dr. ross nobes - Innovation in High-Performance Computing

VISIT 2010 – Fujitsu Forum Europe 1

VISIT 2010 – Fujitsu Forum Europe

Shaping tomorrowwith you.

Innovation Forum – Room 12

Innovation in High-Performance Computing

Dr. Ross NobesAssistant Division Manager, Environment and HealthFujitsu Laboratories

9:00 h


Innovation in High-Performance Computing

Ross NobesFujitsu Laboratories of Europe

4 Copyright 2010 FUJITSU


What is High Performance Computing?

5

Use of parallel computers with low-latency, high-bandwidth networks

Capability computing Large, complex simulations

• Climate modelling, advanced materials, renewable energy, nuclear fusion, aerospace industry, national security, basic science, etc.

Data-intensive computing• Large Hadron Collider, Square Kilometre Array

Now in “petascale” era (1015 operations per second) Moving towards “exascale” computing (1018) by ~2020

Capacity computing Large numbers of smaller compute-intensive jobs

• Digital content creation in entertainment industry, financial applications, etc.

Copyright 2010 FUJITSU

VISIT 2010 – Fujitsu Forum Europe Copyright 2010 FUJITSU

Innovation in Hardware

The “K Computer”

6


30+ Years of Supercomputing



The Next-Generation Supercomputer

8

RIKEN and Fujitsu are jointly developing Japan’s Next-Generation Supercomputer, the “K Computer” 10 PFLOP/s performance Installed at RIKEN’s Advanced

Institute for Computational Science, Kobe

The centrepiece of Japan’s new “Innovative High-Performance Computing Infrastructure”


FY2006 FY2007 FY2008 FY2009 FY2010 FY2011 FY2012

Tuning and improvement

Production, installationand adjustment

Prototype, evaluation

Detailed designConceptual design


The K Computer


Fujitsu Begins Shipping Japan's Next-Generation Supercomputer

Tokyo, September 28, 2010 — Fujitsu announced that today it began shipping the computing units for Japan's Next-Generation Supercomputer, nicknamed the "K computer"


New Technologies


System

Node

CPU

:

CoreCoreCore

:

Tofu Interconnect

VISIMPACT Technology Advanced Packaging

SPARC64TM VIIIfx Multi-Core CPU HPC-ACE Instruction Set Low Power Consumption


Fujitsu’s Advanced Technology

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New HPC-enhanced SPARC64TM VIIIfx CPU 8 cores, 2 GHz, 128 GFLOP/s 58 W peak, 2.2 GFLOP/s per watt

Water cooling• Low current leakage

• Low power consumption and low failure rate Highly reliable design

• Specific logic circuits to detect and correct errors

VISIMPACT Combines hardware enhancements and advanced

compiler technologies to promote hybrid programming models



VISIMPACT: Performance


LS-DYNA on Fujitsu FX1 Supercomputer

www.topcrunch.org


Effect of VISIMPACT


Test Case: Caravan 10-million Elements Car-to-Car Model Time Duration: 10 milliseconds →120 milliseconds

0 500 1000 1500 200005

101520253035404550

Traditional MPI HybridHybrid + VISIMPACT

Cores

Ho

urs

1.54 times speedup by VISIMPACT


High-Performance Computing

Opportunities for Europe

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IDC Report

15

HPC use is indispensable for advancing both scientific and industrial competitiveness

Europe is under-investing in HPC, while other nations are growing their supercomputer investments dramatically

The transition to petascale and exascale computing creates opportunities: For Europe to return to the forefront of development for the next generation of research and HPC software/hardware/storage/networking technologies



IDC Vision for Europe


Provide World-Class HPC Expertise and Resources

To Make EU Scientists, Engineers And Analysts

The Most Productive and Innovative In The World

In Applying HPC To Advance Their Research

In The Pursuit Of Scientific Advancement And Economic Growth


IDC: Outcomes from the Vision


By the year 2020, the EU HPC strategy has enabled the following progress to occur:

1. Europe is recognised as a hotbed for new science and engineering research

2. Europe's leadership in the targeted areas has created many new jobs in science and industry, and has caused the national economies to grow faster

3. Europe is the world leader in important high-end HPC technologiesEurope leads the world in scalable algorithms and software applications, and in tools to make HPC systems easy-to-use and to make researchers highly innovative and productive

FLE’s target


Innovation in Software

The Open Petascale Libraries Project

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Open Petascale Libraries Project


Global collaboration to develop advanced numerical software for supercomputing

Initiated by Fujitsu Laboratories of Europe and Fujitsu Limited

Dedicated forum to promote the open exchange of ideas and the collaborative development of general-purpose and application-specific numerical libraries

Targeted initially at parallel computers built from multi-core processors

All output available as open-source software

Official launch of OPL in November 2010 to coincide with SC10 conference in New Orleans


Exascale Application and Data Initiative


FUJITSUPlatform Solution

R&D Labs

Application users

Application developers

Vendors

Computational scientists,computer scientists and engineers

Computational science society

Open software communities

Exascale

Application

and

Data

Initiative


Bridging Applications and Platforms



OPL: Structure


Advisory PanelEminent figures in HPC

and numerical algorithms

Steering Committeeformed from representative of Network members

Secretariat:Fujitsu Labs Europe / Fujitsu Ltd

Global Members Japanese Members

EESI

Open Petascale Libraries Network


OPL: Members



Contributing to Many Application Areas

Copyright 2010 FUJITSU24


www.openpetascale.org

For More Information



Innovation in Software

Case Study: Improving the Pharmaceutical R&D Pipeline

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Modelling in the Pharmaceutical Industry

We no longer design aeroplanes, bridges, cars or large buildings without first simulating them using computer models

Drugs are developed without modelling their interactions with our bodies

This results in a very expensive pharmaceutical research process Many failures at late stages of

the testing process High health care costs



Lifecycle of a New Medicine

Patent

appli

catio

n

1 medicinal product

0 5 years 10 years 15 years 20 yearsPatent expiry

Acute

toxicity

Pharm

acolo

gy

Chron

ic to

xicit

y

Phase

I cli

nical

trials

Phase I

I

Phase II

I

Regist

ration an

d tran

spare

ncy

Price

Reimbur

semen

t

Pharmac

ovigilance

SPC(supplementary

protection certificate)max. + 5 years

10 years of research

2 to 3 years of administrative procedures

• Average R&D cost for a new medicine: €1 billion• Only 3 out of 10 drugs cover R&D costs before patent expiry



Pharmaceutical R&D

From lab to shelf, development of a new medicine takes 10-13 years

For every 5000 molecules tested: 250 enter pre-clinical testing 10 enter clinical testing 1 approved for use in patients

Half of drugs that enter Stage III clinical testing fail at that stage Often from side-effects in the heart

(arrhythmia and fibrillation which can lead to heart failure and death)

The European project preDiCT aims to eliminate unsuitable drugs early in the R&D pipeline to eliminate wasted time and expenditure



preDiCT Partners



Objectives of preDiCT

Earlier approval of successful drugs, at lower costEarly elimination of unsuitable drug candidatesSystematic inclusion of modelling as well as experiments in the

drug testing processReal time simulation of cardiac electrical activation on a

realistic whole human heart meshModelling environment suitable for use by physiologistsBetter cardiac cell models to describe the interaction of healthy

and unhealthy tissue with drugs Identification of simple biomarkers to indicate the risk of a drug

inducing arrhythmia



Whole-Ventricle Simulator

Scale 2Cell modelling

CellML

Scale 3Organ modelling

Requirements

Research tool

Optimized cellcode

Fast, parallelsimulator

Chaste



Technological Improvements



Performance Improvements

0100200300400500600700800900

1000

0 500 1000 1500 2000 2500

Sp

ee

d-u

p

Processes

Old New



Virtual Physiological Human

preDiCT is part of the VPH Initiative, a flagship eHealth project in FP7

Computational frameworks and ICT-based tools for multiscale models of the human anatomy, physiology and pathology

A key facilitator for: Personalised (patient-specific) healthcare

solutions Early diagnosis and predictive medicine Assessment of safety/efficacy of drugs using

patient-specific computational models Innovative personalised drugs

FLE plans to contribute further to the VPH



Future Innovation

The International Exascale Software Project

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Assumed Exascale Architectures



Assumed Exascale Architectures


x1000

x3

x100

x10

x10

O(1000)

O(1,000,000)

x100

x0.1


Challenges for Exascale


Will need 1 billion simultaneous threads of execution

→ Daunting challenge for algorithm scalability

Power budget will be limited to 20 MW

→ Need for energy efficient algorithms

A node will fail every few hours

→ Need for fault tolerant algorithms

Fujitsu Laboratories intends to work with the computational science community to tackle these challenges

International Exascale Software Project


Summary

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High-performance computing is a vital tool for future scientific and industrial competitiveness and economic prosperity

Fujitsu Limited is developing innovative HPC systems, such as the K Computer

Innovation in software is a challenge that Fujitsu Laboratories is tackling through open collaboration Numerical libraries New applications, especially in health, energy and the environment The road ahead to exascale computing




Business

dr. ross nobes - Innovation in High-Performance Computing