Browse > Article
http://dx.doi.org/10.3745/KTSDE.2013.2.2.081

Design of MAHA Supercomputing System for Human Genome Analysis  

Kim, Young Woo (한국전자통신연구원)
Kim, Hong-Yeon (한국전자통신연구원)
Bae, Seungjo (한국전자통신연구원)
Kim, Hag-Young (한국전자통신연구원 서버플랫폼연구팀)
Woo, Young-Choon (한국전자통신연구원 고성능컴퓨팅시스템연구팀)
Park, Soo-Jun (한국전자통신연구원 바이오의료IT융합연구부)
Choi, Wan (한국전자통신연구원 클라우드컴퓨팅연구부)
Publication Information
KIPS Transactions on Software and Data Engineering / v.2, no.2, 2013 , pp. 81-90 More about this Journal
Abstract
During the past decade, many changes and attempts have been tried and are continued developing new technologies in the computing area. The brick wall in computing area, especially power wall, changes computing paradigm from computing hardwares including processor and system architecture to programming environment and application usage. The high performance computing (HPC) area, especially, has been experienced catastrophic changes, and it is now considered as a key to the national competitiveness. In the late 2000's, many leading countries rushed to develop Exascale supercomputing systems, and as a results tens of PetaFLOPS system are prevalent now. In Korea, ICT is well developed and Korea is considered as a one of leading countries in the world, but not for supercomputing area. In this paper, we describe architecture design of MAHA supercomputing system which is aimed to develop 300 TeraFLOPS system for bio-informatics applications like human genome analysis and protein-protein docking. MAHA supercomputing system is consists of four major parts - computing hardware, file system, system software and bio-applications. MAHA supercomputing system is designed to utilize heterogeneous computing accelerators (co-processors like GPGPUs and MICs) to get more performance/$, performance/area, and performance/power. To provide high speed data movement and large capacity, MAHA file system is designed to have asymmetric cluster architecture, and consists of metadata server, data server, and client file system on top of SSD and MAID storage servers. MAHA system softwares are designed to provide user-friendliness and easy-to-use based on integrated system management component - like Bio Workflow management, Integrated Cluster management and Heterogeneous Resource management. MAHA supercomputing system was first installed in Dec., 2011. The theoretical performance of MAHA system was 50 TeraFLOPS and measured performance of 30.3 TeraFLOPS with 32 computing nodes. MAHA system will be upgraded to have 100 TeraFLOPS performance at Jan., 2013.
Keywords
Genome Analysis; Bio-Informatics; Supercomputer; MAHA Supercomputer; Heterogeneous;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Intel Xeon Processor E5-1600/E5-2600/E5-460 Product Families Datasheet, Intel, 2012, http://www.intel.com/content/www/us/en/processors/xeon/xeon-e5-1600-2600-vol-1-datasheet.html
2 NVIDIA whitepaper, "Tesla@ Kepler GPU Accelerators," NVIDIA, 2012, http://www.nvidia.com/content/tesla/pdf/ Tesla-KSeries-Overview-LR.pdf
3 Intel $Intel^{(R)}$ $Xeon^{(R)}$ Processor X5670, Intel, 2011, http://ark.intel.com/products/47920/Intel-Xeon-Processor-X5670-12M-Cache-2_93-GHz-6_40-GTs-Intel-QPI
4 "Intelの8コア版Sandy Bridgeとモジュラー設計戦略," 後藤弘茂のWeekly海外ニュース, Impress Watch, 2011. 04, http:// pc.watch.impress.co.jp/docs/column/kaigai/20110406_437481.html
5 BY Jeong, et. al., "Data center operating cost savings for the eco-friendly air conditioning methods," Korea Patent pending, 2011.
6 $Intel^{(R)}$ Xeon PhiTM Coprocessor, Intel, 2012, http://ark.intel.com/products/71992/Intel-Xeon-Phi-Coproce ssor-5110P-8GB-1_053-GHz-60-core
7 "Development of Supercomputing system for genome analysis," IT industrial fusion core technology development project, MKE.
8 YW Kim, SW Kim, "Technology and Trends of High Performance Processors," Electronics and Telecommunications Trends, Vol.25, No.5, pp.123-136, 2010.
9 YW Kim, K Park, HY Kim, "Recent Trends on High Performance Computing System Technology," proceedings of the ITFE Summer Conference, pp.23-25, Aug., 2012.
10 TOP500 Supercomputer sites, http://top500.org
11 YW Kim, SW Kim, W Choi, "Summary on Worldwide HPC Developement Strategies and Status," Electronics and Telecommunications Trends, Vol.26, No.6, pp.174-188, 2011.
12 電子情報通信分野 科学技術.研究開発の國際比較, 2011年版, 擉立行政法人科學 技術振興機構研究開發戦略センター, June, 2012. http://crds.jst.go.jp/output/pdf/11ic03s.pdf
13 P. Kogge et al., ExaScale Computing Study: Technology Challenges in Achieving ExaScale Systems, DARPA Information Processing Techniques Office(IPTO) sponsored study, 2008.
14 Kirk Skaugen, "Petascale to Exascale," ISC 2010 Keynote Presentation, Intel, 2010.
15 Human Genome Project, Wikipedia, http://en.wikipedia.org/wiki/Human_Genome_Project
16 Biology 2.0, Special report, The Economist, 2010, http://www. economist.com/node/16349358