Introduction to
Grid Computing with
High Performance Computing
Mike Griffiths
White Rose Grid
e-Science Centre of Excellence
Outline
• Introduction
• High Performance Grid Computing
• e-Science
• The Evolving Grid
• The Local Compute Node Iceberg
• Registration
Objectives
• What is grid computing?
• How the grid assists with problem solving lifecycle
• Identify and Explain Buzzwords
• Remove Hype
Problem solving lifecycle
• Problem definition and requirements capture
• Model development
– Languages (FORTRAN, C, C++, Java etc.)
– Model Building SDK’s
– Matlab and clones
– Packages (ANSYS, FLUENT, CFX)
Problem solving lifecycle
• Problem solving environment
– specialized software for solving one class of problems
– Application user interface, portal
• Model testing
– Validation, verification
• Results production
– Scheduling tasks over the grid
• Analysis and Visualisation
Grid Technologies
Grid Technologies
• Simulation of large complex systems
• Large scale multi site data mining,
distributed data sets
• Shared virtual reality
• Interactive collaboration
• Real-time access to remote resources.
What Is Grid Computing
• Virtualisation of resource
• Increase processing power
• Secure and flexible collaboration
• The Grid Problem
Electric Power Generation Analogy
Access to
Customer
Information
Grid
Information
Information Distributed
Generators
Over the Grid
[Link]
• A form of networking. Unlike conventional networks
that focus on communication among devices, grid
computing harnesses unused processing cycles of
all computers in a network for solving problems too
intensive for any stand-alone machine.
IBM Definition
• Grid computing enables the virtualization of
distributed computing and data resources such as
processing, network bandwidth and storage capacity
to create a single system image, granting users and
applications seamless access to vast IT capabilities.
Just as an Internet user views a unified instance of
content via the Web, a grid user essentially sees a
single, large virtual computer.
Sun Microsystems
• Grid Computing is a computing infrastructure that
provides dependable, consistent, pervasive and
inexpensive access to computational capabilities.
“The Grid Problem”
• “Grid problem,” flexible, secure, coordinated
resource sharing among dynamic collections of
individuals, institutions, and resources—what we
refer to as virtual organizations.
– From “The Anatomy of the Grid” by Foster, Kesselman and
Tuecke.
Virtual
Organisations
Grid Characteristics Computing - Tflops
The
Grid
Networks Data storage
– High Bandwidth Peta byte
Types of Grids
•Cluster Grid
•Beowulf clusters
•Enterprise Grid, Campus
Grid, Intra-Grid
•Departmental clusters,
servers and PC network
•Utility Grid
•Access resources over internet on demand
•Global Grid, Inter-grid
•White Rose Grid, National Grid Service,
Particle physics data grid
Three Uses of Grid Computing
• Compute grids
• Data grids
• Collaborative grids
Distributed Supercomputing
• Compute Clusters
– Schedulers sun grid engine, pbs
• Grid aggregates computational resources to compute large complex
problems
• Fast networks enabling true parallel computation and shared memory
processing
• Select compute resources according to Time and Financial constraints
Architectures for High Performance
Computing
• Supercluster
– e.g. Blue Gene (65536 dual processors in 64 cabinets)
• Clusters
– e.g. iceberg
– Parallel applications using MPI
• Symmetric multiprocessors
– e.g. 4 processor shared memory V40 node on iceberg
– Shared memory programming Open MP
• Vector Processor
– E.g Amdhal VP at MCC (80’s and 90’s)
High Throughput Applications
• Problems divided into many tasks
– Grid schedules tasks
• Seti@home
– The mother of @home projects
– Spin off for companies such as
Entropia and United Devices
• Other @home projects
– Folding@home, fightAIDS@home,
Xpulsar@home
• Condor
– Cycle scavenging from spare PC’s
Statistics for SETI at Home
(13/09/2004)
Total Last 24 Hours
Users 5115495 2715
Results received 1532818080 3248739
Total CPU time 2045520.287 years 2510.9 years
Floating Point 5.562175e +21 1.267008e+19
Operations (146.64 TeraFLOPs/sec)
Average CPU time 11 hr 41 min 24.2 sec 6 hr 46 min 10.6 sec
per work unit
SETI@home’s Most Promising Candidates
Grid Types
Data Grid
Engine flight data
• Computing
Network stores
large volume of London Airport
data across Airline New York Airport
network
• Heterogeneous
Grid
Diagnostics centre
data sources
Maintenance Centre
American data center
European data center
Grid Types - Collaborative
• Internet videoconferencing
• Collaborative Visualisation
e-Science
• More science relies on computational experiments
• More large, geographically disparate, collaborative
projects
• More need to share/lease resources
– Compute power, datasets, instruments, visualization
e-Science Centres
Centres of Excellence
Regional Centres
e-Science Organisations
• National e-Science Centre
– To stimulate and sustain the development of e-Science in
the UK, to contribute significantly to its international
development and to ensure that its techniques are rapidly
propagated to commerce and industry.
• Open Middleware Infrastructure Institute
– Repository for UK Grid Middleware
e-Science Requirements
• Simple and secure access to remote resources
across administrative domains
• Minimally disruptive to local administration policies
and users
• Large set of resources used by a single computation
• Adapt to non-static configuration of resources
The Evolving Grid
• Comprising of two data clusters and two compute clusters.
• Offer a significant resource for the UK e-Science community.
• Clusters are located at
– Manchester (data cluster),
– Oxford (compute cluster),
– CCLRC (data cluster) and
– White Rose Grid (compute cluster).
• More sites
– Lancaster
– Wesc
– Bristol
EGEE
• The EGEE project brings together experts from over 27
countries
– Build on recent advances in Grid technology.
– Developing a service Grid infrastructure in Europe,
• available to scientists 24 hours-a-day.
Available Grid Services
• Access Grid
• White Rose Grid
– Grid research
– HPC Service
• National Grid Service
– Compute Grid
– Data Grid (SRB)
• National HPC Services
– HPCx and CSAR (part of NGS)
• Portal Services
Sheffield Grid Node: Hardware
• AMD based supplied by Sun Microsystems
• Processors: 320
• Performance: 300GFLOPs
• Main Memory: 800GB
• Filestore: 9TB
• Temporary disk space: 10TB
• Physical size: 8 racks
• Power usage: 50KW
Sheffield Grid Node: Hardware,part 2
• 160 Processors Grid pp community
• 160 Processors General Use
– 20 x V40 each with 4x64 bit AMD Opteron (2.4GHz) and 16GB
shared main memory.
– 40 x V20 each with 2x64 bit AMD Opteron (2.4 GHz) and 4GB
shared main memory
• Comparing L2 Cash
– AMD Opteron 1MB
– Ultrac sparc III Cu (Titania) 8MB
Sheffield Grid Node: Hardware, part 3
Inside a V20
unit.
Sheffield Grid Node: Hardware 4
• Two main Interconnect types gigabit (commodity),
Myrinet (more specialist)
– Gigabit – Supported as standard good for job farms, and
small to mid size systems
– Myrinet – High End solution for large parallel applications
has become defacto standard for clusters (4Gb/s)
Sheffield Grid Node: Hardware
• 64bit v 32 bit
– Mainly useful for programs requiring large memory –
available on bigmem nodes
– Greater Floating Point accuracy
– Future-proof: 32-bit systems are becoming obselete in HPC
Sheffield Grid Node: Software 1
Ganglia
DDT
Portland, GNU
Sun Grid
Redhat 64bit Engine v6
Scientific
Linux
MPICH
Opteron
Sheffield Grid Node: Software 2
• Maths and Statistical
– Matlab7.0, scilab 3.1
– R+ 2.0.1
• Engineering and Finite Element
– Fluent 6.2.16, 6.1.25 and 6.1.22 als gambit, fidap and tgrid
– Ansys v90
– Abaqus
– CFX 5.7.1
– DYNA 91a
• Visualisation
– IDL 6.1
– OpenDX
Sheffield Grid Node: Software 3
• Development
– MPI, MPICH-gm
– OpenMP
– Nag, 20
– ACML
• Grid
– Globus 2.4.3 (via gpt 3.0)
– SRB s-client tools to follow
Registration
• Local User Account
• Obtain an e-Science Certificate
• Register with the White Rose Grid
• Apply for NGS Resource
Go to the link
[Link]
Why obtain an e-Science Certificate
• Enables secure single sign on to the White Rose
Grid
• Use portals e.g. the WRG Application portal
• Access WRG, NGS, egee
For More Information
• The White Rose Grid
– [Link]
• The National e-Science Centre
– [Link]
• The Globus Project™
– [Link]
• Global Grid Forum
– [Link]
Grid Computing References
• The Grid: Computing Without Bounds
– Ian Foster, Scientific American, April 2003.
• “The Anatomy of the Grid”
– [Link]
• Grid Services – “The Physiology of the Grid”
– [Link]
[Link]
• Research Agenda for the Semantic Grid
– [Link]
