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Grid computing: An introduction Lionel Brunie National Institute of Applied Science (INSA) LIRIS Laboratory/DRIM Team – UMR CNRS 5205 Lyon, France http://liris.cnrs.fr/lionel.brunie

A Brain is a Lot of Data! (Mark Ellisman, UCSD)

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Grid computing: An introduction Lionel Brunie National Institute of Applied Science (INSA) LIRIS Laboratory/DRIM Team – UMR CNRS 5205 Lyon, France http://liris.cnrs.fr/lionel.brunie. A Brain is a Lot of Data! (Mark Ellisman, UCSD). And comparisons must be made among many. - PowerPoint PPT Presentation

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Page 1: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid computing: An introduction

Lionel Brunie

National Institute of Applied Science (INSA)LIRIS Laboratory/DRIM Team – UMR CNRS 5205

Lyon, France

http://liris.cnrs.fr/lionel.brunie

Page 2: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

And comparisons must bemade among many

We need to get to one micron to know location of every cell. We’re just now starting to get to 10 microns

A Brain is a Lot of Data!

(Mark Ellisman, UCSD)

Page 3: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Data Intensive Physical Sciences

• High energy & nuclear physics• Simulation

– Earth observation, climate modeling– Geophysics, earthquake modeling– Fluids, aerodynamic design– Pollutant dispersal scenarios

• Astronomy- Digital sky surveys: modern telescopes produce over 10 Petabytes per year by 2008 !

• Molecular genomics• Chemistry and biochemistry• Financial applications• Medical images

Page 4: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Performance evolution of computer components

• Network vs. computer performance– Computer speed doubles every 18 months– Network speed doubles every 9 months– Disk capacity doubles every 12 months

• 1986 to 2000– Computers: x 500– Networks: x 340,000

• 2001 to 2010– Computers: x 60– Networks: x 4000

Moore’s Law vs. storage improvements vs. optical improvements. Graph from Scientific American (Jan-2001) by Cleo Vilett, source Vined Khoslan, Kleiner, Caufield and Perkins.

Page 5: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Conclusion: invest innetworks !

Page 6: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Hansel and Gretel are lost in the forest of definitions

• Distributed system• Parallel system• Cluster computing• Meta-computing• Grid computing• Peer to peer computing• Global computing• Internet computing• Network computing• Cloud computing

Page 7: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Distributed system

• N autonomous computers (sites): n administrators, n data/control flows

• an interconnection network

• User view: one single (virtual) system– «A distributed system is a collection of independent computers that

appear to the users of the system as a single computer » Distributed Operating Systems, A. Tanenbaum, Prentice Hall, 1994

• « Traditional » programmer view: client-server

Page 8: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Parallel System

• 1 computer, n nodes: one administrator, one scheduler, one power source

• memory: it depends

• Programmer view: one single machine executing parallel codes. Various programming models (message passing, distributed shared memory, data parallelism…)

Page 9: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Examples of parallel system

CPU CPU

Memory

network

CPU

CPU CPU CPU

Memory

network

CPU

CPU CPU CPU

Memory

network

CPU

CPU

Interconnection network

Periph.

A CC-NUMA architecture

CPU

CPU

CPUMemory

network

Memory

Memory

A shared nothing architecture

Page 10: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Cluster computing

• Use of PCs interconnected by a (high performance) network as a parallel (cheap) machine

• Two main approaches– dedicated network (based on a high performance

network: Myrinet, SCI, Infiniband, Fiber Channel...)– non-dedicated network (based on a (good) LAN)

Page 11: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Where are we today ?

• A source for efficient and up-to-date information: www.top500.org

• The 500 best architectures

• N° 1: 1,8 (2,3) Pflops ! N° 500: 20 Tflops • Sum (1-500) = 20 Pflops

• 1 Flops = 1 floating point operation per second• 1 TeraFlops = 1000 GigaFlops – 1 Pflops = 1000

TeraFlops

Page 12: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

How it grows ?

• in 1993 (prehistoric times!)– n°1: 59.7 GFlops– n°500: 0.4 Gflops– Sum = 1.17 TFlops

• in 2004 (yesterday)– n°1: 70 TFlops (x1118)– n°500: 850 Gflops (x2125)– Sum = 11274 Tflops and

408629 processors

Page 13: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

2007/11 best: http://www.top500.org/http://www.top500.org/

Peak: 596 Tflops !!!

http://www.top500.org/

Page 14: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

2008/11 best: http://www.top500.org/http://www.top500.org/

Peak: 1457 Tflops !!!

http://www.top500.org/

Page 15: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

2009/11 best: http://www.top500.org/http://www.top500.org/

Peak: 2331 Tflops !!!

http://www.top500.org/

Page 16: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Performance evolution

Page 17: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Projected performance

Page 18: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Architecture distribution

Page 19: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Interconnection network distribution

Page 20: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

NEC earth simulator (1st en 2004 ; 30th in 2007)

Single stage crossbar: 2700 km of cables

700 TB disk space1.6 PB mass storageArea: 4 tennis courts, 3 floors

A MIMD withDistributed Memory

Page 21: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

NEC Earth Simulator

Page 22: A Brain is a Lot of Data! (Mark Ellisman, UCSD)
Page 23: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

BlueGene

• 212992 processors – 3D torus

• Rmax = 478 Tflops ; Rpeak = 596 Tflops

Page 24: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

RoadRunner• 3456 nodes (18 clusters) - 2 stage fat tree Infiniband (optical)• 1 node= 2 AMD Opteron DualCore + 4 IBM PowerXCell 8i• Rmax = 1.1Pflops ; Rpeak = 1.5Pflops• 3,9 MW (0,35 Gflops/W)

Page 25: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Jaguar• 224162 cores – Memory: 300 TB – Disk: 10 PB

• AMD x86_64 Opteron Six Core 2600 MHz (10.4 GFlops) • Rmax = 1759 – Rpeak = 2331• Power: 6,950 MW• http://www.nccs.gov/jaguar/

Page 26: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Network computing

• From LAN (cluster) computing to WAN computing

• Set of machines distributed over a MAN/WAN that are used to execute parallel loosely coupled codes

• Depending on the infrastructure (soft and hard), network computing is derived in Internet computing, P2P, Grid computing, etc.

Page 27: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Meta computing (beginning 90’s)

• Definitions become fuzzy...• A meta computer = set of (widely) distributed (high

performance) processing resources that can be associated for processing a parallel not so loosely coupled code

• A meta computer = parallel

virtual machine over a

distributed system Cluster of PCs

SAN

SAN

Cluster of PCs

LAN

WAN

SupercomputerVisualization

Page 28: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Internet computing

• Use of (idle) computer interconnected by Internet for processing large throughput applications

• Ex: SETI@HOME – 5M+ users since launching– 2009/11: 930k users, 2.4M computers; 190k

active users, 278k active computers, 2M years of CPU time

– 234 « countries »– 1021 floating point operations since 1999– 769 Tflops! – BOINC infrastructure (Décrypthon, RSA-

155…)

• Programmer view: a single master, n servants

Page 29: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Global computing

• Internet computing on a pool of sites

• Meta computing with loosely coupled codes

• Grid computing with poor communication facilities

• Ex: Condor (invented in the 80’s)

Page 30: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Peer to peer computing

• A site is both client and server: servent

• Dynamic servent discovery by « contamination »

• 2 approaches: – centralized management: Napster, Kazaa, eDonkey…– distributed management: Gnutella, KAD, Freenet,

Bittorrent…

• Application: file sharing

Page 31: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid computing (1)

“Coordinated resource sharing and problem solving in dynamic, multi-institutional virtual organisations” (I. Foster)

Page 32: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid computing (2)

• Information grid– large access to distributed data (the Web)

• Data grid– management and processing of very large

distributed data sets

• Computing grid– meta computer

Page 33: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Parallelism vs grids: some recalls

• Grids date back “only” 1996 • Parallelism is older ! (first classification in 1972)

• Motivations:– need more computing power (weather forecast, atomic

simulation, genomics…)– need more storage capacity (Petabytes and more)– in a word: improve performance ! 3 ways ...

Work harder --> Use faster hardware

Work smarter --> Optimize algorithms

Get help --> Use more computers !

Page 34: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

The performance ? Ideally it grows linearly

• Speed-up:

– if TS is the best time to process a problem sequentially,

– then the parallel processing time should be TP=TS/P with P processors

– speedup = TS/TP

– the speedup is limited by Amdhal law: any parallel program has a purely

sequential and a parallelizable part TS= F + T//,

– thus the speedup is limited: S = (F + T//) / (F + (T///P)) < P

• Scale-up:

– if TPS is the time to solve a problem of size S with P processors,

– then TPS should also be the time to process a problem of size n*S with n*P

processors

Page 35: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid computing

Page 36: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Starting point

• Real need for very high performance infrastructures

• Basic idea: share computing resources– “The sharing that the GRID is concerned with is not primarily

file exchange but rather direct access to computers, software, data, and other resources, as is required by a range of collaborative problem-solving and resource-brokering strategies emerging in industry, science, and engineering” (I. Foster)

Page 37: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Applications

• Distributed supercomputing

• High throughput computing

• On demand (real time) computing

• Data intensive computing

• Collaborative computing

Page 38: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An Example Virtual Organization: CERN’s Large Hadron Collider

Worldwide LHC Computing Grid (WLCG)8000 Physicists, 170 Sites, 34 Countries

15 PB of data per year; 100,000 CPUs

Page 39: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Why Grid Computing (CERN opinion) ?

• The answer is "money"... In 1999, the "LHC Computing Grid" was merely a concept on the drawing board for a computing system to store, process and analyse data produced from the Large Hadron Collider at CERN. However when work began on the design of the computing system for LHC data analysis, it rapidly became clear that the required computing power was far beyond the funding capacity available at CERN.

• On the other hand, most of the laboratories and universities collaborating on the LHC had access to national or regional computing facilities.

• The obvious question was: Could these facilities be somehow integrated to provide a single LHC computing service? The rapid evolution of wide area networking—increasing capacity and bandwidth coupled with falling costs—made it look possible. From there, the path to the LHC Computing Grid was set.

Page 40: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Why Grid Computing (CERN opinion) ?Additional benefits

• Multiple copies of data can be kept in different sites, ensuring access for all scientists involved, independent of geographical location.

• Allows optimum use of spare capacity for multiple computer centres, making it more efficient.

• Having computer centres in multiple time zones eases round-the-clock monitoring and the availability of expert support.

• No single points of failure.

• The cost of maintenance and upgrades is distributed, since individual institutes fund local computing resources and retain responsibility for these, while still contributing to the global goal.

• Independently managed resources have encouraged novel approaches to computing and analysis.

• So-called “brain drain”, where researchers are forced to leave their country to access resources, is reduced when resources are available from their desktop.

• The system can be easily reconfigured to face new challenges, making it able to dynamically evolve throughout the life of the LHC, growing in capacity to meet the rising demands as more data is collected each year.

• Provides considerable flexibility in deciding how and where to provide future computing resources.

• Allows community to take advantage of new technologies that may appear and that offer improved usability, cost effectiveness or energy efficiency.

Page 41: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

LCG System Architecture• A 4 layers Computing Model

– Tier-0: CERN: accelerator• Data Acquisition and Reconstruction • Data Distribution to Tier-1 (~online)

– Tier-1• 24x7 Access and Availability, • Quasi-online data Acquisition • Data Service on the Grid• “Heavy” Analysis of the data• ~10 countries

– Tier-2• Simulation• Final User, Analysis of the data (batch and

interactive modes)• ~40 Countries

– Tier-3• Final User, Scientific analysis

Tier-0(1)

Tier-1(11)

Tier-2(160)

« Tier-3 » End User

LHCLHC40 millions collisions per second40 millions collisions per second

~100 interesting collisions per second after filtering~100 interesting collisions per second after filtering1-10 MB of data per collision1-10 MB of data per collisionAcquisition rate: 0.1 to 1 GB/secAcquisition rate: 0.1 to 1 GB/sec

1010 collisions recorded every year 1010 collisions recorded every year ~10 PBytes/year~10 PBytes/year

Page 42: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

LCG System Architecture (Cont’d)T

ier-

1

Tier-0

10 Gbps linksOptical Private Network

(to almost all sites)

Trigger and Data

Acquisition System

Tie

r-2

General Purpose/Academic/Research Network

From F. Malek – LCG France

Page 43: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Back to roots (routes)

• Railways, telephone, electricity, roads, bank system

• Complexity, standards, distribution, integration (large/small)

• Impact on the society: how US grown

• Important differences: – clients (the citizens) are NOT providers (states or companies)– small number of actors/providers– small number of applications– strong supervision/control

Page 44: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Computational grid

• “Hardware and software infrastructure that provides dependable, consistent, pervasive and inexpensive access to high-end computational capabilities” (I. Foster)

• Performance criteria:– security– reliability– computing power– latency– throughput– scalability– services

Page 45: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid characteristics

• Large scale• Heterogeneity• Multiple administration domain• Autonomy… and coordination• Dynamicity• Flexibility• Extensibility• Security

Page 46: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Levels of cooperation in a computing grid

• End system (computer, disk, sensor…)– multithreading, local I/O

• Cluster– synchronous communications, DSM, parallel I/O

– parallel processing

• Intranet/Organization– heterogeneity, distributed admin, distributed FS and databases

– load balancing

– access control

• Internet/Grid– global supervision

– brokers, negotiation, cooperation…

Page 47: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Basic services

• Authentication/Authorization/Traceability

• Activity control (monitoring)

• Resource discovery

• Resource brokering

• Scheduling

• Job submission, data access/migration and execution

• Accounting

Page 48: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Layered Grid Architecture(By Analogy to Internet Architecture)

Application

Fabric“Controlling things locally”: Access to, & control of, resources

Connectivity“Talking to things”: communication (Internet protocols) & security

Resource“Sharing single resources”: negotiating access, controlling use

Collective“Coordinating multiple resources”: ubiquitous infrastructure services, app-specific distributed services

InternetTransport

Application

Link

Inte

rnet P

roto

col

Arch

itectu

re

From I. Foster

Page 49: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Resources

• Description

• Advertising

• Cataloging

• Matching

• Claiming

• Reserving

• Checkpointing

Page 50: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Resource management (1)

• Services and protocols depend on the infrastructure

• Some parameters– stability of the infrastructure (same set of resources or not)– freshness of the resource availability information– reservation facilities– multiple resource or single resource brokering

• Example of request: I need from 10 to 100 CE each with at least 512 MB RAM and a computing power of 150 Mflops

Page 51: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Resource management and scheduling (1)

• Levels of scheduling– job scheduling (global level ; perf: throughput)– resource scheduling (perf: fairness, utilization)– application scheduling (perf: response time, speedup, produced data…)

• Mapping/Scheduling process– resource discovery and selection– assignment of tasks to computing resources– data distribution– task scheduling on the computing resources– (communication scheduling)

Page 52: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Resource management and scheduling (2)

• Individual perfs are not necessarily consistent with the global (system) perf !

• Grid problems– predictions are not definitive: dynamicity !– Heterogeneous platforms– Checkpointing and migration

Page 53: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

GRAM GRAM GRAM

LSF Condor NQE

Application

RSL

Simple ground RSL

Information Service

Localresourcemanagers

RSLspecialization

Broker

Ground RSL

Co-allocator

Queries& Info

A Resource Management System Example (Globus)

NQE: Network Queuing Env.(batch management; developedby Cray Research

LSF: Load Sharing Facility(task scheduling and load balancing; Developed by Platform Computing)

Resource Specification Language

Page 54: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Resource information (1)

• What is to be stored ?– virtual organizations, people, computing resources, software packages,

communication resources, event producers, devices…– what about data ???

• A key issue in such dynamics environments

• A first approach : (distributed) directory (LDAP)– easy to use– tree structure– distribution– static– mostly read ; not efficient updating– hierarchical– poor procedural language

Page 55: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Resource information (2)

• Goal:– dynamicity– complex relationships– frequent updates– complex queries

• A second approach: (relational) database

Page 56: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Programming on the grid: potential programming models

• Message passing (PVM, MPI)• Distributed Shared Memory• Data Parallelism (HPF, HPC++)• Task Parallelism (Condor)• Client/server - RPC• Agents• Integration system (Corba, DCOM, RMI)

Page 57: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Program execution: issues

• Parallelize the program with the right job structure, communication patterns/procedures, algorithms

• Discover the available resources

• Select the suitable resources

• Allocate or reserve these resources

• Migrate the data

• Initiate computations

• Monitor the executions ; checkpoints ?

• React to changes

• Collect results

Page 58: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Data management

• It was long forgotten !!!• Though it is a key issue !• Issues:

– indexing– retrieval– replication– caching– traceability– (auditing)

• And security !!!

Page 59: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Bruni, pas BruniE !!!

Page 60: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

From computing grids to information grids

Page 61: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

From computing grids to information grids (1)

• Grids lack most of the tools mandatory to share (index, search, access), analyze, secure, monitor semantic data (information)

• Several reasons:– history– money– difficulty

• Why is it so difficult ?– Sensitivity but openness– Multiple administrative domains, multiple actors, heterogeneousness but a

single global architecture/view/system– Dynamicity and unpredictability but robustness– Wideness but high performance

Page 62: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

From computing grids to information grids (2) ex: Replica Management Problem

• Maintain a mapping between logical names for files and collections and one or more physical locations

• Decide where and when a piece of data must be replicated

• Important for many applications

• Example: CERN high-level trigger data– Multiple Petabytes of data per year– Copy of everything at CERN (Tier 0)– Subsets at national centers (Tier 1)– Smaller regional centers (Tier 2)– Individual researchers have copies of pieces of data

• Much more complex with sensitive and complex data like medical data !!!

Page 63: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

From computing grids to information grids (3):some (still…) open issues

• Security, security, security (incl. privacy, monitoring, traceability…)) at a semantic level

• Access protocols (incl. replication, caching, migration…)• Indexing tools• Brokering of data (incl. accounting) • (Content-based) Query optimization and execution• Mediation of data• Data integration, data warehousing and analysis tools• Knowledge discovery and data mining

Page 64: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Functional View of Grid Data Management

Location based ondata attributes

Location of one ormore physical replicas

State of grid resources, performance measurements and predictions

Metadata Service

Application

Replica LocationService

Information Services

Planner:Data location, Replica selection,Selection of compute and storage nodes

Security and Policy

Executor:Initiates data transfers and computations

Data Movement

Data Access

Compute Resources Storage Resources

A bit simplistic…

Page 65: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid Security (1): Why Grid Security is Hard

• Used resources may be extremely valuable & the problems to be solved extremely sensitive

• Resources are located in distinct administrative domains– Each resource has its own policies & procedures

• Users are diverse

• The set of resources used by a single computation may be large, dynamic, and/or unpredictable

– Not just client/server

• The security service must be broadly available & applicable– Standard, well-tested, well-understood protocols– Integration with wide variety of tools

Page 66: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Grid security (2): Requirements

• Authentication• Authorization and Delegation of authority• Assurance• Accounting • Auditing and Monitoring• Traceability• Integrity and Confidentiality (ACID properties)

Page 67: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Access to data and Mediation

• Ciel, where are the data ?• Use case: Italian tourist – heart accident in Lyon• Data inside the grid # data at the side of the grid !• Basic idea

– use of metadata/indexes. Pb: indexes are (sensitive) information

• Alternative – encrypted indexes, use of views, proxies

• Mediation– no single view of the world mechanisms for interoperability,

ontologies

• Negotiation: a key open issue

Page 68: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

CachingCaching

• Motivation:– Collaborative caching is proved to be efficient– Each institution wants to control the access to its data– No standard exists in Grids for caching

• Proposal:– on demand caching– a two-level cache: local caches and a global virtual cache– use metadata to collaborate / index data

Page 69: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Query optimization and execution

• Old wine in new bottles ?• Yes and no: it seems the problem has not changed but the

operational context has so changed that classical heuristics and methods are not more pertinent

• Key issues: – Dynamicity

– Unpredictability

– Adaptability

• Very few works have specifically addressed this problem

Page 70: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An application example:GGM

Grille Geno-Médicale

Page 71: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An application example: GGM Biomedical grids

• Biomedical applications are perfect candidates for gridification:– Huge volumes of data (an hospital = several TB per year)– Dissemination of data – Collaborative work (health networks)– Very hard requirements (e.g. response time)

• But– Partially structured semantic data– Very strong privacy issues

→ a perfect play field for researchers !

Page 72: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An application example: GGM Motivation (1)

• Dissemination of new “high bandwidth” technologies in genome and proteome research (e.g. micro-arrays)– huge volume of structural (gene localization)– functional (gene expression) data

• Generalization of digital patient files and digital medical images

• Implementation of (regional and inter-national) health networks

• All information is available, people are connected to the network.

• The question is: How can we use it ?

Page 73: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

• Need for an information infrastructure to– index, exchange/share, process all this data– while preserving their privacy at a very large scale

• That is... just a good grid!

• Application objectives:– correlation of genomic and medical data: fundamental research and

later medical decision making process– patient-centered medical data integration: patient’s monitoring in

and out-side the hospital– epidemiology– training

An application example: GGM Motivation (2)

Page 74: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

• References: “Synergy between medical informatics and bioinformatics: facilitating genomic medicines for future healthcare”, – BIOINFOMED Working Group, Jan. 2003, European Commission

• Proceedings of Healthgrid conferences (1st edition in Lyon(2003))

An application example: GGM Motivation (3)

Page 75: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An application example: GGM Scope

“The goal of the GGM project is, on top of a grid infrastructure, to propose a software architecture able to manage heterogeneous and dynamic data stored in distributed warehouses for intensive analysis and processing purposes.”

• Distributed Data Warehouses• Query Optimization• Data Access [and Control]• Data Mining

Page 76: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An application example: GGM Data

• A piece of medical data (age, image, biological result, salient object in an image) has a meaning– It conveys information that can be interpreted (in multiple ways !)

• Meta-data can be attached to medical data… or not– pre-processing is necessary

• Medical data are often private– privacy/delegation

• The medical data of a patient are often disseminated over multiple sites– access rights/authentication problem, collection/integration of data into

partial views, identification of data/users

• Medical (meta-)data are complex and not yet (fully) standardized– no global structure

Page 77: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

An application example: GGM Architecture

GO Medical recordsExperiments

wrappers

DA+CacheNDS

OQS

DW DM

Grid Middleware

DW-GUI DW-GUI

GGM Middleware

Page 78: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Virtual Data Warehouses on the Grid

Page 79: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Virtual Data Warehouses on the Grid (1)

• Almost nothing…

• Why is it so difficult ?– multiple administrative domains– very sensitive data => security/privacy issues– wide distribution– unpredictability– relationship with data replica– heterogeneity– dynamicity (permanent production of large volumes of data)

• Centralized data warehouse ? – Not realistic at a large scale and not acceptable

Page 80: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Virtual Data Warehouses on the Grid (2)

• A possible direction of research: virtual data warehouses on the grid

• Components:– a federated schema– a set of partial views (“chunks”) materialized at the local system level

• Advantages– Flexibility wrt users’ needs– Good use of the storage capacity of the grid and scalability– Security control at the local level– Global view of the disseminated data

Page 81: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Virtual Data Warehouses on the Grid (3)

• Drawbacks and open issues– maintenance protocols– indexing tools– access to data and negotiation– query processing

Page 82: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Access to data and collaborative brokers

Page 83: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Access to data and collaborative brokers (1)

• Brokers act as interfaces between data, services and applications

• Possible locations– at the interface between the grid and the external data repositories– on the grid storage elements– at the interface between the grid and the user– inside the network (e.g. routers)

• Open issues– caching: computation results, query partial results…– data indexing– prefetching– user’s customization– inter brokers collaboration– a key issue: security and privacy

Page 84: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Access to data and collaborative brokers (2): security and privacy

• Medical data belong to the patient that should be able to give access rights to who he wants

• To whom processed (even anonymous) data belong to ?

• How one can combine privacy and dissemination/

replication/caching ?

• What about traceability ?

• What about traceability ?

Page 85: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Datamining and knowledge extraction on the grid

Page 86: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Datamining and knowledge extraction on the grid

• Structure of the data: few records, many attributes

• Parallelizing data mining algorithms for the grid– volatility of the resources (data, processing)– fault tolerance, checkpointing– distribution of the data: local data exploration + aggregation

function to converge towards a unified model– incremental production of the data => active data mining

techniques

Page 87: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

A short overview of some grid middleware

Page 88: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

The Legion system

• University of Virginia• Object-oriented approach. Objects = data, applications,

sensors, computing resources, codes…: all is object !• Loosely coupled codes• Single naming space• Reuse of existing OS and protocols ; definition of message

formats and high level protocols• Core objects: naming, binding, object

creation/activation/desactivation/destruction• Methods: description via an IDL• Security: in the hands of the users• Resource allocation: a site can define its own policy

Page 89: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

High-Throughput Computing: Condor

• High-throughput computing platform for mapping many tasks to idle computers

• Since 1986 !

• Major components– A central manager manages pool(s) of [distributively owned or dedicated]

computers. A CM = scheduler + coordinator– DAGman manages user task pools– Matchmaker schedules tasks to computers using classified ads– Checkpointing and process migration– No simple communications

• Parameter studies, data analysis

• Condor married Globus: Condor-G

• Several hundreds of Condor pools in the world… or in your student room !

Page 90: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Defining a DAG

• A DAG is defined by a .dag file, listing each of its nodes and their dependencies:# diamond.dagJob A a.subJob B b.subJob C c.subJob D d.subParent A Child B CParent B C Child D

• Each node will run the Condor job specified by its accompanying Condor submit file

Job A

Job B Job C

Job D

From Condor tutorial

Page 91: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

The Globus toolkit

• A set of integrated executable management grid services

• Services– resource management (GRAM-DUROC)– communication (NEXUS - MPICH-G2, globus_io)– information (MDS)– data management (replica catalog)– security (GSI)– monitoring (HBM)– remote data access (GASS - GridFTP - RIO)– executable management (GEM)– execution– commodity Grid Kits (Java, Python, Corba, Matlab…)

Page 92: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Components in Globus Toolkit 3.0

GSI

WS-Security

Data Managemen

tSecurity

WSCore

Resource Managemen

t

Information Services

RFT(OGSI)

RLS

WU GridFTPJAVA

WS Core(OGSI)

OGSI C Bindings

MDS2

WS-Index(OGSI)

Pre-WSGRAM

WS GRAM(OGSI)

Page 93: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Components in Globus Toolkit 3.2

GSI

WS-Security

CAS(OGSI)

SimpleCA

Data Managemen

tSecurity

WSCore

Resource Managemen

t

Information Services

RFT(OGSI)

RLS

OGSI-DAI

WU GridFTP

XIO

JAVAWS Core(OGSI)

OGSI C Bindings

MDS2

WS-Index(OGSI)

Pre-WSGRAM

WS GRAM(OGSI)

OGSI Python Bindings

(contributed)

pyGlobus(contributed)

Page 94: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Components in Globus Toolkit 4

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Components in Globus Toolkit 5

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Conclusion (2005)

• Just a new toy for scientists or a revolution ?

• Huge investments

• Classical issues but a functional, operational and applicative context very complex

• Complexity from heterogeneity, wide distribution, security, dynamicity

• Functional shift from computing to information

• Data management in grids: not prehistory, but still middle-ages

• Still much work to do !!!

• A global framework for grid computing, pervasive computing and Web services ?

Page 97: A Brain is a Lot of Data! (Mark Ellisman, UCSD)

Conclusion (2008)Still valid in 2010 (just add a ref to Cloud computing))

• Just a new toy for scientists or a revolution ? Neither of them !

• Huge investments: too much ?!

• Classical issues but a functional, operational and applicative context very complex

• Complexity from heterogeneity, wide distribution, security, dynamicity

• Functional shift from computing to information

• Data management in grids: not middle-ages, but not 21st century => services

• Supercomputing is still alive

• A global framework for grid computing, pervasive computing and Web services… and SOA !

• Some convergence between P2P and grid computing

• The industrialization time