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Computational Science and Infrastructure for Supercomputing in Japan

2006/11/20 Supercomputing Korea 2006 KIAS. Computational Science and Infrastructure for Supercomputing in Japan. Kiyoyuki Terakura Hokkaido University. Supercomputer projects in Japan. Top500 List – November 2006 9. Global Scientific Information and Computing Center, Tokyo Inst. Tech.

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Computational Science and Infrastructure for Supercomputing in Japan

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  1. 2006/11/20Supercomputing Korea 2006 KIAS Computational Science and Infrastructure for Supercomputing in Japan Kiyoyuki Terakura Hokkaido University

  2. Supercomputer projects in Japan Top500 List – November 2006 9. Global Scientific Information and Computing Center, Tokyo Inst. Tech. TSUBAME Grid Cluster – Sun Fire x4,600 cluster, Opteron 2.4/2.6 GHz and ClearSpeed Accelerator, Infiniband NEC/Sun # of proc.: 11,088, Year: 2006, Rmax: 47 Tflops, Rpeak: 82 Tflops main memory: 21 TB 14. The Earth Simulator Center Earth Simulator NEC # of proc.: 5,120, Year: 2002, Rmax: 36 Tflops, Rpeak: 41 Tflops main memory: 10 TB 13 systems in TOP100 30 systems in TOP500

  3. Earth simulator http://www.es.jamstec.go.jp/esc/eng/ AP: arithmetic vector processor PN: processor node

  4. Earth simulator

  5. Atmospheric general circulation model • An atmospheric general circulation model called AFES (AGCM for Earth Simulator) was developed and optimized for the architecture of the Earth Simulator (ES). AFES is based on the CCSR/NIES AGCM and is a global three dimensional hydrostatic model using the spectral transform method. We achieved a high sustained performance by the execution of AFES with T1279L96 resolution on the ES. The performance of 26.58 Tflops was achieved the execution of the main time step loop using all 5120 processors (640 nodes) of the ES. This performance corresponds to 64.9% of the theoretical peak performance 40.96 Tflops. AFES's this performance was recognized as the fastest computation at Super Computing 2002, Baltimore, MD, U.S.A., November 2002, and AFES won Gordon Bell Prize for Peak Performance. Atmosphere and Ocean Simulation Research Group (AOSG), Earth Simulator Center, JAMSTEC

  6. Atmospheric general circulation model Atmosphere and Ocean Simulation Research Group (AOSG), Earth Simulator Center, JAMSTEC

  7. Another example of large simulation Simulation of Typhoon ETAU in 2003 • Software: MSSG(Multi Scale Simulator for Geoenvironment) holistic simulation for coupled atmosphere-ocean model (software developed by Multiscale Simulation Research Group) • resolution 10 km x 10 km over the whole earth 2.78 km x 2.78 km in the region near Japan Time integration over 5 days • Computer resource 768CPU (96 Nodes) memory: about 1TB CPU time: about 7.5 hours http://www.es.jamstec.go.jp/esc/eng/GC/index.html

  8. Supercomputers deployed inInformation Initiative Centers in 7 universities Available to researchers in all universities and national institutes Hokkaido Univ. SR11000/K1(5.4Tflops) Kyoto Univ. PrimePower(8.8Tflops) Tohoku Univ. SX-7(2Tflops) Osaka Univ. SX-8(5.3Tflops) Kyushu Univ. P5(3.25Tflops) Univ. of Tokyo SR11000/K2(19Tflops) Nagoya Univ. PrimePower(12.5Tflops)

  9. Some other supercomputer centers Institute for Materials Research, Tohoku Univ. High Energy Accelerator Research Organization Center for Computational Sciences, Tsukuba Univ. National Institute for Materials Science Institute for Solid State Physics, Tokyo Univ. Advance Center for Computing and Communication, RIKEN Global Scientific Information and Computing Center, TITEC Earth simulator center Japan Aerospace Exploration Agency National Institute for Fusion Science Institute for Molecular Science Japan Atomic Energy Agency ・・ ・・

  10. Next generation supercomputer vs. earth simulator Earth simulator Start of the project: 1997 Start of operation: 2002 number of processors: 5,120 peak performance: 40 Tflops Next generation supercomputer (NGSC) Start of the project: 2006 Start of operation: 2011 number of processors: > 100, 000 peak performance: 10 Pflops total budget : about 1 billion USD

  11. Target of next-generation supercomputer from RIKEN Next-Generation Supercomputer R&D Center

  12. MEXT (Ministry of Education, Culture, Sports, Science and Technology) National Institute for Informatics GRID middleware RIKEN Next-Generation Supercomputer R&D Center http://www.nsc.riken.jp/index-eng.html Institutute for Molecular Science Nano-science RIKEN Life science Structure of the NGSC project Project Leader: T. Watanabe Council for industrial applications of supercomputing (about 160 companies)

  13. Important aspects NGSC project Continuity There was no connection between consecutive developments of supercomputers in Japan, though almost every 10 years new supercomputers have been developed. We have entered a new era in the sense that Japanese Government promised to develop world top level supercomputer consecutively. General purpose Earth simulator was developed for a particular research field, i.e., earth science. The next generation supercomputer is, however, for general purpose. It is expected that the technology development associated with the next generation supercomputer will be utilized for the development of lower rank supercomputers in several computer Centers. Contribution to industry It is expected that the next generation supercomputer will benefit the industries in their research and development.

  14. Supercomputing as a national key technology Supercomputers are extremely expensive: In order to make such a big investment for developing supercomputers, importance of supercomputing has to be well recognized. Council for Science and Technology Policy has set supercomputing as one of the national key technologies. Some by-products Computational sciences are getting more important. Education program will be introduced for training skilled people for software engineering for operating systems and applications.

  15. Grand challenge applications in NGSC • Two grand challenges in application have been set up. • Next Generation Integrated Nanoscience Simulation Software • Institute for Molecular Science • Institute for Solid State Physics, University of Tokyo • Institute for Materials Research, Tohoku University • Nat’l Institute of Advanced Industrial Science and Technology • Research and Development of Next-Generation Integrated Life • Simulation Software • RIKEN • http://www.nsc.riken.jp/p8-eng.html

  16. 東北大 福村裕史 京大 中原勝、榊茂好、加藤重樹、 松林伸幸、石田俊正、佐藤啓文、 中尾嘉秀、木下正弘、松林伸幸 産総研 北浦和夫、三上益弘、古明地勇人、 D.G. Fedorov、石田豊和、都築誠二、 篠田渉、森下徹也、西尾憲吾 大阪府立大 麻田俊雄 阪大 高橋英明 岡山大 田中秀樹、甲賀研一郎 分子研 平田文男、信定克幸、永瀬茂、森田明弘、安池智一、久保田陽二、 鄭誠虎、A. Kobryn,丸山豊、宮田竜彦、生田靖弘、吉田紀生、 大塚勇起、石村和也、Z. Slanina、石田干城、石山達也、 V.V. Sokolov、李洪珍、岡崎進、斉藤真司、三浦伸一、吉井範行、 山田篤志、三上泰治、小林千草、金　鋼、矢ヶ崎琢磨、篠田恵子 東大 北尾彰朗、城地保昌 九大 南部伸孝、青柳睦、 のぎ田理恵、秋山良 早大 中井浩巳、山内祐介 星野稔、菊池那明 慶応 藪下聡 豊田 兵頭志明、金城友之、 鷲津仁志、山本智 名大 岡本祐幸、伊藤暁 大分大 中島俊男 東レ 茂本勇、川上智教 立命館大 今井隆 Chemist members of nano-science WG1-1 About 70 researchers

  17. WG1-2 Physicist members of nano-science 北大 毛利哲夫、大野宗一、 相澤秀昭 東北大 川添良幸、遠山貴巳、前川禎通、 安原洋、本郷研太、水関博志、 高橋まさえ、佐原亮二、筒井健二、 石原純夫、松枝宏明、宮下哲、 横山寿敏、高橋三郎、小山富男、 佐久間昭正、土浦宏紀 About 100 researchers 山形大 富田憲一 仙台電波高専 小椎八重航 筑波大 押山淳、白石賢二、 M. Boero、舘野賢、岡田晋、 小林信彦、矢花一浩 産総研 石橋章司、寺倉清之、橋本保、田村友幸、 香山正憲、田中真吾、三宅隆、西岡圭太、 池庄司民夫、尾崎泰助、土田英二、小野田勝、 今村裕心崎 京大 常次宏一、原田健自 阪大 赤井久純、尾形成信、 草部浩一、小倉昌子 物材機構 小山敏幸、諏訪嘉宏、 前園涼、館山佳尚、 宮崎剛、西野正理 奈良県立医科大 平井國友 理研 古崎昭、有田亮太郎、 小布施秀明、桃井勉 高エネ研 那須奎一郎、吉　凱 大阪府立大 上杉徳照 分子研 米満賢治、信定克幸、 山下靖文 東大 高山一、常行真司、杉野修、永長直人、小形正男、 宮下精二、藤堂眞治、川島直輝、陳　迎、吉本芳英、 赤木和人、村上修一、求幸年、柳瀬陽一、斉藤圭司、 福島孝治、富田裕介、黒田明義、松下勝義、鈴木隆史 愛媛大 土屋卓久 日立 市村雅彦、佐々木直哉、 加賀爪明子、小野木敏之 東芝 石田邦夫 横浜国立大 松井和己 名大 井上順一郎、田中由喜夫、 伊藤博介 富士通 大淵真理、金田千穂子、 山崎隆浩 NEC 広瀬賢二、宮本良之 NTT 田村浩之

  18. 次世代ナノ統合シミュレーションソフトウェアの研究開発次世代ナノ統合シミュレーションソフトウェアの研究開発 Fe-Pd at c=0.5 Nafion T=1020K820K 15nm Water 100nm Ｎａｆｉｏｎ膜のメソスケール構造(DPD) 16.70 3.59 ナノ組織化材料 サブミクロンスケール のトラクションのＭＤ ポリオウイルス ミオシン 5nm Ｎａｆｉｏｎ膜のＭＤ 自己組織化磁性ナノドット セルラーゼ 複合系電子伝導 脂質膜 ミセル タンパク質の 折れ畳み構造 オービトン (軌道波) シリコンの一次元結晶 リゾチームの空洞内の水分子 “off” “on” light light 強磁性ハーフメタル 光スイッチ light 自己集合 カプセル化 フラーレンやカーボンナノ チューブのドーピング functions and materials for information technology energy 非線形光学素子 ナノ量子デバイス スピンエレクトロニクス 超高密度記録デバイス 複合電子デバイス 太陽エネルギー固定 アルコール燃料 燃料電池 電気エネルギー保存 医療・創薬・DDS Nano biological systems ウイルス 抗がん剤 タンパク質制御 DDSナノプロセス DPD FEM 複合系 ﾌｪｰｽﾞﾌｨｰﾙﾄﾞ法 準巨視系 RISM 固体 MD 量子ﾓﾝﾃｶﾙﾛ DFT 分子集合体 ドメイン MO 電子・分子 電子 13 固体電子論 分子動力学 量子化学

  19. Related projects: GRAPE-DR 2004 - • Leader: Kei Hiraki (Univ. Tokyo) http://grape-dr.adm.s.u-tokyo.ac.jp/project-en.html 1. Research Purpose GRAPE-DR project aims to construct an information system infrastructure which combines the high-speed Internet, high-speed computer systems, and high-capacity storage systems to serve the need in the field of scientific researches. Specifically (1) distributed data sharing for experimental science, (2) high-speed computation for various large-scale numerical simulations, and (3) distributed database processing for scientific data. 2. Target By 2008, we construct an information system infrastructure for science with 2PFLOPS computation power and network throughput over 40Gbps. We also provide libraries, applications and database system with mining facilities for various fields of academic research.

  20. GRAPE-DR (2) Hardware design http://grape-dr.adm.s.u-tokyo.ac.jp/project-en.html

  21. GRAPE-DR (3) • Recent achievement They have succeeded in the development of a processor chip (PC) with 512 processor elements with performance of 512 Gflops. This is the world highest performance of one chip. news release: 2006/11/06 Cf: final target: PC with 1024 processor elements with performance of 1Tflops.

  22. Related project: PACS-CS 2005 - 2007 • Leader: Akira Ukawa (Tsukuba Univ.) http://www.ccs.tsukuba.ac.jp/PACS-CS/ (Parallel Array Computer System for Computational Sciences ) The PACS-CS Project aims to advance frontiers of computational sciences through development of a massively parallel cluster PACS-CS and its concentrated usage on the problems that require large-scale simulations. One of the emphases of the Project is placed on the development of first-principles quantum simulations in materials and life sciences capable to treat O(10,000) atoms, thereby allowing an exploration of the connection between the spatial structure and function characteristic of nano materials such as carbon nano-tubes and large bio molecules such as proteins. Another emphasis is advancement of full QCD simulations in particle physics and astrophysics research which forms the core of our fundamental understanding of the creation and history of our Universe. The design targets are a peak performance of 14.3 Tflops with 2,560 nodes connected by a 3-dimensional Hyper-Crossbar Network. The target for the start of operation is July 2006.

  23. Related project • By March 2008, Tokyo Univ. : 150 Tflops Kyoto Univ. : 66 Tflops Tsukuba Univ.: 80 Tflops total 296 Tflops The above universities have set up joint agreement for cooperative operation of these systems.

  24. Summary: Hardware development • Projects involving hardware development PACS-CS 14.6 Tflops, July/2006 joint project among Tokyo, Kyoto and Tsukuba Univ. 300 Tflops, March/2008 GRAPE-DR 2 Pflops, fiscal 2008 (maybe March/2009?) next generation supercomputer (NGSC) project 10 Pflops, March/2011

  25. Other application projects (1) • Grant-in-Aid for Scientific Research in Priority Areas: Ministry of Education, Culture, Sports, Science and Technology (MEXT) Development of New Quantum Simulators and Quantum Design: 2005 – 2008 Hisazumi Akai (Osaka University) http://ann.phys.sci.osaka-u.ac.jp/~tokutei/ Molecular Theory for Real Systems: 2006 – 2009 Shigeyoshi Sakaki (Kyoto University) http://www.riron.moleng.kyoto-u.ac.jp/

  26. WG2 赤字：領域代表者 青字：研究計画代表者 緑字：１８年度公募研究代表者 茶字：評価班メンバー 科研費特定領域 「次世代量子シミュレータ・量子デザイン手法の開発 」 北大 寺倉清之 氏名の後の（実）は実験家 東北大 長尾和多加、白井正文、 三浦良雄、佐久間昭正 金沢大 小田竜樹、長尾秀美 筑波大 押山淳、中務孝、白石賢二、 ボエロ・マウロ、岡田晋、バーバー・サバッシュ 矢花一浩、舘野賢 国際高等研 金森順次郎 北陸先端大 潮田資勝 阪大 赤井久純、鈴木直、森川良忠、笹井秀明、 広瀬喜久治、長柄一誠、佐藤和則、小倉昌子、 草部浩一、白井光雲、濱口幾太郎、柳澤将、 中西寛、D.W. Agerico、R. Muhida、岸智弥、 後藤英和、小野倫也、稲垣耕司、下司雅章、 吉田博、V.A. Dinh、 田畑仁（実）、渡部平司（実）、川合知二 福井工業大 張紀久夫 物・材機構 前園涼、大野隆央、佐々木泰造、 新井正男、宮崎剛、木野日織、 西野正理、奈良純、館山佳尚 産総研 三宅隆、F. Aryasetiawan、 尾崎泰助 信州大 樋口雅彦 茨城大 五十嵐潤一 東大 常行真司、藤原毅夫、今田正俊、 高田康民、吉本芳英 群馬大 高橋学 神戸大 保田英洋（実）、 田中章順（実） 広島大 城健男、樋口克彦、 小口多美夫、田口新、 　獅子堂達也、中田謙吾 東京都立大 酒井治 京都工繊 播磨　弘（実） 東工大 濡木理 慶応 山内淳 奈良医科大 平井國友 東京理科大 福山秀敏 浜田典昭 横浜国立大 大野かおる、石井聡、 野口良史 早稲田 塚田捷 Members in “Quantum Simulator and Quantum Design”

  27. WG3 赤字：領域代表者 青字：研究計画代表者 茶字：評価班メンバー 氏名の後の（実）は実験家 科研費特定領域 「実在系の分子理論」 北大 武次徹也、野呂武司、中山哲 東北大 河野裕彦、大槻幸義 京大 榊茂好、中辻博、小松紘一、 諸熊圭治、中尾嘉秀、加藤重樹、 山本武司、江原正博谷村吉隆 阪大 中野雅由 物・材機構 三島修（実） 東大 中村栄一、西林仁昭（実）、 高塚和夫、牛山浩 兵庫県立大 本間健二（実）、 下条竜夫、松本剛昭 岡山大 田中秀樹、甲賀研一郎 理研 茅幸二 広島大 相田美砂子、松原世明 分子研 中村宏樹、岩田末廣、永瀬茂、 岡崎進、石村和也、斉藤真司、 信定克幸、安池智一、三浦伸一 早大 中井浩巳、星野稔、 山内祐介 慶応 藪下聡 九大 吉澤一成 名大 巽和行、笹井理生 Members in “Molecular Theory for Real Systems”

  28. Other application projects (2) • CREST (Core Research for Evolutional Science and Technology): supported by JST (Japan Science and Technology Agency) New High-Perfomance Information Processing Technology Supporting Information-Oriented Society – Aiming at the Creation of New High-Speed, Large-Capacity Computing Technology Based on Quantum Effects, Molecular Functions, Parallel Processing etc. –: 2001 – 2003 +5 Hidehiko Tanaka (Institute of Information Security) The innovation of Simulation Technology and the Construction of Foundations for Its Practical Use: 2002 – 2004 +5 Norihisa Doi (Chyo University) http://www.simulation.jst.go.jp/ High Performance Computing for Multi-Scale and Multi-Physics Phenomena: 2005 – 2007 + 5 Genki Yagawa (Toyo University) http://www.multi.jst.go.jp/en/index.html Virtual Lab in Nanotechnology Area: 2004 - 2007 For each area, 3 to 5 groups are funded each year.

  29. Exmaples of projects in Doi’s area Development of Multi-scale and Multi-physics Simulation of Heart for Disease Care and Drug Discovery: Toshiaki Hisada (Univ. Tokyo) Normal beat Abnormal beat http://www.sml.k.u-tokyo.ac.jp/

  30. Exmaples of projects in Yagawa’s area Simulations and Dynamics for Nanoscale and Biological Systems Kimihiko Hirao (Univ. Tokyo) UTChem is high-performance software for carrying out ab initio quantum chemistry calculations to calculate electronic wavefunctions, and chemical properties of polyatomic molecules. http://utchem.qcl.t.u-tokyo.ac.jp/

  31. Other application projects (3) • Precursory Research for Embryonic Science and Technolgoy, SAKIGAKE: supported by JST The innovation of Simulation Technology and the Construction of Foundations for Its Practical Use: 2002 – 2004 +3 Norihisa Doi (Chyo University) http://www.simulation.jst.go.jp/ Funded to individual researcher

  32. A plan for Consortium for Computational Materials science WG1 Nanoscience Of NGSC project WG2 Quantum simulator and Quantum design WG7 Council for industrial applications of supercomputing Computer centers for common use ISSP, IMS, IMR, Tsukuba Univ. WG３ Molecular theory for real systems WG6 Materials science （to be formed） WG5 ITBL WG４ JST CREST SAKIGAKE Nano-virtual Lab

  33. Missions for computational science community • Development of linear scale O(N) algorithms If the calculation scales N3, next generation supercomputer can treat only 6 or 7 times bigger system than earth simulator. • Highly parallel computation So far in my community of materials science, the maximum parallelization has been up to about 1,000 processors, while the NGSC will have more than 100,000 processors. • Multi-scale simulations Most problems in real life have aspects of multi-scale. • Overcoming of fundamental difficulties For instance, in the field of nano-bio, vdW interaction is crucially important, while present DFT treatment fails in treating it.

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