• Genomics & Informatics
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• v.20 no.1
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• pp.14.1-14.4
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• 2022

Permutation testing is a robust and popular approach for significance testing in genomic research that has the advantage of reducing inflated type 1 error rates; however, its computational cost is notorious in genome-wide association studies (GWAS). Here, we developed a supercomputing-aided approach to accelerate the permutation testing for GWAS, based on the message-passing interface (MPI) on parallel computing architecture. Our application, called MPI-GWAS, conducts MPI-based permutation testing using a parallel computing approach with our supercomputing system, Nurion (8,305 compute nodes, and 563,740 central processing units [CPUs]). For 10⁷ permutations of one locus in MPI-GWAS, it was calculated in 600 s using 2,720 CPU cores. For 10⁷ permutations of ~30,000-50,000 loci in over 7,000 subjects, the total elapsed time was ~4 days in the Nurion supercomputer. Thus, MPI-GWAS enables us to feasibly compute the permutation-based GWAS within a reason-able time by harnessing the power of parallel computing resources.

• Journal of Korea Society of Industrial Information Systems
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• v.14 no.5
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• pp.19-32
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• 2009

In this paper, we design thin-client framework capable of application sharing & data access on the Internet, and apply related skills, such as X windows system, pseudo server, CODA file system, MPI(Message Passing Interface). We suggest a framework for the thin client to access data produced by working on a server optimally as well as to run server side application, even in the case of network down. Additionally, it needed to reflect all local computing changes to remote server when network is restored. To design thin client framework with these characteristics, in this paper, we apply distributed pseudo server and CODA file system to our framework, also utilize MPI for the purpose of more efficient computing & management. It allows for implementation of network independent computing environment of thin client, also provide scalable application service to numerous user through the elimination of bottleneck on caused by server overload. In this paper, we discuss the implementing method of thin client framework in detail.

• Journal of KIISE:Computer Systems and Theory
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• v.29 no.10
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• pp.539-549
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• 2002

PC cluster-based Information Retrieval (IR) systems improve their performances by parallel processing of query terms using cluster nodes. However TCP/IP based communication used to exchange data between cluster nodes prevents the performance from being improved further. The user-level communication mechanisms solve the problem by eliminating the time-consuming kernel access in exchanging data between cluster nodes. The Virtual Interface Architecture (VIA) is one of the representative user-level communication mechanisms which provide low latency and high bandwidth. In this paper, we propose a VIA-based parallel IR system on a PC cluster. The IR system is implemented using the following three communication methods: Sealable Coherent Interface (SCI) based VIA, MPI on SCI based VIA, MPI on Fast Ethernet based VIA. Through experiments, the performances of the three methods are analyzed in various aspects.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.12 no.10
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• pp.1744-1750
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• 2008

As the computing and network technique move rm and spread widly, the usage of multimedia application becomes in general while the usage of text based application becomes low. Especially the application which treats the streaming media such as video or movie, one of multimedia data, holds a majority in the usage of computing. MPEG, one of the typical compression standard of streaming media, provides very high compression ratio so that general users could be close to the streaming media with easy usage. However, the encoding of MPEG requires lots of computing power and time. In the paper, we design and implement a parallel MPEG encoder with MPI in cluster envrionment to reduce the encoding time of MPEG.

• Journal of ILASS-Korea
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• v.1 no.4
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• pp.32-39
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• 1996

Fuel spray in the MPI gasoline injector and its atomization characteristics are investigated with both macroscopic and microscopic visualization systems. The Bosch injector is inserted into an air-assist spray adapter which is designed to be fabricated and assembled easily. particle motion analysis system is used to measure the SMD of injector, where the assistant air pressure is varied from 0.0 to 1.5bar with fuel pressure 2.8bar. Droplet size decreased with higher air pressure and fine fuel spray with below $60{\mu}m$ of SMD is acquired at the assistant air pressure over 0.5bar.

• Journal of Broadcast Engineering
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• v.11 no.1 s.30
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• pp.100-106
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• 2006

In this paper, we proposed a TxID(Transmitter Identification) system using ZCD (Zero Correlation Duration) code as interference-cancelled spread codes for single frequency network of ATSC terrestrial DTV broadcasting. ZCD codes are simply implemented and have ZCD characteristics. Then, Proposal system can fundamentally solve interference problems caused by ICI(Inter Code Interference) and MPI(Multi-Path Interference) which happens in TxID system using spread coding method. Also, those can cancel truncated error which happens at watermarking for TxID since those can remove its period. In this paper, we identified the availability of TxID system applying interference-cancelled ZCD codes by analyzing DER (Detection Error Rate) which is simulated in various interference environments such as AWGN, ICI, and MPI.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.37B no.9
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• pp.795-805
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• 2012

This paper proposes an algorithm and a hardware architecture for a broadcast communication which has the worst bottleneck among multiprocessor using distributed memory architectures. In conventional system, The pipelined broadcast algorithm is an algorithm which takes advantage of maximum bandwidth of communication bus. But unnecessary synchronization process are repeated, because the pipelined broadcast sends the data divided into many parts. In this paper, the MPI unit for pipeline chain algorithm based on circuit switching removing the redundancy of synchronization process was designed, the proposed architecture was evaluated by modeling it with systemC. Consequently, the performance of the proposed architecture was highly improved for broadcast communication up to 3.3 times that of systems using conventional pipelined broadcast algorithm, it can almost take advantage of the maximum bandwidth of transmission bus. Then, it was implemented with VerilogHDL, synthesized with TSMC 0.18um library and implemented into a chip. The area of synthesis results occupied 4,700 gates(2 input NAND gate) and utilization of total area is 2.4%. The proposed architecture achieves improvement in total performance of MPSoC occupying relatively small area.

• 한국연소학회:학술대회논문집
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• 2002.11a
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• pp.215-222
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• 2002

It has been well acknowledged that intake system plays great role in the performance of reciprocating engine. Well-designed intake system is expected to not only increase engine efficiency but also decrease engine emission, which is one of the most urgent issues in the automotive society. Thorough understanding of the flow in intake system helps great to design adequate intake system. Even though both experimental and numerical methods are used to study intake flow, numerical analysis is more widely used due to its merits in time and economy. Intake system of In-line 6-Cylinder CNG engine was chosen for the analysis ICEM CFD HEXA was used to create 3-D structured grid and FIRE code was used for the flow analysis in the intake system. Due to the complexity of the geometry standard ${\kappa}-{\varepsilon}$ turbulence model was applied. Numerical analysis was performed for various inlet and outlet boundary conditions under both steady and transient flow. Inlet mass flow rate and outlet pressure variation were changing parameters with respect to engine speed. Flow parameters, such as velocity, pressure and flow distribution, were evaluated to provide adequate data of this intake system.

• Journal of the Korean Society for Aeronautical & Space Sciences
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• v.31 no.4
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• pp.16-25
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• 2003

A parallel computing environment based on Windows operating system was constructed and a performance test was mode in comparison with Linux based systems. The Windows 2000 cluster was composed with servers and clients connected by Fast-ethernet, within which two sub-clusters may operates together or separately. Compaq Visual Fortran complier and two MPI libraries, MPICH.NT.1.2.2 and NT-MPICHNT.1.2 were installed as computing tools. Parallel computing performance tests were carried out using two-dimensional preconditioned Navier-Stokes code to examine the dependency on the number of processors, problem size and MPI libraries, those were compared with results from Linux clusters. Results shows that a cluster based on the user-friendly Windows operating system is also useful for the parallel computing and has good performance comparable to the previous Linux clusters.

• Transactions of the Korean Society of Mechanical Engineers B
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• v.38 no.1
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• pp.71-79
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• 2014

A parallelization of the bi-conjugate gradient solver for the pressure equation of the CUPID (component unstructured program for interfacial dynamics) code, which was developed for analyzing the components of a pressurized water-cooled reactor, was studied in a symmetric multi-processing system. The parallel performance was investigated for three typical parallel programming models (MPI, OpenMP, Hybrid) by solving incompressible backward-facing step flow at various grid resolutions. It was confirmed that parallel performance was low when problem size was small or the memory requirement for each thread was considerably higher than the cache memory. Furthermore, it was shown that MPI was better than OpenMP regardless of the problem size, and Hybrid was the best when the number of threads was relatively small.