Data Grids and Data ManagementData Grids and Data Management

Storage Resource BrokerStorage Resource Broker

Reagan W. MooreReagan W. Moore

moore@sdsc.edu

http://www.sdsc.edu/srbhttp://www.sdsc.edu/srb

TopicsTopics

• Data management evolution• Shared collections• Digital Libraries• Persistent Archives

• Building shared collections• Project level / National level / International

• Demonstration of shared collections• Access to collections at SDSC

Shared CollectionsShared Collections

• Data grids support the creation of shared collections that may be distributed across multiple institutions, sites, and storage systems.

• Digital libraries publish data, and provide services for discovery and display

• Persistent archives preserve data, managing the migration to new technology

Storage Resource Broker Collections at SDSC(12/6/2005)

GBs ofdata

stored

Numberof files

Userswith

ACLsData Grid      

NSF/ITR - National Virtual Observatory 93,252 11,189,215 100NSF - National Partnership for Advanced Computational Infrastructure 34,319 7,235,387 380

Static collections – Hayden planetarium 8,013 161,352 227

Pzone – public collections 16,815 9,628,452 68

NSF/NPACI - Biology and Environmental collections 103,849 124,169 67

NSF/NPACI – Joint Center for Structural Genomics 15,731 1,577,260 55

NSF - TeraGrid, ENZO Cosmology simulations 187,684 2,415,397 3,267

NIH - Biomedical Informatics Research Network 12,812 9,078,456 337

Digital Library      

NSF/NPACI - Long Term Ecological Reserve 236 34,594 36

NSF/NPACI - Grid Portal 2,620 53,048 460

NIH - Alliance for Cell Signaling microarray data 733 94,686 21

NSF - National Science Digital Library SIO Explorer collection 2,452 1,068,842 27

NSF/ITR - Southern California Earthquake Center 134,779 2,958,799 73

Persistent Archive      

NHPRC Persistent Archive Testbed (Kentucky, Ohio, Michigan, Minnesota) 96 387,825 28

UCSD Libraries archive 4,147 408,050 29

NARA- Research Prototype Persistent Archive 2,029 1,393,722 58

NSF - National Science Digital Library persistent archive 4,651 45,724,945 136

TOTAL 624 TB 93 million 5,369

Generic InfrastructureGeneric Infrastructure

• Can a single system provide all of the features needed to implement each type of data management system, while supporting access across administrative domains and managing data stored in multiple types of storage systems?

• Answer is data grid technology

Shared CollectionsShared Collections

• Purpose of SRB data grid is to enable the creation of a collection that is shared between academic institutions• Register digital entity into the shared collection• Assign owner, access controls• Assign descriptive, provenance metadata• Manage state information

• Audit trails, versions, replicas, backups, locks• Size, checksum, validation date, synchronization date, …

• Manage interactions with storage systems• Unix file systems, Windows file systems, tape archives, …

• Manage interactions with preferred access mechanisms• Web browser, Java, WSDL, C library, …

SRBserver

SRB agent

SRBserver

Federated Server ArchitectureFederated Server Architecture

MCAT

Read Application

SRB agent

1

2

34

6

5

Logical NameOr

Attribute Condition

1.Logical-to-Physical mapping2.Identification of Replicas3.Access & Audit Control

Peer-to-peer

Brokering

Server(s) SpawningData

Access

Parallel Data Access

R1R2

5/6

Generic InfrastructureGeneric Infrastructure

• Digital libraries now build upon data grids to manage distributed collections• DSpace digital library - MIT and Hewlitt Packard• Fedora digitial library - Cornell University and University

of Virginia

• Persistent archives build upon data grids to manage technology evolution• NARA research prototype persistent archive• California Digital Library - Digital Preservation Repository• NSF National Science Digital Library persistent archive

National Science Digital LibraryNational Science Digital Library

• URLs for educational material for all grade levels registered into repository at Cornell

• SDSC crawls the URLs, registers the web pages into a SRB data grid, builds a persistent archive• 750,000 URLs• 13 million web pages• About 3 TBs of data

Southern California Earthquake CenterSouthern California Earthquake Center

SCEC Community

Library

Select Receiver (Lat/Lon)

OutputTime HistorySeismograms

Select ScenarioFault Model

Source Model

•Intuitive User Interface–Pull-Down Query Menus –Graphical Selection of Source Model–Clickable LA Basin Map (Olsen)–Seismogram/History extraction (Olsen)

•Access SCEC Digital Library

–Data stored in a data grid–Annotated by modelers–Standard naming convention–Automated extraction of selected data and metadata–Management of visualizations

SCEC Digital LibrarySCEC Digital Library

Terashake Data HandlingTerashake Data Handling

• Simulate 7.7 magnitude earthquake on San Andreas fault• 50 Terabytes in a simulation• Move 10 Terabytes per day

• Post-Processing of wave field• Movies of seismic wave propagation• Seismogram formatting for interactive on-

line analysis• Velocity magnitude• Displacement vector field• Cumulative peak maps• Statistics used in visualizations• Register derived data products into

SCEC digital library

HumidityClimateEcologicalWirelessOceanography

Wind SpeedClimateEcologicalWirelessOceanography

SeismicGeophysics

ROADNet Sensor Network Data Integration

Fire startRain start

Frank Vernon - UCSD/SIOFrank Vernon - UCSD/SIO

NARA Persistent ArchiveNARA Persistent Archive

NARA U Md SDSC

MCAT MCAT MCAT

Original data at NARA, data replicated to U Md & SDSC

Replicated copyat U Md for improvedaccess, load balancingand disaster recovery

Active archive atSDSC, user access

Demonstrate preservation environment • Authenticity• Integrity• Management of technology evolution• Mitigation of risk of data loss

• Replication of data• Federation of catalogs

• Management of preservation metadata• Scalability

• Types of data collections• Size of data collections

Federation of Three Independent Data Grids

Worldwide University Network Data GridWorldwide University Network Data Grid

• SDSC• Manchester• Southampton• White Rose• NCSA• U. Bergen

• A functioning, general purpose international Data Grid for academic collaborations

Manchester-SDSC mirror

WUNGrid CollectionsWUNGrid Collections

• BioSimGrid• Molecular structure collaborations

• White Rose Grid • Distributed Aircraft Maintenance Environment

• Medieval Studies• Music Grid• e-Print collections

• DSpace

• Astronomy

BioSimGridBioSimGrid

• Kaihsu Tai, Stuart Murdock, Bing Wu, Muan Hong Ng, Steven Johnston, Hans Fangohr, Simon J. Cox, Paul Jeffreys, Jonathan W. Essex, Mark S. P. Sansom (2004) BioSimGrid: towards a worldwide repository for biomolecular simulations. Org. Biomol. Chem. 2:3219–3221 DOI: 10.1039/b411352g

• University of Oxford• Mark Sansom, Biochemistry• Paul Jeffreys, e-Science• Kaihsu Tai, Biochemistry• Bing Wu, Biochemistry / e-Science

• University of Southampton• Jonathan Essex, Chemistry• Simon Cox, e-Science• Stuart Murdock, Chemistry / e-Science• Muan Hong Ng, e-Science• Hans Fangohr, e-Science• Steven Johnston, e-Science

•Elsewhere•David Moss, Birkbeck, London•Adrian Mulholland, Bristol•Charles Laughton, Nottingham•Leo Caves, York

KEK Data GridKEK Data Grid

• Japan• Taiwan• South Korea• Australia• Poland• US

• A functioning, general purpose international Data Grid for high-energy physics

Manchester-SDSC mirror

BaBar High-energy PhysicsBaBar High-energy Physics

• Stanford Linear Accelerator

• Lyon, France• Rome, Italy• San Diego• RAL, UK

• A functioning international Data Grid for high-energy physics

Manchester-SDSC mirror

Moved over 100 TBs of dataMoved over 100 TBs of data

Astronomy Data GridAstronomy Data Grid

• Chile• Tucson, Arizona• NCSA, Illinois

• A functioning international Data Grid for Astronomy Manchester-SDSC mirror

Moved over 400,000 imagesMoved over 400,000 images

International Institutions (2005)International Institutions (2005)

Project InstitutionData mangement project British Antarctic Survey, UKeMinerals Cambridge e-Science Center, UKSickkids Hospital in Toronto CanadaWelsh e-Science Centre Cardiff University, UKAustralian Partnership for Advanced Computing Data Grid Victoria, AustraliaTrinity College High Performance Computing (HPC-Europa) Trinity College, IrelandNational Environment Research Council United KingdomCenter for Advanced Studies, Research, and Development ItalyLIACS(Leiden Inst. Of Comp. Sci) Leiden University,The NetherlandsPhysics Labs University of Bristol, UKMonash E-Research Grid Monash University, AustraliaComputational Modelling University of Queensland, AustraliaSchool Computing University of Leeds, UKDept. of Computer Science University of Liverpool, UKBelfast e-Science Centre Queen's University, UKWorldwide Universities Network University of Manchester, UKLarge Hadron Collider Computing Grid University of Oxford, UKWhite Rose Grid University of Sheffield. UKProtein structure prediction Taiwan University, Taiwan

Unix Shell

NT Browser,Kepler Actors

http,Portlet,WSDL,

OAI-PMH)

DSpace,OpenDAP,GridFTP,Fedora

Archives - Tape,Sam-QFS, DMF,

HPSS, ADSM,UniTree, ADS

Databases -DB2, Oracle,

Sybase, Postgres, mySQL, Informix

File SystemsUnix, NT,Mac OSX

Application

ORB

Storage Repository AbstractionDatabase Abstraction

Databases -DB2, Oracle, Sybase,

Postgres, mySQL,Informix

CLibrary,

Java

Logical Name Space

LatencyManagement

DataTransport

MetadataTransport

Consistency & Metadata Management / Authorization, Authentication, Audit

Linux I/OC++

DLL /Python,

Perl, Windows

Federation Management

Storage Resource Broker 3.3.1Storage Resource Broker 3.3.1

SRB ObjectivesSRB Objectives

• Automate all aspects of data discovery, access, management, analysis, preservation• Security paramount• Distributed data

• Provide distributed data support for• Data sharing - data grids• Data publication - digital libraries• Data preservation - persistent archives• Data collections - Real time sensor data

SRB DevelopersSRB DevelopersReagan Moore Reagan Moore - PI- PIMichael Wan Michael Wan - SRB Architect- SRB ArchitectArcot Rajasekar Arcot Rajasekar - SRB Manager- SRB ManagerWayne Schroeder Wayne Schroeder - SRB Productization- SRB ProductizationCharlie CowartCharlie Cowart - inQ- inQLucas Gilbert Lucas Gilbert - Jargon- JargonBing Zhu Bing Zhu - Perl, Python, Windows- Perl, Python, WindowsAntoine de Torcy Antoine de Torcy - mySRB web browser- mySRB web browserSheau-Yen Chen Sheau-Yen Chen - SRB Administration- SRB AdministrationGeorge KremenekGeorge Kremenek - SRB Collections- SRB CollectionsArun Jagatheesan Arun Jagatheesan - Matrix workflow- Matrix workflowMarcio Faerman Marcio Faerman - SCEC Application- SCEC ApplicationSifang Lu Sifang Lu - ROADnet Application- ROADnet ApplicationRichard Marciano Richard Marciano - SALT persistent archives- SALT persistent archives

Contributors from UK e-Science, Academia Sinica, Ohio State University, Aerospace Corporation, …

75 FTE-years of support75 FTE-years of supportAbout 300,000 lines of CAbout 300,000 lines of C

HistoryHistory• 1995 - DARPA Massive Data Analysis Systems• 1997 - DARPA/USPTO Distributed Object Computation Testbed• 1998 - NSF National Partnership for Advanced Computational Infrastructure

• 1998 - DOE Accelerated Strategic Computing Initiative data grid• 1999 - NARA persistent archive• 2000 - NASA Information Power Grid• 2001 - NLM Digital Embryo digital library• 2001 - DOE Particle Physics data grid• 2001 - NSF Grid Physics Network data grid• 2001 - NSF National Virtual Observatory data grid• 2002 - NSF National Science Digital Library persistent archive• 2003 - NSF Southern California Earthquake Center digital library• 2003 - NIH Biomedical Informatics Research Network data grid• 2003 - NSF Real-time Observatories, Applications, and Data management Network

• 2004 - NSF ITR, Constraint based data systems• 2005 - LC Digital Preservation Lifecycle Management• 2005 - LC National Digital Information Infrastructure and Preservation program

DevelopmentDevelopment

• SRB 1.1.8 - December 15, 2000• Basic distributed data management system• Metadata Catalog

• SRB 2.0 - February 18, 2003• Parallel I/O support• Bulk operations

• SRB 3.0 - August 30, 2003• Federation of data grids

• SRB 3.4 - October 31, 2005• Feature requests (extensible schema)

Separation of Access Method Separation of Access Method from Storage Protocolsfrom Storage Protocols

Storage SystemStorage System

Storage ProtocolStorage Protocol

Access MethodAccess Method

Access OperationsAccess Operations

Data GridData Grid

Map from the Map from the

operations used byoperations used by

the access methodthe access method

to a standard set ofto a standard set of

operations used to operations used to

interact with theinteract with the

storage systemstorage system

Storage OperationsStorage Operations

Data Grid OperationsData Grid Operations• File access

• Open, close, read, write, seek, stat, synch, …• Audit, versions, pinning, checksums, synchronize, …• Parallel I/O and firewall interactions• Versions, backups, replicas

• Latency management• Bulk operations

• Register, load, unload, delete, …

• Remote procedures• HDFv5, data filtering, file parsing, replicate, aggregate

• Metadata management• SQL generation, schema extension, XML import and export,

browsing, queries, • GGF, “Operations for Access, Management, and Transport at Remote

Sites”

Examples of ExtensibilityExamples of Extensibility• Storage Repository Driver evolution

• Initially supported Unix file system• Added archival access - UniTree, HPSS• Added FTP/HTTP• Added database blob access• Added database table interface• Added Windows file system• Added project archives - Dcache, Castor, ADS• Added Object Ring Buffer, Datascope• Added GridFTP version 3.3

• Database management evolution• Postgres• DB2• Oracle• Informix• Sybase• mySQL (most difficult port - no locks, no views, limited SQL)

Examples of ExtensibilityExamples of Extensibility• The 3 fundamental APIs are C library, shell commands,

Java• Other access mechanisms are ported on top of these interfaces

• API evolution• Initial access through C library, Unix shell command• Added iNQ Windows browser (C++ library)• Added mySRB Web browser (C library and shell commands)• Added Java (Jargon)• Added Perl/Python load libraries (shell command)• Added WSDL (Java)• Added OAI-PMH, OpenDAP, DSpace digital library (Java)• Added Kepler actors for dataflow access (Java)• Added GridFTP version 3.3 (C library)• Added Fedora

Logical Name SpacesLogical Name Spaces

Storage Repository

• Storage location

• User name

• File name

• File context (creation date,…)

• Access constraints

Data Access Methods (C library, Unix, Web Browser)

Data access directly between

application and storage

repository using names

required by the local

repository

Logical Name SpacesLogical Name Spaces

Storage Repository

• Storage location

• User name

• File name

• File context (creation date,…)

• Access constraints

Data Grid

• Logical resource name space

• Logical user name space

• Logical file name space

• Logical context (metadata)

• Control/consistency constraints

Data Collection

Data Access Methods (C library, Unix, Web Browser)

Data is organized as a shared collection

Federation Between Data GridsFederation Between Data Grids

Data Grid

• Logical resource name space

• Logical user name space

• Logical file name space

• Logical context (metadata)

• Control/consistency constraints

Data Collection B

Data Access Methods (Web Browser, DSpace, OAI-PMH)

Data Grid

• Logical resource name space

• Logical user name space

• Logical file name space

• Logical context (metadata)

• Control/consistency constraints

Data Collection A

Access controls and consistency constraints on cross registration of digital entities

Types of Risk Types of Risk

• Media failure• Replicate data onto multiple media

• Vendor specific systemic errors• Replicate data onto multiple vendor products

• Operational error• Replicate data onto a second administrative domain

• Natural disaster• Replicate data to a geographically remote site

• Malicious user• Replicate data to a deep archive

How Many ReplicasHow Many Replicas

• Three sites minimize risk• Primary site

• Supports interactive user access to data

• Secondary site• Supports interactive user access when first site is

down• Provides 2nd media copy, located at a remote site,

uses different vendor product, independent administrative procedures

• Deep archive• Provides 3rd media copy, staging environment for

data ingestion, no user access

Deep ArchiveDeep Archive

Z2Z2 Z1Z1Z3Z3

Z2:D2:U2Z2:D2:U2

RegisterRegister

Z3:D3:U3Z3:D3:U3

RegisterRegister

PullPull PullPull

FirewallFirewall

Server initiated I/OServer initiated I/O

DeepDeep

ArchiveArchive

StagingStaging

ZoneZone

Remote ZoneRemote Zone

No access byNo access by

Remote zonesRemote zones

PVNPVN

For More InformationFor More Information

Reagan W. Moore

San Diego Supercomputer Center

moore@sdsc.edu

http://www.sdsc.edu/srb/