Vicky Rowley

1
The Biomedical Informatics Research Network
Creation and Management of Grid Systems for
Biomedical ResearchUK E-Science AHM - September
10, 2008

• Vicky Rowley
• Solution Architect
• BIRN Coordinating Center - University of
  California San Diego

2
Infrastructure for a Biomedical Grid

• What is the BIRN project?
• Current project status
• Infrastructure description
• Hardware
• Software deployment
• Software development and integration
• Operations
• Monitoring
• Community Support

3
Biomedical Informatics Research Network

• A shared biomedical IT infrastructure to hasten
  the derivation of new understanding and treatment
  of disease through use of distributed knowledge
• Collaboration between groups with different
  expertise and resources (technical, scientific,
  social and political)
• Technical infrastructure to support collaboration
  and data sharing
• Open access and dissemination of data and tools
  (i.e. Open Source)
• Designed to be extensible to other biomedical
  communities

4
Biomedical Informatics Research Network

• All the components required to effectively share
  and collaboratively analyze and explore data
• The BIRN Portal
• The BIRN Data Grid
• The BIRN Rack (BIRN site infrastructure)
• The BIRN Data Integration Infrastructure
• The BIRN Computational GRID
• The system integration, development, deployment
  and management of this infrastructure is the main
  focus of activities within the BIRN Coordinating
  Center

5
BIRN Community Test Beds

• Functional Imaging Research of Schizophrenia
  (fBIRN)
• Researching cause of schizophrenia
• Constructing a large, multi-site, publicly
  available data repository
• Morphometry BIRN (mBIRN)
• Researching neuroanatomy correlates of disease
• Primarily depression, Alzheimers disease and
  mild cognitive impairment
• Mouse BIRN
• Studying animal models of disease
• Range of anatomical scales

6
BIRN Interactions

• Users include
• Researchers
• Software developers
• Managers
• Site administrators
• Coordinating center admins
• Researchers are very important, but their needs
  are primarily met by the software developers that
  work for/with them

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The BIRN Collaborative Today
Enabling collaborative research at 28 research
institutions comprised of 40 research groups.
8
Typical BIRN Hardware

• At each site
• Gpop - General Point-of-Presence
• Gcomp - Processing Node
• NAS - Data Storage
• UPS - Uninterruptable Power Supply
• Switches (network, VPN, KVM)
• At BIRN-CC
• Central Services (Auth, DB, Web, etc.)
• HPC/cluster resources

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Major System Components
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Desired System Qualities

• Agile
• Fast response with updates
• Self-help for developers
• Repeatable
• Tracking of versions
• Tracking of deployments
• Modular/Flexible
• Handles unique site requirements
• Handles unique project requirements
• Customizable
• Scalable
• Highly automated
• Supports addition of several sites per year, plus
  additional projects over 5 years

• Basic System Software
• Operating System
• Security

BIRN/Rocks Software Stack

• Server Definition Software
• Apache/Tomcat
• Globus

• Application Software
• Gridsphere
• HID
• Mediator
• Scientific Applications

Custom BIRN Server
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Software Deployment - Rocks Clusters

• Rocks facilitates construction and management of
  large clusters
• Invest heavily in a frontend then kickstart other
  nodes
• Manage cluster information in a MySQL database on
  the frontend
• Support/Utilize Virtualization
• Use a graph/nodes approach to system modularity
• Automate everything!
• scalability
• repeatability
• robustness

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Benefits of Rocks

• Highly automated installation of all servers
• Installation of remote servers with relatively
  little impact on remote site admins
• Ability to remotely (re)-install frontend via
  WAN/Central server
• Ability to remotely (re)-install any node other
  than gpop via gpop

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Software Development Integration
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Software Development Integration
SRB Oracle Postgres Mysql Condor
Rocks Server (yum updates)
3D Slicer AFNI AIR Brains2 BrainSuite Caret Freesu
rfer FSL LDDMM LONI mipav
CVS SRB
Testbeds
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BIRN Cyber Environment
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Software Deployment

• Staging Area
• Verify interoperation of latest code
• Support demonstration of latest development
  efforts without disruption to production
• Functional system/Beta Testing

• Development Area
• Integrate software for many diverse sources
• Version control at system and sub-component
  levels
• Rolling baseline
• Integration and Functional Testing

• Production Area
• Stable
• - Reliable
• Facilitates research

Rocks Development Server
Rocks Staging Server
Rocks Production Server
CVS
SRB
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Operations and Monitoring
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Support of Research Community

• Technical Support
• Publications

• Training and Documentation
• Facilitation of Collaboratory Meetings

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NDAR
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www.nbirn.net