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Computing boundary element method's matrices on GPU 1

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8th international conference on Large-Scale Scientific Computations,LSSC 2011

作者： Haase, Gundolf Schanz, Martin Vafai, Samar Institute of Mathematics and Scientific Computing University of Graz Austria Institute of Applied Mechanics Graz University of Technology Austria

ISBN: (数字)9783642298431

ISBN: (纸本)9783642298424

Matrices resulting from standard boundary element methods are dense and computationally expensive. To speed up the computational time, the matrix computation is done on a GPU. the parallel processing capability of the Graphics processing Unit (GPU) allows us to divide complex computing tasks into several thousands of smaller tasks that can be run concurrently. We achieved an acceleration of 31-36 in comparison to a computation performed on the CPU, serially. © 2012 Springer-Verlag.

关键词： Graphics processing unit

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Highly Efficient parallel Approach to the Next-Generation DNA Sequencing

Highly Efficient Parallel Approach to the Next-Generation DN...

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9th international conference on parallel processing and Applied Mathematics (PPAM)

作者： Blazewicz, Jacek Bosak, Bartosz Gawron, Piotr Kasprzak, Marta Kurowski, Krzysztof Piontek, Tomasz Swiercz, Aleksandra Poznan Univ Tech Inst Comp Sci Poznan Poland Polish Acad Sci Inst Bioorgan Chem Poznan Poland Poznan Supercomputing & Networking Ctr Poznan Poland

ISBN: (纸本)9783642314995;9783642315008

Due to the rapid development of the technology, next-generation sequencers can produce huge amount of short DNA fragments covering a genomic sequence of an organism in short time. there is a need for the time-efficient algorithms which could assembly these fragments together and reconstruct the examined DNA sequence. Previously proposed algorithm for de novo assembly, SR-ASM, produced results of high quality, but required a lot of time for computations. the proposed hybrid parallel programming strategy allows one to use the two-level hierarchy: computations in threads (on a single node with many cores) and computations on different nodes in a cluster. the tests carried out on real data of Prochloroccocus marinas coming from Roche sequencer showed, that the algorithm was speeded up 20 times in comparison to the sequential approach with the maintenance of the high accuracy and beating results of other algorithms.

关键词： hybrid programming paradigm de novo assembly

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TOWARDS LARGE SCALE AUTOMATED INTERPRETATION OF CYTOGENETIC BIODOSIMETRY DATA

TOWARDS LARGE SCALE AUTOMATED INTERPRETATION OF CYTOGENETIC ...

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IEEE 6th international conference on Information and Automation for Sustainability (ICIAFS)

作者： Li, Yanxin Wickramasinghe, Asanka Subasinghe, Akila A. Samarabandu, Jagath Knoll, Joan Wilkins, Ruth Flegal, Farrah Rogan, Peter Western Univ London ON Canada Cytognomix Inc London ON Canada Hlth Canada London ON Canada Atom Energy Canada Ltd London ON Canada

ISBN: (纸本)9781467319751;9781467319768

Cytogenetic biodosimetry is the definitive test for assessing exposure to ionizing radiation. It involves manual assessment of the frequency of dicentric chromosomes (DCs) on a microscope slide, which potentially contains hundreds of metaphase cells. We developed an algorithm that can automatically and accurately locate centromeres in DAPI-stained metaphase chromosomes and that will detect DCs. In this algorithm, a set of 200-250 metaphase cell images are ranked and sorted. the 50 top-ranked images are used in the triage DC assay (DCA). To meet the requirement of DCA in a mass casualty event, we are accelerating our algorithm through parallelization. In this paper, we present our finding in accelerating our ranking and segmentation algorithms. Using data parallelization on a desktop system, the ranking module was up to 4-fold faster than the serial version and the Gradient Vector Flow module (GVF) used in our segmentation algorithm was up to 8-fold faster. Large scale data parallelization of the ranking module processed 18,694 samples in 11.40 hr. Task parallelization of Image ranking with parallelized labeling on a desktop computer reduced processing time by 20% of a serial process, and GVF module recoded with parallelized matrix inversion reduced time by 70%. Overall, we estimate that the automated DCA will require around 1 min per sample on a 64-core computing system. Our long-term goal is to implement these algorithms on a high performance computer cluster to assess radiation exposures for thousands of individuals in a few hours.

关键词： cellular biophysics dosimetry genetics image segmentation matrix inversion medical image processing parallel processing

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Word sense disambiguation based on example sentences in dictionary and automatically acquired from parallel corpus

Word sense disambiguation based on example sentences in dict...

引用

8th international conference on Natural Language processing, JapTAL 2012

作者： Kathuria, Pulkit Shirai, Kiyoaki Japan Advanced Institute of Science and Technology Japan

ISBN: (纸本)9783642339820

this paper presents a precision oriented example based approach for word sense disambiguation (WSD) for a reading assistant system for Japanese learners. Our WSD classifier chooses a sense associated with the most similar sentence in a dictionary only if the similarity is high enough, otherwise chooses no sense. We propose sentence similarity measures by exploiting collocations and syntactic dependency relations for a target word. the example based classifier is combined with a Robinson classifier to compensate recall. We further improve WSD performance by automatically acquiring bilingual sentences from a parallel corpus. According to the results of our experiments, the accuracy of automatically extracted sentences was 85%, while the proposed WSD method achieves 65% accuracy which is 7% higher than the baseline. © 2012 Springer-Verlag Berlin Heidelberg.

关键词： Natural language processing systems

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An Adaptive, Scalable, and Portable Technique for Speeding Up MPI-Based Applications

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18th international conference on Euro-Par parallel processing

作者： Filgueira, Rosa Atkinson, Malcolm Nunez, Alberto Fernandez, Javier Univ Edinburgh Sch Informat Edinburgh EH8 9AB Midlothian Scotland Univ Complutense Madrid Dept Sistemas Informat Computac Madrid 28040 Spain Univ Carlos III Madrid Dept Arquitectura Comp Leganes 3028911 Spain

ISBN: (纸本)9783642328206

this paper presents a portable optimization for MPI communications, called PRAcTICaL-MPI (Portable Adaptive Compression Library- MPI). PRAcTICaL-MPI reduces the data volume exchanged among processes by using lossless compression and offers two main advantages. Firstly, it is independent of the MPI implementation and the application used. Secondly, it allows for turning the compression on and off and selecting the most appropriate compression algorithm at runtime, depending on the characteristics of each message and on network performance. We have validated PRAcTICaL-MPI in different MPI implementations and HPC clusters. the evaluation shows that compressing MPI messages with the best algorithm and only when it is worthwhile, we obtain a great reduction in the overall execution time for many of the scenarios considered.

关键词： MPI Library parallel techniques High-Performance Computing Compression algorithms Adaptive systems Portable optimizations

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Processor farming in homogenization of coupled heat and moisture transfer

Processor farming in homogenization of coupled heat and mois...

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8th international conference on Engineering Computational Technology, ECT 2012

作者： Kruis, J. Krejčí, T. Sýkora, J. Šejnoha, M. Department of Mechanics Czech Technical University in Prague Czech Republic

ISBN: (纸本)9781905088553

Coupled heat and moisture transport in extremely heterogeneous materials like a masonry still cannot be solved for large strucutres. Multi-scale methods with the macro and meso-scale levels are usually used. the biggest disadvantage of such methods stems from their enormous computational demands. Small coupled problem on the meso-scale level has to be solved for every integration point of the macro-scale problem. the number of the integration points is in thousands or tens of thousands. the multi-scale method can be efficiently implemented in parallel because the particular computations connected with the integration points are totally independent. the strategy denoted the processor farming can be used. © Civil-Comp Press, 2012.

关键词： parallel processing systems

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Application of GPU-based computing to large scale finite element analysis of three-dimensional structures

Application of GPU-based computing to large scale finite ele...

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8th international conference on Engineering Computational Technology, ECT 2012

作者： Akbariyeh, A. Carrigan, T.J. Dennis, B.H. Chan, W.S. Wang, B.P. Lawrence, K.L. University of Texas Arlington United States Pointwise Inc. Fort Worth TX United States

ISBN: (纸本)9781905088553

Finite element analysis for stress and deformation prediction has become routine in many industries. However, the analysis of complex three-dimensional geometries composed of millions of degrees of freedom is beyond the computing capacity of the typical desktop computer. Recent advances in commodity graphics processing units (GPUs) have opened a new route for computing large scale finite element solutions on the desktop computer in a timely fashion. the current generation of advanced GPU hardware is equipped with hundreds of streaming processors and offers the potential of teraflops performance. It is no surprise that this hardware is becoming increasingly popular for general scientific computing because of their high performance to cost ratio. However, the peak performance of the GPU is difficult to obtain and requires careful consideration regarding algorithms and implementation. In the case of finite element analysis, the most time consuming step is solving the resulting linear system of equations. this system is typically large, sparse, and unstructured. Often these systems are solved iteratively with a domain decomposition technique used to distribute the computational load among parallel processors. In this paper the benefits of using GPUs to improve the performance of the iterative sparse matrix solver for a finite element program is explored. We focus specifically on hexahedral elements for linear elasticity with trilinear basis functions for displacement. this does not require domain decomposition, so it is simpler than the corresponding implementation for distributed memory parallel computers. In addition, the performance of the GPU implementation is compared with the corresponding serial version run on a conventional processor for various mesh sizes and sparse matrix storage schemes. © Civil-Comp Press, 2012.

关键词： Graphics processing unit

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Power efficiency evaluation of block ciphers on GPU-integrated multicore processor

Power efficiency evaluation of block ciphers on GPU-integrat...

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12th international conference on algorithms and architectures for parallel processing, ICA3PP 2012

作者： Nishikawa, Naoki Iwai, Keisuke Kurokawa, Takakazu Departmemt of Computer Science and Engineering National Defense Academy of Japan 1-10-20 Hashirimizu Yokosuka-shi Kanagawa-ken 239-8686 Japan

ISBN: (纸本)9783642330773

Computer systems with discrete GPUs are expected to become the standard methodology for high-speed encryption processing, but they require large amounts of power consumption and are inapplicable to embedded devices. therefore, we have specifically examined a new heterogeneous multicore processor with CPU-GPU integration architecture. We first implemented three 128-bit block ciphers (AES, Camellia, and SC2000) from several symmetric block ciphers in an e-government recommended ciphers list by CRYPTREC in Japan using OpenCL on AMD E-350 APU with CPU-GPU integration architecture and two traditional systems with discrete GPUs. then we evaluated their respective power efficiencies. Result showed that performance per watt of AES-128 on the APU including 80 cores were 743.0 Mbps/W and 44.0 % increases compared with those on a system equipped with a discrete AMD Radeon HD 6770 including 800 cores. this paper is the first to describe a study to evaluate the per-watt performance of block ciphers on GPUs. © 2012 Springer-Verlag.

关键词： Graphics processing unit

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A regularization network committee machine of isolated regularization networks for distributed privacy preserving data mining

A regularization network committee machine of isolated regul...

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8th IFIP WG 12.5 international conference on Artificial Intelligence Applications and Innovations, AIAI 2012

作者： Kokkinos, Yiannis Margaritis, Konstantinos G. Parallel and Distributed Processing Laboratory Department of Applied Informatics University of Macedonia 156 Egnatia str. 54006 Thessaloniki Greece

ISBN: (纸本)9783642334085

In this paper we consider large scale distributed committee machines where no local data exchange is possible between neural network modules. Regularization neural networks are used for both the modules as well as the combiner committee in an embedded architecture. After the committee training no module will know anything else except its own local data. this privacy preserving obligation is a challenging problem for trainable combiners but crucial in real world applications. Only classifiers in the form of binaries or agents can be sent to others to validate their local data and sent back average classification rates. From this fully distributed and privacy preserving mutual validation a coarse-grained matrix can be formed to map all members. We demonstrate that it is possible to fully exploit this mutual validation matrix to efficiently train another regularization network as a meta learner combiner for the committee. © 2012 IFIP international Federation for Information processing.

关键词： Data mining

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parallel implementation of the TestU01 statistical test suite

Parallel implementation of the TestU01 statistical test suit...

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IEEE international conference on Intelligent Computer Communication and processing (ICCP)

作者： Alin Suciu Radu Alexandru Toma Kinga Marton Department of Computer Science Technical University of Cluj Napoca Cluj-Napoca Romania

As the need of high quality random number generators is constantly increasing especially for cryptographic algorithms, the development of high throughput randomness generators has to be combined with the development of high performance statistical test suites. Unfortunately the implementations of the most popular batteries of test suites are not focused on efficiency and high performance, do not benefit of the processing power offered by today's multi-core processors and tend to become bottlenecks in the processing of large volumes of data generated by various random number generators. Hence there is a stringent need for providing highly efficient statistical tests and our research efforts and results on improving and parallelizing the TestU01 test suite intend to fill this need. Experimental results show that the parallel version of TestU01 takes full advantage of the system's available processing power, reducing the execution time up to 4 times on the tested multicore systems.

关键词： Batteries Rabbits Generators Libraries Instruction sets Multicore processing Algorithm design and analysis

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