• Proceedings of the Korea Information Processing Society Conference
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• 2023.11a
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• pp.81-84
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• 2023

최근의 인텔의 새로운 CPU 아키텍처의 도입으로 Singularity 컨테이너 내에서 cgroup 설정으로 인해 특정 작업의 성능에 영향을 초래할 수 있다. 특히 Singularity 컨테이너에서 HPC(고성능 컴퓨팅) 작업은 cgroup 정책에 의해 작업 효율이 달라질 수 있고 아직 새로운 CPU 환경에서의 HPC 작업에 대한 연구가 충분치 않다. 따라서, 본 논문은 Singularity 컨테이너 생성 시 새로운 CPU 아키텍처에 설계된 CPU 코어 유형별 cgroup 지정이 HPC 응용을 포함하여 다양한 유형의 작업 성능에 미치는 영향을 비교 분석하였고, 이를 통해 HPC 사용자에게 가이드라인을 제공하는 것이 목적이다.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.97-106
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• 2013

Since human genome project finished, the cost for human genome analysis has decreased very rapidly. This results in the sharp increase of human genome data to be analyzed. As the need for fast analysis of very large bio data such as human genome increases, non IT researchers such as biologists should be able to execute fast and effectively many kinds of bio applications, which have a variety of characteristics, under HPC environment. To accomplish this purpose, a biologist need to define a sequence of bio applications as workflow easily because generally bio applications should be combined and executed in some order. This bio workflow should be executed in the form of distributed and parallel computing by allocating computing resources efficiently under HPC cluster system. Through this kind of job, we can expect better performance and fast response time of very large bio data analysis. This paper proposes a workflow-based data analysis system specialized for bio applications. Using this system, non-IT scientists and researchers can analyze very large bio data easily under HPC environment.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.2
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• pp.107-112
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• 2013

With the progress of NGS technologies, large genome data have been exploded recently. To analyze such data effectively, the assistance of HPC technique is necessary. In this paper, we organized a genome analysis pipeline to call SNP from NGS data. To organize the pipeline efficiently under HPC environment, we analyzed the CPU utilization pattern of each pipeline steps. We found that sequence alignment is computing centric and suitable for parallelization. We also analyzed the performance of parallel open source alignment tools and found that alignment method utilizing many-core processor can improve the performance of genome analysis pipeline.

• Proceedings of the Korea Information Processing Society Conference
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• 2018.10a
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• pp.93-96
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• 2018

메시지 전달 인터페이스(MPI)는 분산 및 병렬 처리에서 정보의 교환에 대해 기술하는 표준으로 사용자에게 표준 인터페이스를 제공한다. 그러나, 사용자 레벨의 표준화를 지원하고 있으나 MPI 라이브러리와 런타임 환경은 버전과 종류마다 상이하여 호환이 되지 않아 실행 환경 측면에서의 이식성에 대한 문제가 존재한다. 이러한 MPI 어플리케이션의 이식성 문제를 해결하는 방안으로 컨테이너 기반의 HPC 환경이 가능한 솔루션 중 하나이다. 본 연구에서는 컨테이너 기반의 HPC 환경을 제공하는 대표적인 도구인 Docker, Singularity, Shifter에 대한 MPI 어플리케이션의 이식성에 필요한 고려사항과 실행 방법을 비교 분석한다.

• Proceedings of the Korea Information Processing Society Conference
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• 2022.05a
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• pp.25-27
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• 2022

컨테이너 런타임 환경에서 HPC 작업을 실행하는 수요가 증가하고 있으며, 이에 따라 컨테이너 자원 관리의 중요성이 높아지고 있다. 본 연구에서는 HPC 작업 실행에 최적화된 컨테이너 런타임 환경인 Singularity를 대상으로 cgroups 지정 여부에 따른 실행시간을 측정하는 실험을 진행하고 결과를 분석하였다. 이러한 결과는 Singularity 컨테이너 런타임 환경에서 다양한 HPC 작업을 운영할 시 성능 효율을 높일 수 있는 자원 관리 방향을 제시한다.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.995-1004
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• 2017

Culture-dependent methods, such as heterotrophic plate counting (HPC), are usually applied to evaluate the bacteriological quality of hemodialysis water. However, these methods cannot detect the uncultured or viable but non-culturable (VBNC) bacteria, both of which may be quantitatively predominant throughout the hemodialysis water treatment system. Therefore, propidium monoazide (PMA)-qPCR associated with HPC was used together to profile the distribution of the total viable bacteria in such a system. Moreover, high-throughput sequencing of 16S rRNA gene amplicons was utilized to analyze the microbial community structure and diversity. The HPC results indicated that the total bacterial counts conformed to the standards, yet the bacteria amounts were abruptly enhanced after carbon filter treatment. Nevertheless, the bacterial counts detected by PMA-qPCR, with the highest levels of $2.14{\times}10^7copies/100ml$ in softener water, were much higher than the corresponding HPC results, which demonstrated the occurrence of numerous uncultured or VBNC bacteria among the entire system before reverse osmosis (RO). In addition, the microbial community structure was very different and the diversity was enhanced after the carbon filter. Although the diversity was minimized after RO treatment, pathogens such as Escherichia could still be detected in the RO effluent. In general, both the amounts of bacteria and the complexity of microbial community in the hemodialysis water treatment system revealed by molecular approaches were much higher than by traditional method. These results suggested the higher health risk potential for hemodialysis patients from the up-to-standard water. The treatment process could also be optimized, based on the results of this study.

• Journal of the Korean Society of Groundwater Environment
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• v.2 no.2
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• pp.85-92
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• 1995

This study was conducted to find out the relationship between microflora in groundwater and its physico-chemical environmental factors at the 59 sites, where distributed at 3 cities and 18 counties in Jeonranam-Do, Korea. The average values of environmental factors were as followings; pH 6.9, temperature 20.1 $^{\circ}C$, dissolved oxygen 6.5 mg/1, the depth of wells 80.1 m, and nitrate 10.7 mg/1. The average value of microbial population size; Heterotrophic bacteria-NA (HPC-NA) and heterotrophic bacteria-YEPD (HPC-YEPD) were 1.4${\times}$10$^3$CFU/ml and 0.59${\times}$10$^3$ CFU/ml respectively HPC-YEPD numbers were 42.1% of HPC-YEPD. Coliform bacteria were detected at 16 sites, and its average numbers were 6.7 CFU/ml. General fungi were detected at 14 sites, and its had average numbers were 3.9 CFU/ml. The correlation coefficient was calculated value as relation index between the microbial population sizes and environmental factors in groundwater. In case of HPC-NA, the correlation coefficient value with dissolved oxygen was 0.087 But it showed negative correlation coefficient with other factors. In case of HPC-YEPD, the correlation coefficient value with pH, temperature and nitrate were 0.0957, 0.0019 and 0.0151 respectively. It was concluded that the population size of HPC-NA were influenced by the order of temperature, dissolved oxygen, pH and the depth of wells and that HPC-YEPD were influenced by the order of pH, dissolved oxygen, nitrate, the depth of wells and temperature.

• Proceedings of the Korea Information Processing Society Conference
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• 2017.04a
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• pp.190-191
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• 2017

정보통신기술(ICT)의 발전으로 원격지에서 고속으로 HPC(High Performance Computing) 서비스를 이용할 수 있게 되었지만, HPC 서비스 환경을 대상으로 하는 사이버 공격도 끊이지 않고 발생하고 있다. 본 논문에서는 슈퍼컴퓨터 4호기 서비스 환경에서 탐지/차단된 사이버 공격 증가 추이를 살펴보고, 2016년 사이버 공격 탐지 데이터와 슈퍼컴퓨팅서비스 네트워크 내부로 유입된 트래픽 데이터를 분석하여 급격히 증가한 공격지 IP 주소의 분포 및 특징을 확인한다.

• Journal of the Korea Society of Computer and Information
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• v.27 no.9
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• pp.121-129
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• 2022

In this paper, the virtual environment using rack server type HPC and 3U VPX server type HPC was applied and tested to the basic functions of the Jangbogo-III class submarine combat system developed for the first time in Korea. Based on this test results, the possibility of applying virtualization to the domestic submarine combat system to be developed in the future is confirmed. Existing studies have been limited to deriving applicable virtualization solutions through simple performance analysis of virtualization solutions or applying virtualization to some functions of the surface ship combat system, but in this paper, the application of virtualization is expanded to the submarine combat system through testing.

• Proceedings of the Korea Information Processing Society Conference
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• 2017.04a
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• pp.68-70
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• 2017

KISTI 슈퍼컴퓨터 4호기 Tachyon2는 SUN Blade 6275 시스템을 기반으로 구성된 초병렬 컴퓨팅 시스템으로 이론최고성능(Rpeak) 300TFlops를 보이고 있으며 3,200대의 컴퓨팅 노드와 인프라 노드로 구분된다. Tachyon2 시스템은 국내 산학연 연구자들을 위한 공공 목적의 시스템으로 만여 명의 사용자와 200여개의 기관이 사용 중에 있다. 이런 슈퍼컴퓨터와 같은 대형 HPC 환경에서는 대규모의 사용자 작업을 원활하게 수행하기 위해서는 IB의 안정성이 우선적으로 보장되어야 한다. 본 논문에서는 Tachyon2 시스템에서 발생하는 IB 상태를 파악하고 관리하기 위한 자동화 도구를 개발하였다. 이로써 인터커넥션의 상태를 주기적으로 모니터링 할 수 있고, 장애내역 또한 신속하게 파악할 수 있다.