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Computational Science at Edinburgh. From Excellence to Enterprise Dr Arthur Trew Director. Theory- Greece 400 BC. Simulation - Edinburgh 1,980 AD. For problems which are: - too large/small - too fast/slow - too complex - too expensive. on the shoulders of giants.

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computational science at edinburgh

Computational Science at Edinburgh

From Excellence to Enterprise

Dr Arthur Trew


on the shoulders of giants



400 BC

Simulation -


1,980 AD

For problems which are:

- too large/small

- too fast/slow

- too complex

- too expensive ...

on the shoulders of giants
  • for centuries science has relied on experiment and theory, but
    • theory is best suited to a reductionist approach
    • experiment is limited in its range of applicability
  • there is a need for a complementary approach: simulation  study of emergent phenomena

Experiment -


1,500 AD

becoming the best


52.86 HPCx

1.0 Donofrio

.4 Eades

1.68 SRIF

2.3 eDIKT

1.0 SUR

2.3 NeSC/eSI


0.2 GSC

0.35 e-Strom

0.6 GridNet

becoming the best
  • in 1990 Edinburgh established EPCC as its focus for HPC simulation
    • following a decade of research in Physics
  • in 1992 EPCC set itself a mission “to be Europe’s top HPC centre within 5 years”
    • we succeeded
    • today, that success is benefiting Scottish research and industry
  • in 2001 Edinburgh & Glasgow created NeSC to extend that vision
    • over the past 18 months EPCC & NeSC have brought in £65M of research grants/contracts
      • of which £2.3M from SHEFC for eDIKT
    • Edinburgh & Glasgow backed this with £3M
    • … and foundation departments lead major UK Grid projects


UoE = 3.19 - 1.68 UoG = 1.45

(AK’s figures)

what s that to me

£53M: 3 machines

whole earth



solar weather

eddy resolution



materials design


whole aircraft

drug design

protein structures



what’s that to me?
  • as computer performance improves, the range of applications increases
linking to data
linking to data
  • but simulation is only part of the story …
  • linking computer modelling to experiment is vital to the interpretation of many large experiments, eg LHC
  • … and with big experiments set to generate Pbyte/year data management is critical
  • … but we have the web, don’t we?
epcc overview

Technology Transfer


o Projects

o Consultancy

o Standards


o National HPC facilities

o Research

o Support


o Academia

o Industry

European leadership:

o Visitor programmes

o Technology Transfer

o Strategic Planning

EPCC overview
  • 70 staff, £3M turnover
  • … possible through the “win-win-win” model
hpcx rationale
HPCx rationale
  • UK academic research is increasingly dependent upon high-end compute facilities
  • recent technological and Grid advances highlighted the need to upgrade UK resources
  • HPCx objectives are thus:
    • aim “to deliver optimum service resulting in world-leading science”
    • address “the problems involved in scaling to the capability levels required”
what is hpcx
What is HPCx?
  • Consortium of leading UK organisations committed to creating and managing the new resource for the next 6 years
    • led by University of Edinburgh
  • multi-stage project to deliver a world-class academic computing resource, the largest in Europe
  • £54M/$100M budget
  • Grid-enabled, a key component in the UK e-Science programme
hpcx consortium members

UoE HPCx Ltd – wholly-owned subsidiary of the University of Edinburgh and lead contractor

  • EPCC, University of Edinburgh
  • Daresbury Laboratory, CCLRC
  • IBM
HPCx Consortium Members
the University of Edinburgh is one of the top 5 research universities in the UK
  • EPCC is the leading computer centre in Europe, bridging the gap between academia and industry
  • … and provides both HPC and novel computing solutions to a wide range of problems and users
  • long experience of providing national HPC services including:
    • Meiko Computing Surfaces
    • Thinking Machines CM200
    • Cray T3D/T3E
daresbury laboratory
Daresbury Laboratory
  • A multi disciplinary research lab with over 500 people
  • Provides large-scale research facilities both for UK academic and industrial research communities
  • Runs the UK’s Collaborative Computational Projects
  • Daresbury hosts the HPCx hardware

IBM provides the technology for HPCx

  • Long standing involvement in HPC including the development of a number of ASCI machines and 4 of the top dozen machines in the 21st TOP500 list:
    • ASCI White: Rmax = 7.3 TFlop/s
    • SP Power3 (6656 Processors): Rmax = 7.3 TFlop/s
    • xSeries (1920 Processors): Rmax = 6.6 TFlop/s
    • HPCx (1280 processors): Rmax = 3.2 TFlop/s
  • IBM has the long term technology road map essential to a 6 year project such as HPCx
hpcx phase 1
HPCx: Phase 1
  • System will be commissioned in three main stages Phase 1 covering 2002-2004 consists of:
    • 40 Regatta-H SMP nodes, 1280 processors
    • Peak performance 6.6 TFlop/s, with 3.4 Tflop/s sustained Linpack
      • currently 16th in the Top500
  • 1.28 TB total memory capacity
  • Over 50 TB of storage capacity
  • Double plane Colony switch with total peak bandwidth of 250 MB/s per processor
hpcx phases 2 3
HPCx Phases 2 & 3
  • Phase 2 (2004-2006)
    • aiming for 6TFlop/s sustained on Linpack and 2.5TFlop/s on sPPM
    • O(48) Regatta-H+ SMP nodes
    • interconnect upgraded to Federation switch
    • doubling of I/O and storage
      • already built a cluster with 8 Regatta-H+ frames and a pre-release Federation switch
      • undertaking a phased upgrade during 1H2004
  • Phase 3 (2006-2008)
    • target of 12 TFlop/s sustained on Linpack
    • may be additional nodes or alternative technology
hpcx science support



Applications Support

Helpdesk Training

Liaising with users

Life sciences

New applications


Capability applications

Scalable algorithms Performance optimisation

Software Engineering

Underpinning technology Grid/e-Science

Systems & Networking

Flexible and responsive capability computing service

Smooth transitions between phases


HPCx Science Support
  • 18 staff in 5 dual-centre functional support teams
hpcx status application areas
HPCx Status: Application Areas
  • currently 28 active consortia, and over 450 users
  • Life Sciences outreach activity supported by IBM
atomic and molecular physics
Atomic and Molecular Physics
  • The UK Multiphoton, Electron Collision and Bose Einstein Condensates (MECBEC) HPC Consortium
  • Two flagship projects model two-electron atoms (helium) and molecules (hydrogen) exposed to intense, ultra-short laser pulses
  • Modelling involves the grid solution of multi-dimensional, time-dependent partial differential equations)
  • Requires large amounts of computing power
  • Visualisation techniques crucial in extracting information

Simulation of Double Ionization of laser-driven helium performed at Queen’s University Belfast

environmental science polcoms
Environmental Science: POLCOMS
  • POLCOMS is a multi-disciplinary model developed at the Proudman Oceanographic Laboratory
  • … a 3-D hydrodynamic model integrating coasts and oceans using a wide range of associated models
  • POLCOMS is a step towards real time modelling of coastal zones, enabling better analysis of impacts to, and sustainability of, the marine environment

A simulation of Chlorophyll density in UK

waters using the POLCOMS model

material science crystal
Material Science: Crystal
  • CRYSTAL computes electronic structure and related properties of periodic systems
  • Developed jointly by Daresbury and the University of Turin
  • A Fortran90 and MPI program that performs Hartree-Fock, density functional and other approximation calculations
  • On HPCx, CRYSTAL used to calculate the structure of the Crambin molecule, the largest Hartree-Fock calculation ever converged (1284 atoms)
    • next, the Rusticyanin molecule (6284 atoms)
engineering uktc
Engineering: UKTC
  • UK Turbulence Consortium is developing world leading turbulence simulation codes using HPCx
  • essential that they can easily facilitate the scientific usage of the resulting data
  • the calculated data are transferred from HPCx to a remote site for analysis
  • so, the Grid is becoming increasingly important
chemistry realitygrid
Chemistry: RealityGrid
  • RealityGrid is a UK collaboration
    • which aims to grid-enable the realistic modelling and simulation of complex condensed matter structures at the meso and nanoscale levels
  • HPCx terascaling team has worked on parallelisation & optmisation of RealityGrid codes, such as LB3D
  • RealityGrid also uses the Grid for data transfer, computational steering, and remote visualisation
    • using Globus on HPCx
    • TeraGyroid won award at SC2003
the vision

The Vision
  • we want Edinburgh to lead the e-science revolution
    • to become the European equivalent of one of the big US centres, eg San Diego Supercomputer Center