Ye Li, Jiang Anhui Province Key Laboratory on High Performance Computing School of Computer Science and Technology University of Science and Technology of China Hefei Anhui 230027 China Department of Systems and Computer Science Howard University Washington DC 20059 United States

ISBN: (纸本)9780984589333

In this paper, we sought to understand the reasons causing failures and delays of message delivery in Delay Tolerant Networks (DTN), and to use this understanding for improving the network. By studying two real-world datasets, we found that node isolation is prevalent, which largely accounts for the inefficiencies in DTN's message delivery. In addition, by analyzing nodes' contact-location relationship, we found that individual and system-wide key locations exist and their existence suggests potential improvements. Motivated by our observations, we designed a location aware routing scheme for DTN networks. With simulation-based experiments, we compared our proposal with other representative DTN routing schemes, and showed that with the awareness of the location information, our solution can deliver more messages within shorter delays, therefore improves the network intensively.

关键词： Delay tolerant networks

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A heuristic algorithm for minimum-recombinant haplotyping in pedigrees: Implementation and parallelization

A heuristic algorithm for minimum-recombinant haplotyping in...

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International Conference on Information Sciences and Interaction Sciences (ICIS)

作者： Haitao Jiang Yun Xu Yuzhong Zhao Guoliang Chen Key Laboratory on High performance Computing Anhui University of Science and Technology Hefei Anhui China

Haplotype inference based on pedigree data under the Mendelian law of inheritance and the minimum recombination principle is important for the construction of haplotype maps and the study of disease genes. But this problem has been proven to be NP-hard, exact algorithms previously known can't be applied to handle large scale genotype datasets, so heuristic and parallel algorithms are imperative. This paper presents an algorithm named Zero recombinant block algorithm (ZRBA) based on a new strategy using zero recombinant blocks (ZRB) as intermediate structure to reconstruct the haplotype configurations, theoretical analysis shows that this strategy can reduce the possible haplotype configurations, and compared with the dynamical programming strategy used in existing rule-based algorithms, the using of zero recombinant blocks increases the parallelism enormously. Following experiments demonstrate the superiority of our algorithm in both serial and parallel performance.

关键词： Heuristic algorithms Inference algorithms Partitioning algorithms Diseases Parallel algorithms Dynamic programming Humans Laboratories high performance computing Large-scale systems

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An efficient parallel algorithm for longest common subsequence problem on GPUs

An efficient parallel algorithm for longest common subsequen...

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作者： Yang, Jiaoyun Xu, Yun Shang, Yi Key Laboratory on High Performance Computing Anhui Province China College of Computer Science and Technology University of Science and Technology of China Heifei Anhui China Department of Computer Science University of Missouri Columbia MO United States

ISBN: (纸本)9789881701299

Sequence alignment is an important problem in computational biology and finding the longest common subsequence (LCS) of multiple biological sequences is an essential and effective technique in sequence alignment. A major computational approach for solving the LCS problem is dynamic programming. Several dynamic programming methods have been proposed to have reduced time and space complexity. As databases of biological sequences become larger, parallel algorithms become increasingly important to tackle large size problems. In the meantime, general-purpose computing on graphics processing units (GPGPU) has emerged as a promising technology for cost-effective high performance computing. In this paper, we develop an efficient parallel algorithm on GPUs for the LCS problem. We propose a new technique that changes the data dependency in the score table used by dynamic programming algorithms to enable higher degrees of parallelism. The algorithm takes advantage of the large number of processing units and the unique memory-accessing properties of GPUs to achieve high performance. The algorithm was implemented on Nvidia 9800GT GPUs and tested on randomly generated sequences of different lengths. The experiment results show that the new algorithm is about 6 times faster on GPUs than on typical CPUs and is 3 times faster than an existing efficient parallel algorithm, the diagonal parallel algorithm.

关键词： Parallel algorithms

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Bayesian cognitive trust model based self-clustering algorithm for MANETs

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Science China(Information Sciences) 2010年第3期53卷 494-505页

作者： WANG Wei1,2,3 & ZENG GuoSun1,2,31Department of Computer Science & technology, Tongji University, Shanghai 200092, China 2Tongji Branch, National Engineering & technology Center of high performance Computer, Shanghai 200092, China 3key Loboratory of Embedded System and Service computing, Ministry of Education, Shanghai 200092, China 1. Department of Computer Science & Technology Tongji University Shanghai 200092 China2. Tongji Branch National Engineering & Technology Center of High Performance Computer Shanghai 200092 China3. Key Loboratory of Embedded System and Service Computing Ministry of Education Shanghai 200092 China

With the introduction of mobile Ad hoc networks (MANETs), nodes are able to participate in a dynamic network which lacks an underlying infrastructure. Before two nodes agree to interact, they must trust that each will satisfy the security and privacy requirements of the other. In this paper, using the cognition inspired method from the brain informatics (BI), we present a novel approach to improving the search efficiency and scalability of MANETs by clustering nodes based on cognitive trust mechanism. The trust relationship is formed by evaluating the level of trust using Bayesian statistic analysis, and clusters can be formed and maintained autonomously by nodes with only partial knowledge. Simulation experiments show that each node can form and join proper clusters, which improve the interaction performance of the entire network. The essence of the underlying reason is analyzed through the theory of complex networks, revealing great scalability of this method.

关键词： trust model MANET self-clustering Bayesian method cognitive mobile

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Broadcast Scheduling Based on Network Coding in Time Critical Wireless Networks

Broadcast Scheduling Based on Network Coding in Time Critica...

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Workshop on Network Coding, Theory and Applications (NetCod)

作者： Cheng Zhan Yinlong Xu School of Computer Science and Technology Key Laboratory on High Performance Computing University of Science and Technology Hefei Anhui China

ISBN: (纸本)9781424471898;9781424471904

Using network coding in wireless networks can increase throughput and reduce energy consumption. Recently there are many works focusing on how to utilize network coding to increase throughput, however there are few works considering the quality of service such as delay which is important to time critical applications. This paper focuses on network coding based broadcast scheduling problem in time critical wireless networks with packet delay constraint and aims at minimizing the number of packets which miss their deadlines. Using a weighted graph model, we formulate the problem with an integer linear programming and prove that it is NP-hard. By assigning vertex weight as a decreasing function of packet deadline, we propose a packet encoding and broadcasting algorithm based on the maximum weight clique in the graph. Detailed analysis shows that some typical application requirements can be realized with different weight functions, which can be useful for Qos design. Simulation results show that our algorithm significantly reduce the deadline miss ratio in most cases, which is an important performance metric in time critical applications.

关键词： Broadcasting Network coding Wireless networks Throughput Quality of service Delay effects Energy consumption Integer linear programming Encoding Measurement

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Delay Aware Broadcast Scheduling in Wireless Networks Using Network Coding

Delay Aware Broadcast Scheduling in Wireless Networks Using ...

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International Conference on Networks Security, Wireless Communications and Trusted computing, NSWCTC

作者： Zheng Dong Cheng Zhan Yinlong Xu School of Computer Science and Technology Key Laboratory on High Performance Computing University of Science and Technology Hefei Anhui China

ISBN: (纸本)9781424465972;9780769540115

Using network coding in wireless networks can increase throughput and reduce energy consumption. Recently there are many works focusing on how to utilize network coding to increase throughput while there are few works considering the quality of service such as delay. This paper focuses on network coding based broadcast scheduling in wireless networks with the packet delay constraint and aims at minimizing the number of packets which miss their deadlines. Every client needs some packets and has already had some packets in the cache, we propose a graph model to describe the relationship between these packets. By assigning vertex weight as a decreasing function of packet deadline, we propose an encoding algorithm based on the maximum weight clique in the graph to help the sender decide how to broadcast. Simulation results show that our algorithm can reduce the deadline miss ratio which is an important performance metric in the delay sensitive applications.

关键词： Broadcasting Wireless networks Network coding Throughput Delay Decoding Energy consumption Quality of service Wireless communication high performance computing

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