• 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 KIISE:Computer Systems and Theory
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• v.29 no.4
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• pp.192-200
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• 2002

The performance of a PC cluster system is limited by the use of traditional communication protocols, such as TCP/IP because these protocols are accompanied with significant software overheads. To overcome the problem, systems based on user-level interface for message passing without intervention of kernel have been developed. The VIA(Virtual Interface Architecture) is one of the representative user-level interfaces which provide low latency and high bandwidth. In this paper, a VIA system is implemented on an SCI(Scalable Coherent Interface) network based PC cluster. The system provides both message-passing and shared-memory programming environments and shows the maximum bandwidth of 84MB/s and the latency of $8{\mu}s$. The system also shows better performance in comparison with other comparable computer systems in carrying out parallel benchmark programs.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2002.05a
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• pp.197-200
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• 2002

The current Inn technique is many problems that is permission of radio station using RF Wireless Modem, that is influence of geographic obstacle using radio wave, that is frequency interference, that is finiteness of frequency resources. In this paper, we are solved many elements, IM replaces RF Wireless Modem, we suggest transmission technique of correction message using mobile phone, we researched Interface Module development which is linkage of DGPS receiver and mobile phone. IM can transmit correction message passing RS-232 port and modem communication control. IM of base station is initialized RS-232 port and modem to move station for correction message transmission, IM waited response mode. IM of move station is initialized RS-232 port and modem, IM requests hand shaking to base station, completed connection establishment. Users are worked Differential surveying using receiving correction message between mobile phones.

• The KIPS Transactions:PartA
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• v.13A no.6 s.103
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• pp.533-540
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• 2006

This paper describes the design and implementation of a grid system META (Metacomputing Environment using Test-run of Application) which facilitates the execution of a CFD (Computational Fluid Dynamics) analysis program on distributed environment. The grid system META allows the CFD program developers can access the computing resources distributed over the network just like one computer system. The research issues involved in the grid computing include fault-tolerance, computing resource selection, and user-interface design. In this paper, we exploits an automatic resource selection scheme for executing the parallel SPMD (Single Program Multiple Data) application written in MPI (Message Passing Interface). The proposed resource selection scheme is informed from the network latency time and the elapsed time of the kernel loop attained from test-run. The network latency time highly influences the executional performance when a parallel program is distributed and executed over several systems. The elapsed time of the kernel loop can be used as an estimator of the whole execution time of the CFD Program due to a common characteristic of CFD programs. The kernel loop consumes over 90% of the whole execution time of a CFD program.

• Journal of the Korea Institute of Information and Communication Engineering
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• v.10 no.5
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• pp.921-927
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• 2006

The current DGPS technique is many problems that is permission of radio station using RF Wireless Modem, that is influence of geographic obstacle using radio wave, that is frequency interference, that is finiteness of frequency resources. In this paper, we are solved many elements, IM(Interface Module) replaces RF Wireless Modem, we suggest transmission technique of correction message using mobile phone, we researched Interface Module development which is linkage of DGPS receiver and mobile phone. IM can transmit correction message passing RS-232 port and modem communication control. IM of base station is initialized RS-232 port and modem to move station for correction message transmission, IM waited response mode. IM of move station is initialized RS-232 port and modem, IM requests hand shaking to base station, completed connection establishment. Users are worked Differential surveying using receiving correction message between mobile phones.

• Journal of KIISE:Computer Systems and Theory
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• v.27 no.2
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• pp.160-168
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• 2000

In this paper, we present a performance monitor to trace and evaluate the performance of programs running on networked computers. The performance monitor of the JaNeC is online/batch as well as event/time driven. Since it is implemented with the Java programming language, it provides us with high portability among heterogeneous computer systems, and friendly graphical user interface. This performance monitor consists of various views such as 'Task/Event Filter' and 'TimeLine', 'Task View', 'Task Hoistory', 'Message Passing View', 'Host Cpu View', which allow the user to easily analyze event and time during the program execution.

• Journal of information and communication convergence engineering
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• v.8 no.1
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• pp.13-18
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• 2010

The composite stock cutting problem is defined as allocating rectangular and irregular patterns onto a large composite stock sheet of finite dimensions in such a way that the resulting scrap will be minimized. In this paper, we introduce a novel approach to hybrid optimization algorithm called MGA in MPI (Message Passing Interface) environments. The proposed MGA combines the benefit of rapid convergence property of Mean Field Annealing and the effective genetic operations. This paper also proposes the efficient data structures for pattern related information.

• 한국전산유체공학회:학술대회논문집
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• 2003.10a
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• pp.88-90
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• 2003

We implement Realtime Air Diffusion Prediction System which is designed for air diffusion simulations with four-dimensional data assimilation. For realtime running, we parallelize the system using MPI (Message Passing Interface) on distributed-memory parallel computers and build a cluster computer which links high-performance PCs with high-speed interconnection networks. We use 162­CPU nodes and a Myrinet network for the cluster

• Journal of the Computational Structural Engineering Institute of Korea
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• v.23 no.6
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• pp.693-702
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• 2010

In this paper, FETI(Finite Element Tearing and Interconnecting) method is introduced in order to improve numerical efficiency of Staggered method. The porous media theory, the Staggered method and the FETI method are briefly introduced in this paper. In addition, we account for the MPI(Message Passing Interface) library for parallel analysis, and the proposed combined Staggered method with FETI method. Finally Lagrange multipliers and CG(Conjugate Gradient) algorithm to solve decomposed domain are proposed, and then the proposed method is verified to be numerically efficient by MPI library.

• Proceedings of the IEEK Conference
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• 1998.10a
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• pp.289-440
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• 1998

This paper describes an interconnection network structure which transports information among processors through a high speed ATM switch. To efficiently use the high speed ATM switch for the message-based multiprocessor, we implemented the cell router that performs multiplexing and demultiplexing of cells from/to processors. In this system, we use the expanded internal cell format including 3bytes for switch routing information. This interconnection network has 3 stage routing strategies: ATM switch routing using switch routing information, cell router routing using a virtual path identifier (VPI) and cell reassembly routing using a virtual channel indentifier (VCI). The interconnection network consists of the NxN folded switch and N cell routers with the M processor interface. Therefore, the maximum number of NxM processors can be interconnected for message communication. This interconnection network using the ATM switch makes a significant improvement in terms of message passing latency and scalability. Additionally, we evaluated the transmission overhead in this interconnection network using ATM switch.