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K-computer and Supercomputing Projects in Japan

K-computer and Supercomputing Projects in Japan. Makoto Taiji Computational Biology Research Core R IKEN Planning Office for the Center for Computational and Quantitative Life Science & Processor Research Team RIKEN Advanced Institute for Computational Science taiji@riken.jp. Agenda.

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K-computer and Supercomputing Projects in Japan

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  1. K-computer and Supercomputing Projects in Japan Makoto Taiji ComputationalBiology Research Core RIKEN Planning Office for the Center for Computational and Quantitative Life Science & Processor Research Team RIKEN Advanced Institute for Computational Science taiji@riken.jp

  2. Agenda • K-computer • Advanced Institute for Computational Science • High Performance Computing Infrastructure • My own perspective in future HPC, and MDGRAPE-4 (in short)

  3. My Backgrounds • Physics • Special-purpose computers for scientific simulations (1986~) • Monte Carlo simulations of spin systems (1986, m-TIS I) • FPGA-based reconfigurable machine (1990, m-TIS II) • Gravitational N-body problems (1992~96, GRAPE-4,5) • Molecular Dynamics simulations • (1994~, MD-GRAPE, MDM, MDGRAPE-3,4) • Dense Matrix Calculation, quasi-general-purpose machine • (MACE, 2000) • Ultrafast laser spectroscopy (1987~92) • Conjugated Polymers • Rhodopsin and Bacteriorhodopsin • Learning process as dynamical systems, multi-agent dynamics (1996~2002) • Physical Random Number Generator (1997~2004)

  4. World situation of HPC (Top 500) Country Share of Japan: Down to 6th position

  5. Next-Generation Supercomputer Project • National project to develop a leading general-purpose supercomputer in Japan • Not for single purpose – cf. Earth Simulator • Location: Kobe PortIsland • Developer: Fujitsu • Linpack 10 PetaFLOPS • Partial operation: Spring 2011 • Full service: Autumn 2012 K computer system (CG)

  6. Location of K computer Mt. Rokko Shinkansen-Line Shin-Kobe Station Ashiya Sannomiya Kobe Medical Industry Development Project Core Facilities Port Island About 5km from Sannomiya 12 min. by Portliner K-computer & Advanced Institute for Computational Sciences Kobe Sky Bridge Portliner To Osaka To Akashi / Awaji-Island Kobe Airport Photo: June, 2006

  7. RIKEN Advanced Institutefor Computational Science National Center to cover wide fields of computational scienceand engineering

  8. Formation of Central Hub in Kobe Advanced Institute for Computational Science 【Strategic Use】 【Public Use】 StrategicRegion Director: Dr. KimihikoHirao StrategicRegion Academia StrategicRegion Industry StrategicRegion Operation and sophistication of the supercomputer, Computational Sciences Interdisciplinary research Interdisciplinary Research, Computer Science Registered OrganizationSelection of applications User Support Operation Sophistication 【Operation Organization Use】 8

  9. RIKEN Advanced InstituteforComputational Science Computational Science Research Computer Science Research

  10. Grand Challenge Applications Nafion Water 46 nm 27 nm Next-Generation Integrated Life-Science Simulation Software (2006–2012) Next-Generation Integrated Nano-ScienceSimulation Software (2006–2011) Next-Generation Energy Next-Generation information Function Materials Toward therapeutic technology Surgical procedures Catheters Micromachines Hyperthermia High Intensity Focused Ultrasound Medicines, New drug, and DDS Drug Delivery System Regenerative medicine Nonlinear optical Device Nano quantum devices Spin electronics Ultra high-density storage devices Integrated electronic devices Solar energy fixation Fuel alcohol Fuel cells Electric energy storage Drug development Tailor-made medicine Next-Generation Nano Biomolecules Viruses Anticancer drugs Protein control Nano processes for DDC Molecular scale Cellular scale Organ and body scale Proteins/DNA 15nm Mesoscale structure of naflon membrane Whole body Cardiovascular system Electronic conduction in integrated systems Integrated system Semi-macroscopic Organs Cells Tissues 10-8~-6 10-5~-4 10-3~-2 10-1 100 5nm Brain Function Polio virus Self- organized magnetic nanodots Size Liposome Nafion membrane Meso Micro Macro Condensed matters Molecular assembly Protein structural analysis Drug response analysis Molecular network analysis Fluids, heat, structures Achievement of chemical reactions Vascular system modeling Skeleton model Orbiton (orbital waves) Domain One-dimensional crystal of silicon Protein folding Microscopic approach Macroscopic approach Water molecules inside lisozyme cavity Ferromagnetic half-metals “off” “on” light light Self-assembly Doping of fullerene and carbon nanotubes Capsulation Optical switch light MD/first principle/quantum chemistry simulations Continuous entity simulations Electrons and molecules Molecular dynamics Electrons Quantum chemistry Electron theory of solids <Multi-scale human body simulations> Base site: Institute for Molecular Science Base site: RIKEN Wako Institute To provide new tools for breakthroughs against various problems in life science by means of petaflops-class simulation technology, leading to comprehensive understanding of biological phenomena and the development of new drugs/medical devices and diagnostic/therapeutic methods To create next-generation nano-materials (new semiconductor materials, etc.) by integrating theories (such as quantum chemistry, statistical dynamics and solid electron theory) and simulation techniques in the fields of new-generation information functions/materials, nano-biomaterials, and energy

  11. Appointment of Strategic Regions Computational resources and budget will be allocated for the following regions “Strategic organization” will organize the research Region 1. Foundations for predictive life sciences, medical care, and drug design Region 2. Innovation of new materials and new energies Region 3.Prediction of global change for disaster prevention and reduction Region 4. Next-generation manufacturing Region 5. Origin and structure of matter and the universe 2009-2010: Feasibility Studies 2011-2015: Strategic Researches

  12. Prototype and evaluation Conceptual design Schedule of Project Partial operation within FY2010, Full operation starts from FY2012 FY2006 FY2007 FY2008 FY2009 FY2010 FY2011 FY2012 Detailed design Production, installation, and adjustment Processing unit System Front-end unit (total system software) Detailed design Basic design Tuning and improvement Production and evaluation Shared file system Basic design Production, installation, and adjustment Detailed design Next-Generation Integrated Nanoscience Simulation Development, production, and evaluation Verification Applications Next-Generation Integrated Life Simulation Development, production, and evaluation Verification Feasibility Studies Strategic Researches Preparatory Researches Research Promotion Computer building Buildings Design Construction Research building Design Construction

  13. Features of K computer • 京 = “K” means 1016 • High Performance : Linpack 10 PFLOPS • Massive Parallelization • > 80,000 Processors, > 640,000 Cores • SPARC64 VIIIfx: Processor designed for HPC • VISIMPACT / HPC-ACE extensions • 16GB / node, 2GB / core • ~20MW

  14. K-Computer System • Number of nodes : > 80,000 • Number of Processors: > 80,000 • Number of Cores: > 640,000 • Peak Performance: > 10 PFLOPS • Memory Capacity: > 1PB (16GB/node) • Network: Tofu interconnect (6-dim. Torus) • User view: 3D-Torus • Bandwidth: 5GB/s bidirectional for each six direction • 4 Simultaneous Communication • Bisection Bandwidth: >30TB/s (bidirectional, nominal peak) 5GB/s x Bidirectional 5GB/s x Bidirectional ノード CPU: 128GFLOPS (8 Core) 5GB/s x Bidirectional 5GB/s x Bidirectional Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFlops Core SIMD(4FMA) 16GFLOPS L2$: 5MB 5GB/s x Bidirectional 64GB/s z MEM: 16GB y 5GB/s x Bidirectional x 3D-Torus Network

  15. Cabinet of K computer • 24 boards/cabinet • 192 CPUs • 24 TFLOPS

  16. What is special in K computer? • Network • High Bandwidth, Low Latency • Processor for HPC • VISIMPACT • Shared Cache & Hardware Barrier • Multi-core parallelization of inner loop • HPC-ACE • Register Extension • SIMD 2FMA, 2 issue/cycle (4FMA/Core) • Instructions for special functions (trigonometric, inverse, square-root, inverse square-root etc.)

  17. T. Maruyama, Proc. Hot Chips 2009.

  18. Software • OS: Linux • Compiler • Fujitsu compiler will support • Fortran(2003), C(1999), C++(2003) • GNU C/C++ extensions • Automatic vectorization for SPARC64 VIIIfx • OpenMP 3.0 • MPI-2.1 • gcc may also be available. However, it cannot generate CPU specific instructions (e.g SIMD) and poor performance is expected.

  19. How to use it? • Five “Strategic Regions” has been selected. For these fields, MEXT will fund some research budget, and machine time will be delivered. • General Use For general use, “registered organization” will control distribution of machine time. • Commercial Use RIKEN does not responsible for the usage of the machine, basically.

  20. HPCI:High Performance Computing Infrastructure • System to utilize academic supercomputers in Japan • 2012~ • User Communities • 5 strategic regions, Industrial Consortiums, National Universities and Institutes • Computing Resource Provider • RIKEN AICS, University Centers, National Institutes

  21. Basic Idea of HPCI 25 Organization 13 Organization Logical Structure Physical Structure

  22. Problem in Future of HPC Hardware • If the problem can be parallelized… Computing performance is cheap. • However, in every aspects… Data movements dominates costs. • CoreーCache • CacheーMain Memory • NodeーNode • NodeーDisk • SystemーSystem/Apparatus/Internet

  23. Future Processors for HPC • Gap between top-end HPC processors and commodity will increase • What are needed for HPC • Many-core processors, Accelerators for “dense problems” • Chip stacking for bandwidth • Network integration • Network will be the most important factor in HPC

  24. Future Directions (1) • Network integration is essential both for general-purpose machines and special-purpose ones • Platform for Accelerators • General-purpose processor cores • Cache or local memory • Fast, low-latency on-chip and off-chip networks Accelerator Memory ＞100GB/s Network >30GB/s PU On-chip Network >100GB/s/router Memory

  25. Future Directions (2) • High Memory Bandwidth System • “Single-chip BlueGene/L” by System-on-Chip or Chip stacking by TSV • B/F〜1 • B/F〜0.1 for remote node >500GFLOPS PU Network >50GB/s Memory >500GB/s

  26. Problem in Network • Molecular Dynamics: Strong Scaling is important • 〜50,000 FLOP/particle/step • N=105 • 5 GFLOP/step • 5TFLOPS effective performance 1msec/step = 170nsec/day Rather Easy • 5PFLOPS effective performance 1μsec/step = 200μsec/day??? Difficult, but important

  27. Anton • D. E. Shaw Research • Special-purpose pipeline + General-purpose core +Dedicated Network • By decreasing communication latency, it can achieve high sustained performance even for small systems R. O. Dror et al., Proc. Supercomputing 2009, in USB memory.

  28. MDGRAPE-4 • Special-purpose computer for molecular dynamics simulations • Test bed for future HPC hardware • FY2010-FY2012 • System-on-Chip • Accelerator • Memory • General-purpose processor • Network • ~4Tflops / chip

  29. Fin

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