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Nano Grid in NAREGI. Mutsumi AOYAGI Kyushu Univ. & Institute for Molecular Science [email protected] Na tional Re search G rid I nitiative. Working with other national and international initiatives,. Goals. To establish a Grid Infrastructure in Japan.

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nano grid in naregi
Nano Grid in NAREGI

Mutsumi AOYAGI

Kyushu Univ.

&

Institute for Molecular Science

[email protected]

na tional re search g rid i nitiative
National Research Grid Initiative

Working with other national and international initiatives,

Goals

To establish a Grid Infrastructure in Japan

To deploy nano- and bio-applications on the Grid

Period & Budget

Starts April 1st of 2003 →2007

~$16 million / year + Supplementary Budget, depending on Economy condition.

Ministry of Education, Culture, Sports, Science and Technology

slide3

Key Institutes and mission

National Institute of Informatics(NII)&Institute for Molecular Science(IMS)&Institute of Physical and Chemical Research(RIKEN)

Conduct of NAREGIDevelop Grid Infrastructure

Develop nano-science applications on Grid

Develop bio-science applications on Grid

Grid Tech. Research Center, Many Universities and Companies will participate in

slide4

Facilities plan for nano team

  • Grid applications use distributed resources such as
    • High-performance computers
    • Large storage systems
    • High-end visualization environments

For nano Grid applications,IMS has a plan to install new computer resources~10TFLOPS/0.3PB, by the end of 2003 fiscal year.

slide5

ゲート

(金属)

a

b

制御電圧

絶縁体

ドレイン

ソース

Nチャネル

基板

電流

d

制御電圧

c

炭素

酸素

窒素

水素

硫黄

電流

Target applications(1) of nano team

Large scale Electronic Structure Simulations of Soft Materials and Molecular Assemblies.

Molecular Motors

Self-assembled

slide6

Target applications(2) of nano team

Large scale Molecular Dynamics Simulations of Bio-Materials and Solvent.

形態形成

構造予測

ポストゲノム

拡張アンサンブル法

プロティン

G B1

統計力学

分子動力学法

m

10,000個、100

s

Protein holding

membrane

slide7

Developments of Application platform

Nano structure

Platform

MD and MC engine

Nano design

Interaction potential

Nano componets

MO

FMO

Reaction path

DFT

Nano structure Editor

Potential Function

Average Force

Nano Functionality

Zooming engine

OCTA

COGNAC

PASTA

SUSHI

MUFFIN

Joint : Dr. Mikami, (AIST)

slide8

Initial guess,…

Evaluate Integrals

Construct Fock Matrix

no

New Density Converged?

yes

Populations,…

Direct SCFMOmethod

O(N4) integral Calcs.

vs

O(N2) Fock, Density Comm.

N: size of problem

o n 4 integral calcs
O(N4) integral Calcs.

tei(4,4,4,4)=(((3+2*p*(4*PAx*PBx+PBx**2+PAx**2*(1+2*p*PBx**2)))*(3+2*q*(4*QCx*QDx+QDx**2+QCx**2*(1+2*q*QDx**2)))*f(0,t))/(p**2*q**2)+(4*(3+2*p*(4*PAx*PBx+PBx**2+PAx**2*(1+2*p*PBx**2)))*PQx*(QCx+QDx)*(3+2*q*QCx*QDx)*f(1,t))/(p*q*(p+q))(4*(PAx+PBx)*(3+2*p*PAx*PBx)*PQx*(3+2*q*(4*QCx*QDx+QDx**2+QCx**2*(1+2*q*QDx**2)))*f(1,t))/(p*q*(p+q))(8*(PAx+PBx)*(3+2*p*PAx*PBx)*(QCx+QDx)*(3+2*q*QCx*QDx)*(((p+q)*f(1,t))+2*p*PQx**2*q*f(2,t)))/(p*q*(p+q)**2)+(2*(3+2*p*(4*PAx*PBx+PBx**2+PAx**2*(1+2*p*PBx**2)))*(3+q*(QCx**2+4*QCx*QDx+QDx**2))*(((p+q)*f(1,t))+2*p*PQx**2*q*f(2,t)))/(p*q**2*(p+q)**2)+(2*(3+p*(PAx**2+4*PAx*PBx+PBx**2))*(3+2*q*(4*QCx*QDx+QDx**2+QCx**2*(1+2*q*QDx**2)))*(((p+q)*f(1,t))+2*p*PQx**2*q*f(2,t)))/(p**2*q*(p+q)**2)+(4*(3+2*p*(4*PAx*PBx+PBx**2+PAx**2*(1+2*p*PBx**2)))*PQx*(QCx+QDx)*(3*(p+q)*f(2,t)+2*p*PQx**2*q*f(3,t)))/(q*(p+q)**3)\+(8*(3+p*(PAx**2+4*PAx*PBx+PBx**2))*PQx*(QCx+QDx)*(3+2*q*QCx*QDx)*(3*(p+q)*f(2,t)+2*p*PQx**2*q*f(3,t)))/(p*(p+q)**3)(8*(PAx+PBx)*(3+2*p*PAx*PBx)*PQx*(3+q*(QCx**2+4*QCx*QDx+QDx**2))*(3*(p+q)*f(2,t)+2*p*PQx**2*q*f(3,t)))/(q*(p+q)**3)(4*(PAx+PBx)*PQx*(3+2*q*(4*QCx*QDx+QDx**2+QCx**2*(1+2*q*QDx**2)))*(3*(p+q)*f(2,t)+2*p*PQx**2*q*f(3,t)))/(p*(p+q)**3)+((3+2*p*(4*PAx*PBx+PBx**2+PAx**2*(1+2*p*PBx**2)))*(3*(p+q)**2*f(2,t)+4*p*PQx**2*q*(3*(p+q)*f(3,t)+p*PQx**2*q*f(4,t))))/(q**2*(p+q)**4)(8*(PAx+PBx)*(3+2*p*PAx*PBx)*(QCx+QDx)*(3*(p+q)**2*f(2,t)+4*p*PQx**2*q*(3*(p+q)*f(3,t)+p*PQx**2*q*f(4,t))))/(q*(p+q)**4)(8*(PAx+PBx)*(QCx+QDx)*(3+2*q*QCx*QDx)*(3*(p+q)**2*f(2,t)+4*p*PQx**2*q*(3*(p+q)*f(3,t)+p*PQx**2*q*f(4,t))))/(p*(p+q)**4)+(4*(3+p*(PAx**2+4*PAx*PBx+PBx**2))*(3+q*(QCx**2+4*QCx*QDx+QDx**2))*(3*(p+q)**2*f(2,t)+4*p*PQx**2*q*(3*(p+q)*f(3,t)+p*PQx**2*q*f(4,t))))/(p*q*(p+q)**4)+((3+2*q*(4*QCx*QDx+QDx**2+QCx**2*(1+2*q*QDx**2)))*(3*(p+q)**2*f(2,t)+4*p*PQx**2*q*(3*(p+q)*f(3,t)+p*PQx**2*q*f(4,t))))/(p**2*(p+q)**4)(4*p*(PAx+PBx)*(3+2*p*PAx*PBx)*PQx*(15*(p+q)**2*f(3,t)+4*p*PQx**2*q*(5*(p+q)*f(4,t)+p*PQx**2*q*f(5,t))))/(q*(p+q)**5)+(8*(3+p*(PAx**2+4*PAx*PBx+PBx**2))*PQx*(QCx+QDx)*(15*(p+q)**2*f(3,t)+4*p*PQx**2*q*(5*(p+q)*f(4,t)+p*PQx**2*q*f(5,t))))/(p+q)**5+(4*PQx*q*(QCx+QDx)*(3+2*q*QCx*QDx)*(15*(p+q)**2*f(3,t)+4*p*PQx**2*q*(5*(p+q)*f(4,t)+p*PQx**2*q*f(5,t))))/(p*(p+q)**5)(8*(PAx+PBx)*PQx*(3+q*(QCx**2+4*QCx*QDx+QDx**2))*(15*(p+q)**2*f(3,t)+4*p*PQx**2*q*(5*(p+q)*f(4,t)+p*PQx**2*q*f(5,t))))/(p+q)**5+(8*(PAx+PBx)*(QCx+QDx)*(15*(p+q)**3*f(3,t)+30*p*PQx**2*q*(p+q)*(3*(p+q)*f(4,t)+2*p*PQx**2*q*f(5,t))8*p**3*PQx**6*q**3*f(6,t)))/(p+q)**6+(2*(3+p*(PAx**2+4*PAx*PBx+PBx**2))*(15*(p+q)**3*f(3,t)30*p*PQx**2*q*(p+q)*(3*(p+q)*f(4,t)+2*p*PQx**2*q*f(5,t))+8*p**3*PQx**6*q**3*f(6,t)))/(q*(p+q)**6)+(2*(3+q*(QCx**2+4*QCx*QDx+QDx**2))*(15*(p+q)**3*f(3,t)30*p*PQx**2*q*(p+q)*(3*(p+q)*f(4,t)+2*p*PQx**2*q*f(5,t))+8*p**3*PQx**6*q**3*f(6,t)))/(p*(p+q)**6)(787 MUL, 261 ADD,69 FUNC)

Amount of Floating point operations differ significantly depending on the type of integrals.

tei(3,1,1,1)=((PAy*(1+2*p*PAx*PBx)*(1+2*q*QCx*QDx)*f(0,t))/q+((((p+q)**4*((PAy+PQy)*q*(1+2*q*QCx*QDx)+p*(PAy+2*PAx*PAy*PQx*q+2*PAy*PBx*PQx*q+2*PAx*PBx*PQy*q2*PAx*PAy*q*QCx2*PAy*PBx*q*QCx2*PAy*PQx*q*QCx+2*q*((PAy*(PAx+PBx+PQx))+2*(PAy*(PAx+PBx)*PQx+PAx*PBx*PQy)*q*QCx)*QDx)2*p**2*PAx*PAy*PBx*(1+2*PQx*q*(QCx+QDx)))*f(1,t))/q)+(p+q)*((p+q)*((p+q)*(3*p*PAy+6*p**2*PAx*PAy*PQx+6*p**2*PAy*PBx*PQx+2*p**2*PAy*PQx**2+4*p**3*PAx*PAy*PBx*PQx**2+p*PQy+2*p**2*PAx*PBx*PQy+2*p*PAy*PQx**2*q+PQy*q+2*p*PAx*PQx*PQy*q (116 MUL, 31 ADD, 2FUNC)

load balancing
Load Balancing

Number of Integrals Calculated

# Computing node index

slide11

Composite Simulations

Examples

QM/MM model

Particle/Continuum model

Data exchanges only at

Physical boundary

MD simulation combined with electro-static simulation to evaluate defect rate of nano devices.

Hitachi Lab. 2001

slide12

Grid meets Multi-Scale/ Multi-Physics?

Structure Analysis

Fluid Dynamics

Coarse-Grain Dynamics

MD

MC

Reaction Dynamics

MO

Band Struct.

Different space and time scales

slide13

Concluding remarks

A solution based on

Research Grid will have significant advantages for customizing

interdisciplinary simulations,

and also..

Grid will make a big chance for the

Collaboration between Computational Scientists and Computer Scientists in HPC field.

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