riken’s peta-scale supercomputer project and grand challenges … · 2008-06-25 · riken’s...

Ryutaro Himeno

RIKEN’s Peta-scale Supercomputer Project and Grand Challenges in Life Science

1) Group Director of R&D group, NGS R&D Center

2) Deputy Program Director for Computational Science

3) Director of Advance Center for Computer &

Communication

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RIKEN Next-Generation Supercomputer R&D Center

Contents

1. The status of 10 Peta FLOPS supercomputer development project

2. Introduction of the Grand Challenge in Life Science in the supercomputer project

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Policy and Outline of A Next Generation Supercomputer Project

Purpose of policy:development, installation and application of an advanced high performance supercomputer system, as one of Japan’s “Key Technologies of National Importance”

Total Budget: about 115 billion Yen ( 1.0 billion US dollars )

Period of Project: FY2006 – FY2012

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4


Formation of the 10 Peta R&D Project

Evaluation Scheme

EvaluationCommittees

Industries

Industrial Forumfor Promotion

of Supercomputing

R&D Scheme

Advisory

Board

Computer Companies

RIKEN: Project HQNext-Generation

Supercomputer R&D Center (Ryoji Noyori)

NII: Grid Middleware and Infrastructure

IMS: Nano Science Simulation

Riken Wako Institute: Life Science Simulation

(Note) NII: National Institute of Informatics, IMS: Institute for Molecular Science

Project Leader: Tadashi Watanabe

MEXT: Policy & FundingOffice for Supercomputer Development Planning

Project Committee

(MEXT and CSTP)

Visiting Researchers from Univ. & National Labs.

R&D G.: Ryutaro Himeno

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Goals of the Next Generation Supercomputer Project

1. Development and installation of the most advanced

high performance supercomputer system

2. Development and wide use of application software to

utilize the supercomputer to the maximum extent

3. Provision of flexible computing environment by sharing

the next generation supercomputer through connection

with other supercomputers located at universities and

research institutes

4. Establishment of “Advanced Computational Science

and Technology Center (tentative name)”

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6


Investigation

Enhancement

Geographical investigation,Construction

Design Construction

File Systems and others

Design Production

Enhancement

Hardware

Basic Design Detail Design Production

Grand ChallengeApplication Software

Next Generation Nano-Science Simulation,Design & Production Evaluation

Next Generation Life Science Simulation, Design & Production Evaluation

System Software

GRID middleware Design & Production Evaluation

Software

FY 2006 2007 2008 2009 2010 2011 2012

Full Operation ★

Operation

R&DStart Operation ★

Current Schedule

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Optimization of Computer Design

Technology LimitSpin off to the consumer electronics

Other Project Watch

Requirement from Grand Challenges

Nano Sci. Life Sci. Others(Engineering etc)

Technology Survey

LSI process

Power savvingSOI

Low-kHigh-k

Light transmit.tech.

SoftwareOS, compiler///

FMO

RISM

MO

Popular numerical scheme

Linear Solver

FVM

FEM

Requirement from Computer Centers

0

200

400

600

800

1000

1200

1400

0 500 1000 1500 2000 2500 3000 3500

電力（kW）

設置

面積

（㎡

)

Power, Space

Reliability, operability

Cost (development, manufacturing, maintenance

Computer center in Japan

Optimum system

Fastest in the world

Operation & Utilization

Essential Element technologies

Real space density function

method

Fast transform

Monte Carlo

Searching algorism

Life Science（6）

Engineering.（4）

Env./ Desasterprev. （3）

Nano Science（6)

Physics, Astro.（2）

21 Selected Target applications

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Target applications and BM suitThe application software committee started selecting target applications for making a benchmark suit in January, 2006.

21 codes were selected in March and NextBMT suit was developed.

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NextBMT and Peta-scale BMT(1/2)

Coarse-Grained Molecular Dynamics CalculationOcta

First-Principles Molecular Dynamics Simulation within the Plane-Wave Pseudopotential formalismPHASE

Analysis of Electron States of Proteins in Solution with the 3D-RISM/FMO MethodRISM/3D-RISM

Ab-initio Molecular Dynamics Calculation in Real SpaceRSDFT

Massively-parallel multipurpose software for molecular dynamics calculationModylas

FMO Molecular Orbital CalculationGAMESS/FMO

Nono(6)

Ab-initio Molecular Dynamics Calculation in Large-Scale Protein SystemsProteinDF

Docking simulation of protein and drugsievgene/myPresto

Simulation for blood-flow analysisMC-Bflow

Validation of statistical significance for development of individualized medicineMLTest

Inference of Genetic Networks from Experimental Data of Gene ExpressionGNISC

Prediction of Protein StructureSimFold

Life (6)

DescriptionProgram nameFields

Peta-scale BMT

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NextBMT and Peta-scale BMT(2/2)

Unsteady Flow Analysis based on Large Eddy Simulation (LES)FrontFlow/Blue

Structural Calculation by Finite Element Method (FEM)FrontSTR

Computation of compressible fluid in aircraft and spacecraft analysisLANS

Computation of Unsteady Cavitation Flow by the Finite Difference MethodCavitation

Engineering(4)

Super-resolution Ocean General Circulation ModelCOCO

Simulation of Seismic-Wave Propagation and Strong Ground MotionsSeism3D

Nonhydrostatic ICosahedral Atmospheric Model (NICAM) for Global-Cloud Resolving Simulations

NICAM

Geophysics (3)

Super large-scale gravitational many-body simulation for finding the celestial origin

NINJA/ASURA

Study of elementary particle and nuclear physics based on Lattice QCD simulation

LatticeQCDPhysics

Astronomy(2)

Peta-scale BMT

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Approval of the Basic Design of Supercomputer System by MEXT

The committee set up by MEXT accepted the following:

3. Fujitsu, Hitachi and NEC join the project as the system developers.

1. The hardware system consists of scalar and vector processor units.

2. The target performance of LinpackBMT is 10 Peta FLOPS.

Scalar Unit Vector Unit

Shared File System Local FileSystem

Local FileSystem

Frontend Unit

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Vector unit is suitable for continuum physics simulationScalar unit is suitable for Data Base application, perticle-based simulationHybrid system has both strong points for users to choose better units for different

applications

Scalar UnitData base, homology searchSimilarity with PC

• high speed low power CPU

• New strong network for enormous parallelism

Vector UnitVector processor based on the Earth Simulatorstrong for continuum physics simulation

• New generation low-power vector processor with optical network

Hybrid Supercomputer System composed of Scalar and Vector Units

Front end computer(Integrated OS)

Scalar Unit Vector Unit

共有ファイル

Nono device

Local fileGlobal file

Control unitProcessing unit

Local file

Disk unit

Solar cell

Plazma Physics

Climate change CFD

- -e-e-I3-

I -

Characteristics

Homology search

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Major Applications of Next Generation Supercomputer

Targeted as grand challenges

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Basic Concept for Simulations in Nano-Science

Institute for Molecular Science is leading this

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Basic Concept for Simulations in Life Sciences

GenesGenes

Vascular Vascular SystemSystem

OrganismOrganismOrganOrgan

TissueTissueCellCell

ProteinProtein

GenomeGenomeGenome

Bio-MDBioBio--MDMD

Tissue StructureTissue Tissue

StructureStructureMulti-physicsMultiMulti--physicsphysics

ChemicalProcess

ChemicalChemicalProcessProcess

Blood Circulation

Blood Blood CirculationCirculation

DDSDDSDDS

Gene TherapyGene TherapyGene Therapy

HIFUHIFUHIFU

Micro-machineMicroMicro--machinemachine

CatheterCatheterCatheter

Micro

MesoMacro

Under total combination of Under total combination of simulation physics simulation physics ……

http://ridge.icu.ac.jp

http://info.med.vale.edu/

RIKEN

RIKEN

RIKEN is leending this

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Total Simulation of Living Matter

GoalUnderstand the life phenomena: reproducing life program on computerDevelop new medicine and medical equipment

Approachcombination of analytical approach and Data-driven approach on Peta-scale computer Data-Based

approach to analysisAnalytical

approach

Molecule scale

Cell scale

Organ/Whole body scale

Basic principal (Equations)

Experimental data

New methodology

•Understand the life phenomena: reproducing life program on computer•Develop new medicine and medical equipment

Fusion of Data based approach and Anaytical approach

Peta scale simulation

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MoleculeMolecule--Scale ResearchScale Research

ObjectivesObjectivesSimulating protein function in life Simulating protein function in life phenomena to reveal important phenomena to reveal important subjects in molecular and cell biologysubjects in molecular and cell biology

Method for the MoleculeMethod for the Molecule--Scale Research: Combination of the following three modelsScale Research: Combination of the following three models

Quantum ChemistryQuantum Chemistry Molecular DynamicsMolecular Dynamics Coarse Grained Model.Coarse Grained Model.

Amino acid as fundamental degrees of freedomAmino acid as fundamental degrees of freedomEmpirical potential obtained from databaseEmpirical potential obtained from database

Smaller size, shorter time, Smaller size, shorter time, and greater accuracyand greater accuracy

Larger size, longer time, Larger size, longer time, and less accuracyand less accuracy

AbAb--initio calculationinitio calculation Calc. of molecular force fieldCalc. of molecular force field

Example: Example: PhosphorylPhosphoryl transfer reaction of transfer reaction of adenylicadenylic asidasid kinasekinase

ATPATP

AMPAMP

((11)) BondingBonding

((22)) Structure changeStructure change

((33)) Chemical reactionChemical reaction

ADPADP xx 22

Dynamics of moleculesDynamics of molecules

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Diffusion coefficientVelocity of matter Organelle velocity vector Metabolic pathway

LeverHepatocyte

Erythrocyte

Pancreatic cell

Cardiac muscle cell

Blood disc

Pancreas

Heart

Differentiated cell m

odel

Cell membrane

Ion channel

Aquaporin

Mitochondria

Local simulation

Fundamental research forcell model construction

Realization of integrated simulationin the intracellular coordinate system

Construction of a differentiated cell modelExtension of each program

Coupled analysis of various simulation

Support of integrated simulation

Live cell model

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Organ/WholeOrgan/Whole body simulationbody simulation

Medical images Whole bodyLocal precise model

Cerebral artery model

Eyeball model

Leg model

coronal

Blood tubebloodmuscle

Stress-strain

Muscle force

velocity

Multi physics model

Surface modelWhole body voxel model

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Planned simulation based on precise Human model

and more….

Ex) Ultrasound propagation simulation for HIFU

By Prof. Hisada and Prof. Sugiura

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Overview of data analysis researchFusion of large-scale heterogeneous data analysis and life-science simulation

Exponential increase of experimental data- Higher dimensions: from gene to exon- Heterogeneity: array, structure, dynamics,…- Invisibility: deficit of information

Expected outcome- Order-made medicine and therapy based on optimized peta-scale data analysis- Peta-scale analysis of gene network for drug target discovery and validation

Modeling of functionsPeta-scale data-analysis

・Fusion of simulation models and experimental data based on data assimilation

- Automation of large-scale modeling- Information technology for fusion of

simulation and data analysis

Data-driven large-scale

simulation technology

PPARα1049 genes

In-silico analysis of drug-target gene

Estimation of gene network

Peta scale computing

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Grand Challenge Goal

Molecular scale

Each software development

Common software platform and optimization

GUI / Workflow Easy to use from user’s point of view

Common libraries + Core software

Support to derive higher performance

Software family optimized for the supercomputer

Improve software for commercial use

Academic and industrial usage

Software house

Improve by ourselves

others

Support to utilize developed codes

Feedback after applying real phenomena

HPC Team for development of common software platform and HPC Team for development of common software platform and optimization on the new supercomputeroptimization on the new supercomputer

Cell scaleOrgan / whole body

Data-Analysis

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CACST: Center for Advanced Computational Science and Technology (tentative name)

Computer science and Computational scienceBoth researchers will gather and expect to develop new research fields and methodologiesCurrently, we are designing the center and operation policy of the supercomputer

The users will be chosen by a new committee independent from RIKEN to pick up valuable subjects

Kobe Port-Island

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COEセ

ンター

Nono

Astro

Nuclear

Life

Geo

Eng.

Physics

Meteology

CACSTIndustrial use

Computer Science

Tentative our Plan of the center

Hub of the Computer Science and Computational Science in Japan and Asia.

Cross point of various sciences and technologies using HPCOperation of 10-Peta FLOPS SupercomputerUser support and spreading the usage in various fieldDevelopment of the next-next supercomputerResearch on computational science Education

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Facilities

Computer Wing Research Wing

Computer WingTotal Floor Area:17,500m2

Area of one floor: 6,300m2

4 Floors (1 underground floor)

Research WingTotal floor area: 8,500m2

Area of 1floor: 1,900m2

7 floors (1 underground floor)(cafeteria is planned on the 6th floor)

Construction: started in March, 2008 and will complete in May, 2010

Image sketch

Other FacilitiesCo-generation SystemWater chiller systemElectric Subsystem

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SummaryThis project is a key for Japan to keep capability of developing supercomputer and supercomputing in application.The supercomputer will be completed in March, 2012 with more than 1 PFLOPS effective performance and serve as a national infrastructureWe made a benchmark suit with 21 application software and evaluate system performance of proposed designs.We fixed the basic design in 2007and are in a progress of detailed design.Focused application areas: Nano and Life sciencesApplication development of Nano science is lead by Molecular Science Institute, Life Science by Wako Institute, RIKENNew center for advanced computational science and technology is being planed and its building construction startedThe life science application currently includes,

Molecular scale simulationCell scale simulationOrgan/whole body simulationData analysis researchHPC team

We are quite open and welcome any idea and corroboration

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riken’s peta-scale supercomputer project and grand challenges … · 2008-06-25 · riken’s...

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