• Genomics & Informatics
• /
• 제20권1호
• /
• pp.14.1-14.4
• /
• 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.

• 한국전산유체공학회:학술대회논문집
• /
• 한국전산유체공학회 2000년도 추계 학술대회논문집
• /
• pp.92-100
• /
• 2000

At the end of 1999. the TeraCluster project has started in the KORDIC Supercomputer center to study PC clusters for parallel computing. The aim is to replace the Cray T3E with a new cluster system in 2002. The PC cluster without a fast network is well suited for applications which do not require large amount of global communications. Since CFD problems are not very communication intensive, whole test cluster may be efficiently used. As an example of practical CFD simulations. the flow past the ONERA M6 wing and the flow past infinite wing are simulated on a cluster of Linux workstations.

• 한국전산유체공학회:학술대회논문집
• /
• 한국전산유체공학회 1999년도 추계 학술대회논문집
• /
• pp.187-192
• /
• 1999

A metacomputing system is constructed by integrating the heterogeneous supercomputers at KORDIC supercomputer center. The implementation is directed toward building up an easy-to-use supercomputing environment for Computational Fluid Dynamics (CFD) simulations. The key feature is an automatic resource selection According to the predicted performance, the system assigns the request job to the most suitable resource which satisfies the user's demands. Verification tests are conducted by using example CFD applications. An overview of the system is given and derivation of performance prediction models is described in details. Discussion is made of the test results to illustrate applicability and usefulness of the proposed models.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• 제3권2호
• /
• pp.134-146
• /
• 2009

Traffic classification seeks to assign packet flows to an appropriate quality of service(QoS) class based on flow statistics without the need to examine packet payloads. Classification proceeds in two steps. Classification rules are first built by analyzing traffic traces, and then the classification rules are evaluated using test data. In this paper, we use self-organizing map and K-means clustering as unsupervised machine learning methods to identify the inherent classes in traffic traces. Three clusters were discovered, corresponding to transactional, bulk data transfer, and interactive applications. The K-nearest neighbor classifier was found to be highly accurate for the traffic data and significantly better compared to a minimum mean distance classifier.

• 한국해안해양공학회지
• /
• 제5권1호
• /
• pp.19-24
• /
• 1993

슈퍼컴과 워크스테이션을 사용하여 해양과정의 모델링 결과를 고화질의 컴퓨터 영상으로 제시할 수 있게 되었다. 본 연구에서는 근년에 발생한 지진진파(쯔나미)에 대한 수치모형을 적용하여 산정된 수위를 3차원적으로 연속적인 동화로서 제시하였다. 이 결과 광원, 반사 및 음영을 나타내는 최신 렌더링 기법에 의한 사진과 같은 효과를 갖는 영상들을 구축하였다. 비디오동화에 의한 수치모형의 결과는 실제적인 쯔나미의 파급거동을 잘 제시하였다.

• Journal of Information Science Theory and Practice
• /
• 제10권spc호
• /
• pp.76-85
• /
• 2022

At the 8th National High-Performance Computing (HPC) Committee convened in 2021, the "National High-Performance Computing Innovation Strategy (draft) for the 4th Industrial Revolution Era" was deliberated and the original draft was approved. In this proposal, the Ministry of Science and ICT in KOREA announced three major plans and nine detailed projects with the vision of "Realizing the 4th industrial revolution quantum jumping by leaping into a high-performance computing powerhouse." Thereby the most important policy about national mid-term and long-term HPC development was established and called the HPC innovation strategy (hereinafter "the innovation strategy"). The three plans of the innovation strategy proposed by the government are: Strategic HPC infrastructure expansion; Secure source technologies; and Activate innovative HPC utilization. Each of the detailed projects has to be executed nationally and strategically. In this paper, we propose a strategy for the implementation of two items ("Strategic HPC infrastructure expansion" and "activate innovative HPC utilization") among these detailed plans.

• 인터넷정보학회논문지
• /
• 제17권3호
• /
• pp.129-136
• /
• 2016

Crucial aspects to successfully realizing the re-emergence of a contemporary and sustainable supercomputing community in South Korea will involve the devoted efforts and support from key government and R&D organizations. We suggest various supplementation plans regarding the roles of support for the statutory plan. This includes the committee and the plans which are often missing necessary support systems that help competent ministries to plan properly according to the missions of the research center. This dissertation suggests that adjustment in the HPC trends will depend upon exposing and correcting problems in the law as well as overall improvement of the law. Also, the total development of a super computing market is necessary. The results of these guidelines will create a spread of demand for supercomputing for national IT resource sharing, and will foster the development of supercomputer specialists worldwide. Other major end results include significant increases in research productivity and increased rates of product development.

• 천문학회보
• /
• 제44권1호
• /
• pp.33.2-33.2
• /
• 2019

Horizon Run 5 is the most massive cosmological hydrodynamic simulation ever performed until now. Owing to the large spatial volume ($717{\times}80{\times}80[cMpc/h]^3$) and the high resolution down to 1 kpc, we may study the cosmological effects on star and galaxy formations over a wide range of mass scales from the dwarf to the cluster. We have modified the public available Ramses code to harness the power of the OpenMP parallelism, which is necessary for running simulations in such a huge KISTI supercomputer called Nurion. We have reached z=2.3 from z=200 for a given simulation period of 50 days using 2500 computing nodes of Nurion. During the simulation run, we have saved snapshot data at 97 redshifts and two light cone space data, which will be used later for the study of various research fields in galaxy formation and cosmology. We will close this talk by listing possible research topics that will play a crucial role in helping us take lead in those areas.

• KSII Transactions on Internet and Information Systems (TIIS)
• /
• 제12권10호
• /
• pp.4738-4753
• /
• 2018

Efficient rendezvous node selection and routing algorithm (RNSRA) for wireless sensor networks with mobile sink that visits rendezvous node to gather data from sensor nodes is proposed. In order to plan an optimal moving tour for mobile sink and avoid energy hole problem, we develop the RNSRA to find optimal rendezvous nodes (RN) for the mobile sink to visit. The RNSRA can select the set of RNs to act as store points for the mobile sink, and search for the optimal multi-hop path between source nodes and rendezvous node, so that the rendezvous node could gather information from sensor nodes periodically. Fitness function with several factors is calculated to find suitable RNs from sensor nodes, and the artificial bee colony optimization algorithm (ABC) is used to optimize the selection of optimal multi-hop path, in order to forward data to the nearest RN. Therefore the energy consumption of sensor nodes is minimized and balanced. Our method is validated by extensive simulations and illustrates the novel capability for maintaining the network robustness against sink moving problem, the results show that the RNSRA could reduce energy consumption by 6% and increase network lifetime by 5% as comparing with several existing algorithms.

• Ocean and Polar Research
• /
• 제43권3호
• /
• pp.179-192
• /
• 2021

In this study, an integrated wave model from global to coastal scales was developed to improve the operational wave prediction performance of the Korean Meteorological Administration (KMA). In this system, the wave model was upgraded to the WaveWatch III version 6.07 with the improved parameterization of the source term. Considering the increased resolution of the wind input field and the introduction of the high-performance KMA 5^th Supercomputer, the spatial resolution of global and regional wave models has been doubled compared to the operational model. The physical processes and coefficients of the wave model were optimized for the current KMA global atmospheric forecasting system, the Korean Integrated Model (KIM), which is being operated since April 2020. Based on the sensitivity experiment results, the wind-wave growth parameter (β_max) for the global wave model was determined to be 1.33 with the lowest root mean square errors (RMSE). The value of β_max showed the lowest error when applied to regional/coastal wave models for the period of the typhoon season when strong winds occur. Applying the new system to the case of August 2020, the RMSE for the 48-hour significant wave height prediction was reduced by 13.4 to 17.7% compared to the existing KMA operating model. The new integrated wave prediction system plans to replace the KMA operating model after long-term verification.