• Title/Summary/Keyword: Parallel Computing

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Developing a Bioinformatics Tool for Peptide Nucleic Acid (PNA) antisense Technique Utilizing Parallel Computing System (Peptide Nucleic Acid(PNA)를 이용한 antisense 기법에 적용할 병렬 컴퓨팅용 Bioinformatics tool 개발)

  • Kim Seong-Jo;Jeon Ho-Sang;Hong Seung-Pyo;Kim Hyon-Chang;Kim Han-Jip;Min Churl-K
    • Proceedings of the Korean Information Science Society Conference
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    • 2006.06a
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    • pp.43-45
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    • 2006
  • Unlike RNA interference, whose usage is limited to eukaryotic cells, Peptide Nucleic Acid (PNA) technique is applicable to both eukaryotic and prokaryotic cells. PNA has been proven to be an effective agent for blocking gene expressions and has several advantages over other antisense techniques. Here we developed a parallel computing software that provides the ideal sequences to design PNA oligos to prevent any off-target effects. We applied a new approach in our location-finding algorithm that finds a target gene from the whole genome sequence. Message Passing Interface (MPI) was used to perform parallel computing in order to reduce the calculation time. The software will help biologists design more accurate and effective antisense PNA by minimizing the chance of off-target effects.

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Nonlinear Shell Finite Element and Parallel Computing Algorithm for Aircraft Wing-box Structural Analysis (항공기 Wing-box 구조해석을 위한 비선형 쉘 유한요소 및 병렬계산 기법 개발)

  • Kim, Hyejin;Kim, Seonghwan;Hong, Jiwoo;Cho, Haeseong
    • Journal of the Korean Society for Aeronautical & Space Sciences
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    • v.48 no.8
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    • pp.565-571
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    • 2020
  • In this paper, precision and efficient nonlinear structural analysis for the aircraft wing-box model is developed. Herein, nonlinear shell element based on the co-rotational (CR) formulation is implemented. Then, parallel computing algorithm, the element-based partitioning technique is developed to accelerate the computational efficiency of the nonlinear structural analysis. Finally, computational performance, i.e., accuracy and efficiency, of the proposed analysis is evaluated by comparing with that of the existing commercial software.

A Parallel Genetic Algorithm for Solving Deadlock Problem within Multi-Unit Resources Systems

  • Ahmed, Rabie;Saidani, Taoufik;Rababa, Malek
    • International Journal of Computer Science & Network Security
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    • v.21 no.12
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    • pp.175-182
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    • 2021
  • Deadlock is a situation in which two or more processes competing for resources are waiting for the others to finish, and neither ever does. There are two different forms of systems, multi-unit and single-unit resource systems. The difference is the number of instances (or units) of each type of resource. Deadlock problem can be modeled as a constrained combinatorial problem that seeks to find a possible scheduling for the processes through which the system can avoid entering a deadlock state. To solve deadlock problem, several algorithms and techniques have been introduced, but the use of metaheuristics is one of the powerful methods to solve it. Genetic algorithms have been effective in solving many optimization issues, including deadlock Problem. In this paper, an improved parallel framework of the genetic algorithm is introduced and adapted effectively and efficiently to deadlock problem. The proposed modified method is implemented in java and tested on a specific dataset. The experiment shows that proposed approach can produce optimal solutions in terms of burst time and the number of feasible solutions in each advanced generation. Further, the proposed approach enables all types of crossovers to work with high performance.

The Parallel ANN(Artificial Neural Network) Simulator using Mobile Agent (이동 에이전트를 이용한 병렬 인공신경망 시뮬레이터)

  • Cho, Yong-Man;Kang, Tae-Won
    • The KIPS Transactions:PartB
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    • v.13B no.6 s.109
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    • pp.615-624
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    • 2006
  • The objective of this paper is to implement parallel multi-layer ANN(Artificial Neural Network) simulator based on the mobile agent system which is executed in parallel in the virtual parallel distributed computing environment. The Multi-Layer Neural Network is classified by training session, training data layer, node, md weight in the parallelization-level. In this study, We have developed and evaluated the simulator with which it is feasible to parallel the ANN in the training session and training data parallelization because these have relatively few network traffic. In this results, we have verified that the performance of parallelization is high about 3.3 times in the training session and training data. The great significance of this paper is that the performance of ANN's execution on virtual parallel computer is similar to that of ANN's execution on existing super-computer. Therefore, we think that the virtual parallel computer can be considerably helpful in developing the neural network because it decreases the training time which needs extra-time.

Development of Mobile Volume Visualization System (모바일 볼륨 가시화 시스템 개발)

  • Park, Sang-Hun;Kim, Won-Tae;Ihm, In-Sung
    • Journal of KIISE:Computing Practices and Letters
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    • v.12 no.5
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    • pp.286-299
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    • 2006
  • Due to the continuing technical progress in the capabilities of modeling, simulation, and sensor devices, huge volume data with very high resolution are common. In scientific visualization, various interactive real-time techniques on high performance parallel computers to effectively render such large scale volume data sets have been proposed. In this paper, we present a mobile volume visualization system that consists of mobile clients, gateways, and parallel rendering servers. The mobile clients allow to explore the regions of interests adaptively in higher resolution level as well as specify rendering / viewing parameters interactively which are sent to parallel rendering server. The gateways play a role in managing requests / responses between mobile clients and parallel rendering servers for stable services. The parallel rendering servers visualize the specified sub-volume with rendering contexts from clients and then transfer the high quality final images back. This proposed system lets multi-users with PDA simultaneously share commonly interesting parts of huge volume, rendering contexts, and final images through CSCW(Computer Supported Cooperative Work) mode.

Parallel Computing Based Design Framework for Multidisciplinary Design Optimization (병렬 컴퓨팅 기반 다분야통합최적설계 지원 설계 프레임워크)

  • Chu, Min-Sik;Lee, Yong-Bin;Lee, Se-Jung;Choi, Dong-Hoon
    • Journal of the Korean Society for Aeronautical & Space Sciences
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    • v.33 no.8
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    • pp.34-41
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    • 2005
  • A parallel computing technique was applied to large scale structure analysis or aerodynamic design and it is a essential element in reducing the huge computation time for large scale design problem. We can use a many computers for reducing the analysis time of multidisciplinary design optimization. But previous MDO frameworks can not support a parallel design process technique so still existing which calls an analysis program continuously. In this paper, We developed a MDO framework(MLR) which supports a parallel design process to solve sequential analysis call. Finally, three sample cases are presented to show the efficiency of design time using the suggested MDO framework.

Parallel damage detection through finite frequency changes on multicore processors

  • Messina, Arcangelo;Cafaro, Massimo
    • Structural Engineering and Mechanics
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    • v.63 no.4
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    • pp.457-469
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    • 2017
  • This manuscript deals with a novel approach aimed at identifying multiple damaged sites in structural components through finite frequency changes. Natural frequencies, meant as a privileged set of modal data, are adopted along with a numerical model of the system. The adoption of finite changes efficiently allows challenging characteristic problems encountered in damage detection techniques such as unexpected comparison of possible shifted modes and the significance of modal data changes very often affected by experimental/environmental noise. The new procedure extends MDLAC and exploits parallel computing on modern multicore processors. Smart filters, aimed at reducing the potential damaged sites, are implemented in order to reduce the computational effort. Several use cases are presented in order to illustrate the potentiality of the new damage detection procedure.

Interprocedural Transformations for Parallel Computing

  • Park, Doo-Soon;Choi, Min-Hyung
    • Journal of Korea Multimedia Society
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    • v.9 no.12
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    • pp.1700-1708
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    • 2006
  • Since the most program execution time is consumed in a loop structure, extracting parallelism from loop programs is critical for the taster program execution. In this paper, we proposed data dependency removal method for a single loop. The data dependency removal method can be applied to uniform and non-uniform data dependency distance in the single loop. Procedure calls parallelisms with only a single loop structure or procedure call most of other methods are concerned with the uniform code within the uniform data dependency distance. We also propose an algorithm, which can be applied to uniform, non-uniform, and complex data dependency distance among the multiple procedures. We compared our method with conventional methods using CRAY-T3E for the performance evaluation. The results show that the proposed algorithm is effective.

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Application of computational technologies to R/C structural analysis

  • Hara, Takashi
    • Computers and Concrete
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    • v.8 no.1
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    • pp.97-110
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    • 2011
  • In this paper, FEM procedure is applied to the static and dynamic analyses of R/C structures. Simple R/C shell structure is solved by using FEM procedures and the experimental evaluations are performed to represent the applicability of FEM procedure to R/C structures. Also, R/C columns are analyzed numerically and experimentally. On the basis of these results, FEM procedures are applied to the R/C cooling tower structures assembled by huge R/C shell structure and a lot of discrete R/C columns. In this analysis, the parallel computing procedures are introduced into these analyses to reduce the computational effort. The dynamic performances of R/C cooling tower are also solved by the application of parallel computations as well. From the numerical analyses, the conventional FEM procedures combined with computational technologies enables us to design the huge R/C structures statically and dynamically.

A PARALLEL ALGORITHM FOR CONSTRUCTING THE CONVEX-HULL OF A SIMPLE POLYGON

  • Min, Young-Sik;Lee, Kyeong-Sin
    • Journal of applied mathematics & informatics
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    • v.6 no.1
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    • pp.279-289
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    • 1999
  • Given n points in the plane the planar convex hull prob-lem in that of finding which of these points belong to the perimeter of the smallest convex region (a polygon) containing all n points. Here we suggest two kinds of methods. First we present a new sequential method for constructing the pla-nar convex hull O(1.5n) time in the quadratic decision tree model. Second using the sequential method we suggest a new parallel algo-rithm which solve the planar convex hull O(1.5n/p) time on a maspar Machine (CREW-PRAM) with O(n) processors. Also when we run on a maspar Machine we achieved a 37. 156-fold speedup with 64 pro-cessor.