• Journal of the Computational Structural Engineering Institute of Korea
• /
• v.33 no.3
• /
• pp.171-178
• /
• 2020

In this study, we develop MPI-OpenMP hybrid parallelization for multibody peridynamic simulations. Peridynamics is suitable for analyzing complicated dynamic fractures and various discontinuities. However, compared with a conventional finite element method, nonlocal interactions in peridynamics cost more time and memory. In multibody peridynamic analysis, the costs increase due to the additional interactions that occur when computing the nonlocal contact and ghost interlayer models between adjacent bodies. The costs become excessive when further refinement and smaller time steps are required in cases of high-velocity impact fracturing or similar instances. Thus, high computational efficiency and performance can be achieved by parallelization and optimization of multibody peridynamic simulations. The analytical code is developed using an Intel Fortran MPI compiler and OpenMP in NURION of the KISTI HPC center and parallelized through MPI-OpenMP hybrid parallelization. Further parallelization is conducted by hybridizing with OpenMP threads in each MPI process. We also try to minimize communication operations by model-based decomposition of MPI processes. The numerical results for the impact fracturing of multiple bodies show that the computing performance improves significantly with MPI-OpenMP hybrid parallelization.

• Journal of the Korea Convergence Society
• /
• v.8 no.8
• /
• pp.9-15
• /
• 2017

With the development of semiconductor integration technology, central processing units and storage devices have been miniaturized and performance has been rapidly developed, interconnection network technology is becoming a more important factor in terms of the performance of high performance computing system. In this paper, we analyze the trend of interconnection network technology used in high performance computing. Interconnect technology, which is the most widely used in the Supercomputer Top 500(2017. 06.), is an Infiniband. Recently, Ethernet is the second highest share after InfiniBand due to the emergence of 40/100Gbps Gigabit Ethernet technology. Gigabit Ethernet, where latency performance is lower than InfiniBand, is preferred in cost-effective medium-sized data centers. In addition, top-end HPC systems that demand high performance are devoting themselves from Ethernet and InfiniBand technologies and are attempting to maximize system performance by introducing their own interconnect networks. In the future, high-performance interconnects are expected to utilize silicon-based optical communication technology to exchange data with light.

• Proceedings of the Korea Contents Association Conference
• /
• 2007.11a
• /
• pp.522-526
• /
• 2007

Since newly emerged disease, the Severe Acute Respiratory Syndrome (SARS), spread from Asia to North America and Europe rapidly in 2003, many researchers have tried to determine where the virus came from. In the phylogenetic point of view, SARS virus has been known to be one of the genus Coronavirus, but, the overall conservation of SARS virus sequence was not highly similar to that of known coronaviruses. The natural reservoirs of SARS-CoV are not clearly determined, yet. In the present study, the genomic sequences of SARS-CoV were analyzed by bioinformatics techniques such as multiple sequence alignment and phylogenetic analysis methods as well multivariate statistical analysis. All the calculating processes, including calculations of the relative synonymous codon usage (RSCU) and other genomic parameters using 30,305 coding sequences from the two genera, Coronavirus, and Lentivirus, and one family, Orthomyxoviridae, were performed on SMP cluster in KISTI, Supercomputing Center. As a result, SARS_CoV showed very similar RSCU patterns with feline coronavirus on the both axes of the correspondence analysis, and this result showed more agreeable results with serological results for SARS_CoV than that of phylogenetic result itself. In addition, SARS_CoV, human immunodeficiency virus, and influenza A virus commonly showed the very low RSCU differences among each synonymous codon group, and this low RSCU bias might provide some advantages for them to be transmitted from other species into human beings more successfully. Large-scale genomic analysis using bioinformatics techniques may be useful in genetic epidemiology field effectively.