na-mic national alliance for medical image computing ucsd: engineering core 2 portal and grid...

NA-MICNational Alliance for Medical Image Computing http://na-mic.org

UCSD: Engineering Core 2

Portal and Grid Infrastructure

National Alliance for Medical Image Computing http://na-mic.org

NAMIC Grid Infrastructure

• Leverage BIRN infrastructure development and deployment– Security Architecture– Data Grid – Computational Grid Resources– Portal

– Grid Deployment


Overview of the BIRN Roadmap

• Deliver and maintain a robust and scalable PRODUCTION Grid for the collaborative sharing, analysis and interrogation of biomedical data

• Provide integrated solutions for core domain science research

• Provide a consistent and scalable delivery mechanism• Be a vehicle for bringing biomedical sciences and scientists to

the Grid • Be the biomedical applications driver for the global Grid

community“Enforce the AEIOU’s – Accessibility, Extensibility, Interoperability, Openness,

Usability, Scalability”


Current Grid Infrastructure


BIRN Core Software Infrastructure

GASS GRAMGSI SRBGridFTPNWSMDS/GRIS

File/DataJob ManagementAuthentication Information

Grid Middleware Services

BIRN Portal

Data SourcesApplicationsComputation

Remote Servers / Sites

Custom APIs mediator client

GridPort Services

registry planner

PortletsGrid Services

Web Server / Applications Server

Collaboration Data ManagementViewing/VisualizationPipelines Queries/Results

BIRN Toolkit

mediatorgateway

executor

Statistics/Analysis Spatial Ontology

PACS

Distributed Resources

• BIRN builds on evolving community standards for middleware

• Adds new capabilities required by projects

•Does System Integration of domain-specific tools building a distributed infrastructure

• Utilizes commodity hardware and stable networks for baseline connectivity


Security Infrastructure• Security based on Grid standards (i.e. GSI - Grid

Security Infrastructure)– Each user is assigned their own private credentials by

the BIRN Certificate Authority

• Users don’t see complexity of infrastructure - single sign-on via a secure username and password– Certificate Authority– Escrow of user credentials– Management of proxy credentials

• Authentication service available to any application or service


Single Sign-On via Authentication Service

• Authentication service available to all applications

• Multiple implementations available– e.g. Java, PERL

AuthenticationService

Certificate

Authority

Proxy Management

DelegateProxy

Fetch NewProxy

ValidateProxy

1

2

3

4


Authentication for Applications

• Single sign-on authentication can be accomplished from non-Grid tools

• Initiates Portal session to handle common services

AuthenticationService

AuthenticateUser

Issue Proxy

Certificate

Authority

Proxy Management 1

2

3


BIRN Data Grid• Defines a Distributed Data

Handling System

• Integrates Storage Resources in the BIRN network

• Provides a Uniform Interface to Users

• Users interact with data in a logical file space (i.e. location of files is hidden from the user)


Sharing data using BIRN

Data Access Control & Auditing

Metadata Search

Data Management

The BIRN Portal and Data Grid provides secure and audited access to NAMIC data from Core 3 sites with a Single Login from any Internet capable location.

The BIRN Portal and Data Grid provides secure and audited access to NAMIC data from Core 3 sites with a Single Login from any Internet capable location.


Data Grid Access

• A coordinated suite of tools and interfaces to are available that interact with the BIRN Data Grid– Programmatic interfaces - e.g. JARGON Java API– Command Line access – Graphical User Interface

• Java Data Grid Browser (local client)• Web Data Grid Browser (remote server)

– Contributed tools - e.g. SRBwrap from JHU

• Allows users to tailor access to the data grid based on their requirements


Grid Computing Infrastructure

• Provide an open resource for grid computing– Production computational grid – Research and development grid

• Provisioning middleware and services for large scale grid computation– Authentication– Scheduling– resource discovery– Resource management

Needed for Grid Workflows


Grid Based Workflows Authentication, resource discovery

and scheduling! Currently there are many standards

for the description of workflows.• Grid workflow environment must be

open and able to interact with multiple workflow tools and languages.

• Collaborating with grid community (e.g. Telescience, GEON, UK e-Science)– Definition of grid-based workflow

description languages

– Development of grid based workflow execution environment


Portal Job Management

•Portal based user interfaces•Job management functions provide detailed job information for execution on remote resource


BIRN Portal

•Application environment that provides transparent and pervasive access to the BIRN infrastructure (i.e. tools, applications, resources) with a Single Login from any Internet capable location

•Provides simple, intuitive access to distributed resources for data storage, distributed computation, and visualization

•Support for dynamic collaborative projects such as NAMIC

•Built on standard Portal framework


BIRN Portal Framework

• Future -> GridSphere portal framework– Based on a portlet model: gives developers an

open way of creating and adding new elements to the portal

– JSR-168 compatible: Java portlet standard that enables interoperability between Portlets and Portals

– Open Source– Community development across many Grid

based projectsDistributed Portal development and deployment


• Allow continual improvement of the BIRN software infrastructure in terms of performance, robustness and interoperability,

• Support use of latest development efforts without disruption to development effort or production operation

• Separately instantiated development, staging and production environments provide robust, yet flexible areas for developing, testing, and deploying BIRN system software

• Twice yearly, in April and October, a complete production integrated BIRN software stack is released (and deployed on the BIRN physical hardware infrastructure)

Development Environment


Grid System Deployment• BIRN specific extensions to Rocks grid management

software, means automated, repeatable deployment of any version of the BIRN system

• We’ve created BIRN “rolls” that integrate – BIRN domain tools (e.g. 3DSlicer, LONI Pipeline, FreeSurfer)– Database (Oracle) and Data Grid Configuration

• Rocks, with BIRN extensions, includes automated deployment mechanism for– Middleware (Security, Computational, Data)– Data mediation/integration– Application codes– Portal

na-mic national alliance for medical image computing ucsd: engineering core 2 portal and grid...

Documents