Title: Vicky Rowley
1The 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
2Infrastructure 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
3Biomedical 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 -
4Biomedical 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
5BIRN 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
6BIRN 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
7The BIRN Collaborative Today
Enabling collaborative research at 28 research
institutions comprised of 40 research groups.
8Typical 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
9Major System Components
10Desired 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
11Software 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
12Benefits 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
13Software Development Integration
14Software 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
15BIRN Cyber Environment
16Software 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
17Operations and Monitoring
18Support of Research Community
- Technical Support
- Publications
- Training and Documentation
- Facilitation of Collaboratory Meetings
19NDAR
20www.nbirn.net