HPC at Warwick and in the Midlands
Rudolf A Roemer
Centre for Scientific Computing,
Computing, University of Warwick
•The Centre for Scientific Computing (CSC) at the University of Warwick
•The Midlands Alliance for Research Computing (MARC)
The Centre for Scientific Computing
Rudolf A Roemer (Director)
Peter Taylor (Facilities Coordinator)
Elke Thonnes (Teaching Coordinator)
csc-director@warwick.ac.uk
csc-facilities@warwick.ac.uk
csc-teaching@warwick.ac.uk
• interdisciplinary research centre
• national teaching and training centre
• HPC facilities @ Warwick
www.warwick.ac.uk/go/CSC
CSC, a research centre
•
../go/csc/research
CSC Core Academic Staff
• Chemistry (Rodger, Taylor, Troisi, Walsh)
• Computer Science (Jarvis, Feng)
• Engineering (Chung, Kerr)
• Mathematics (Barkley, Elliot, Kerr, Kirkilionis,
Stuart)
• Physics (Allen, Arber, Quigley, Roemer)
• Statistics (Thonnes) • Biology (Thalassinos)
•
Research Report 2005-07:
–
–
–
–
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12 conferences/workshops
20+ visitors
72 conference presentation
17+ successful research grants
180+ publications
www.warwick.ac.uk/go/CSC
30/03/2009
what we provide
../go/csc/people
Interdisciplinary Environment
•
We are based around 17 core academic staff and 22
affiliate academics from 7/11 departments. Currently
research activity is focused on:
– Molecular Dynamics and Modelling (Allen, Quigley, Rodger,
Stuart, Taylor, Troisi, Walsh)
– Quantum Simulations (Rodger, Roemer, Quigley, Taylor, Troisi,
Walsh)
– Computational Fluid Dynamics (Arber, Chung, Barkley, Kerr)
– Computational Systems Biology (Feng, Kirkilionis,Thalassinos)
– Monte Carlo Methods (Allen, Roemer, Stuart, Thonnes)
– Computational PDEs (Barkley, Chung, Elliott, Kerr, Kirkilionis,
Plechac, Stuart)
+ faculty and students from SysBio, Complexity DTC, MOAC DTC, …
www.warwick.ac.uk/go/CSC
30/03/2009
where we are and when
• CSC@Lunch:
../go/csc/
Physical Sciences Building
Mondays, 13-14:00 PS017a
• CSC@Tea&Cookies:
Fridays, 14-15:00 in PS
Common Room
• PG seminars
Thursdays, 10-11:00 in
PS017a with breakfast
+ faculty and students from SysBio, Complexity DTC, MOAC DTC, …
www.warwick.ac.uk/go/CSC
30/03/2009
Molecular Dynamics and Modelling
Synopsis
• In the broadest sense, molecular
dynamics is concerned with particle
motion which is inherent to many
natural processes. Examples are simple
molecular vibrations, like bond
stretching and angle bending.
People
• Allen, Rodger, Stuart, Taylor, Quigley,
Walsh
Projects
• The Biological Interface with Materials
• Differential Equations With Random
Initial Data
www.warwick.ac.uk/go/CSC
Polyhedral cages within a
methane hydrate crystallite
30/03/2009
Monte Carlo Methods
Synopsis
• Monte Carlo methods provide approximate solutions
to quantitative problems by inferring from samples
produced through stochastic simulation. While the
method itself is based on statistical simulation the
problems solved can be both deterministic or
probabilistic. A very popular Monte Carlo method is
based on Markov chains and known as MCMC
(Markov chain Monte Carlo).
People
• Allen, Roemer, Stuart, Thönnes
Projects
• Molecular simulation
• Disordered quantum systems
• Algorithms and Analysis for models of inertial
particles
• Infinite dimensional sampling
• Efficient Markov chain Monte Carlo for models in
stochastic geometry
www.warwick.ac.uk/go/CSC
Snapshot of a MC simulation of
elongated particles used to model
liquid crystals
30/03/2009
Computational PDEs
Synopsis
• Partial Differential Equations
(PDEs) arise throughout science
and engineering. In many contexts
a solution is known to exist, but is
not known explicitly. It is then
desirable to approximate the
solution numerically.
People
• Barkley, Chung, Elliott, Kerr,
Kirkilionis, Plechac, Stuart
Projects
• Computational Fluid Dynamics
• Pattern formation and reactiondiffusion equations
• Multiscale computation
www.warwick.ac.uk/go/CSC
Pattern formation in reactiondiffusion systems
30/03/2009
Quantum Simulations
Synopsis
• Ultimately, quantum mechanics governs
how the world around us evolves. Thus
we study quantum effects at the
microscopic and mesoscopic levels and
how these manifest themselves in
macroscopic behavior.
People
• Quigley, Rodger, Roemer, Taylor, Troisi,
Walsh
Projects
• Disordered Quantum Systems
• Molecular Structures, Energetics and
Properties
• Molecular Interactions at Surfaces
• Structure, Dynamics and Reactivity of
Transition Metal Nanoclusters
www.warwick.ac.uk/go/CSC
Electronic charge density at the
quantum Hall transition
30/03/2009
Computational Fluid Dynamics
Synopsis
• CFD is predicting what will happen,
quantitatively, when fluids flow, often with
the complications of, e.g., simultaneous
flow of heat, mass transfer, chemical
reaction (eg combustion, rusting),
mechanical movement (eg of pistons,
fans, rudders), stresses, etc.
People
• Arber, Chung, Barkley, Kerr
Projects
• Fluid Dynamics Research Centre
• Turbulence
• Computational Mathematics
• Computational MHD
• Solar MHD simulations
www.warwick.ac.uk/go/CSC
Adaptive mesh high resolution
image of Rayleigh-Taylor unstable
flows
30/03/2009
Computational Systems Biology
Synopsis
•
Systems biology is the study of living organisms in
terms of their underlying network structure in
addition to their individual molecular components. A
"system" can be anything from a gene regulatory
network to a cell, a tissue, or an entire organism.
Computational approaches are particularly useful to
handle and interpret the volumes of data necessary
to understand complex biological systems.
People
• Feng, Kirkilionis, Roemer, Thalassinos
Projects
• Complex phenomena arising from biological
systems
• Electronic Transport in DNA
• Modelling & Simulation in the Life Sciences
www.warwick.ac.uk/go/CSC
Structure of oxytonic neural
networks
30/03/2009
National EPSRC Training Centre
Training and the MSc
../go/csc/teaching
•
We run a taught-MSc in Scientific Computing based around five core
modules (all dual purpose with home departments):
• CY900: Foundations of Scientific Computing
• CY901: High Performance Scientific Computing
• CY902: Computational Linear Algebra and Optimization
• CY503: Data Structure and Algorithms
• CY904: Monte Carlo Methods
• CY905: Computational PDE’s (Numerics)
•
other degrees are
–
–
MSc in Scientific Computing (Research)
PhD in Scientific Computing
www.warwick.ac.uk/go/CSC
30/03/2009
HPC@Warwick
Computer Resources
../go/csc/facilities
We operate three High Performance Computers:
1. Shared Memory: An SGI Altix 3700BX2 with 56
Intel Itanium2 1.6 GHz processors and 112 GB of
memory.
2. Distributed Memory: 960 x 3 GHz Intel Xeon
"Woodcrest" cores arranged as 240 x 2-way dual
core nodes, 1.92 TB of RAM and QLogic InfiniPath
interconnect [195 in TOP500 in 2008].
3. Task Farm: A dedicated cluster-of-workstation
solution for small-scale scientific computing.
www.warwick.ac.uk/go/CSC
30/03/2009
HPC@Warwick
../go/csc/facilities
Further Resources
• Two more HPC clusters for national
consortia and an e-Science grid site
• We operate a managed LINUX scientific
desktop system for 300+ users from all CSC
participating departments.
• Other technologies include an Access Grid
Node, EPrints server, Linux development
hardware, Bugzilla, HPC software, etc.
www.warwick.ac.uk/go/CSC
30/03/2009
Intermission ...
www.warwick.ac.uk/go/CSC
30/03/2009
CSC and MARC
• Strong partners in the region
• A vision for high-end computing
• A sustainable model for
academia/industry interactions
MARC
www.warwick.ac.uk/go/CSC
30/03/2009
Midlands Alliance for Research Computing (MARC)
2009
2009--2014
Institutional IT Needs for
Science City Collaborative
Research
Project Update
Monday 26th Jan 2009
RA Roemer, J Staunton, J Tuck UW
S Decent, J Rowe, G Theodoropoulos, P Reddy UB
Science Cities @ Birmingham/Warwick
 an exciting new large-scale initiative with £80M investment:
 encouraging increase in internationally leading research in the West
Midlands
 driving a vibrant knowledge-led economy
 deliver new models of partnership with the industrial base
 funding joint equipment and research by the Regional Development
Agency, Advantage West Midlands (AWM) for 3 themes:
Medicine
Materials
Energy
MARC in a nutshell
Unlocking the academic IT potential
for industry in the Midlands
MARC’s partners
Clinical Trials Unit
VIN (Birmingham University)
Staffordshire University
Birmingham City University
The Midlands Energy Consortium
MidSim
The Science City fit
Energy
Medicine
Materials
• Business Engagement and
Delivery
– Various services (modelling,
optimization etc)
– Access to expertise via
referrals (Science City
Programmes, regional
brokerage services e.g
Business Link)
– Various engagement / delivery
mechanisms (collaborative
projects, seminars, events etc)
Materials
– Project Manager (1)
– Support Officers (2)
– Research Technologists (4)
Medicine
• Project Management and
Delivery
Energy
People and more
Project Demand within Science City
Collaborative Project
• state-of-the-art today:
– plane semiconductor device modelling heat flow in power
semiconductor cooling system
– 2D mechanical stress and fracture processes in power
semiconductor packaging
• AWM Science City tomorrow:
–
3D semiconductor device
modelling
–
3D calculation of mechanical
stress and fracture processes in
power semiconductor
packaging
–
Optimisation of coupled multiphysics problems in the energy
efficiency and renewables
EX1
Project Demand within Science
City Collaborative Project
EX2
Materials Modelling in Disordered
Systems
1997: 125.000 atoms in a
disordered system
2002: 1.000.000 atoms
2006: 43.000.000 atoms
[single-proc CSC system]
2010: >1.000.000.000 atoms (?)
[AWM HPC system]
industry spin-off: now part of MKL for
IBM systems
Who does it…
data mining,
optimization,
simulation
modelling,
highperformance
computing, ..
modelling, highperformance computing
data mining,
optimization
,…
national training centre
in HPC
AWM Science City
Summary MARC
• indispensable IT infrastructure for the
3 AWM themes
• a step-change
 for research computing in the Midlands (with
MARC as the focus)
 for research computing and industry
engagement at Warwick and Birmingham
• unlocking future industrial income
in line with university strategy
Supercomputer
• memory-rich
massively-parallel
cluster with taskfarm
component
Storage Farm
Research Collaboration
• working as a team
– between researchers
– between campuses
• working in the region
– access to AWM SC
facilities
• working in the world
– midlands as IT
research hub
• Access Grid
Nodes
• CVS/Subversion
document
control/exchange
tools
• Web services
• demonstrators