ucsd / birn coordinating center namic group
DESCRIPTION
UCSD / BIRN Coordinating Center NAMIC Group. Site PI: Mark H. Ellisman Site Project Lead: Jeffrey S. Grethe. Faculty Mark Ellisman Jeffrey Grethe Grid Application Development Integration of Slicer3 Execution model with Grid infrastructure Marco Ruiz Algorithm Development - PowerPoint PPT PresentationTRANSCRIPT
NA-MICNational Alliance for Medical Image Computing http://na-mic.org
UCSD / BIRN Coordinating CenterNAMIC Group
Site PI: Mark H. Ellisman
Site Project Lead: Jeffrey S. Grethe
National Alliance for Medical Image Computing http://na-mic.org
Who are we – people • Faculty
– Mark Ellisman– Jeffrey Grethe
• Grid Application Development* Integration of Slicer3
Execution model with Grid infrastructure
– Marco Ruiz
• Algorithm Development* N-Channel Automated
Colocalization Analysis
• Portal Development* Integration of Slicer / NA-MIC
Toolkit components w/ User Portal
– Ramil Manansala
• Application Integration* Integration of NA-MIC Toolkit
with BIRN environment– Vicky Rowley
• Systems Support* Support for NA-MIC
components of BIRN grid– Bao Nguyen
National Alliance for Medical Image Computing http://na-mic.org
What do we contribute - Collaboration
• Provide collaborative portal environment
• Enable researchers to store and interact with large collections of federated data within a distributed data grid
National Alliance for Medical Image Computing http://na-mic.org
What do we contribute - Algorithm Development
• N-Channel Automated Colocalization Analysis– Quantitative tools to assess the co-distributions of molecular markers
within individual cells and immuloabeled tissue slices.
– Colocalization and spatial distribution analysis module within Slicer3
National Alliance for Medical Image Computing http://na-mic.org
Slice view
Surface view
File readers to deal with variety of image file formats generated at NCMIR
Developing Slicer interface for existing tools used by NCMIR researchers (eg. IMOD, TxBR, etc)
Create a single, user-friendly application to unify image processing, visualization, analysis and annotation
Incorporating Microscopy Processing and Analysis Into 3-D Slicer
National Alliance for Medical Image Computing http://na-mic.org
Grid Execution Module
What do we contribute - Grid Computation
• Provide researchers with customizable access to a computing environment that takes advantage of Grid-based infrastructures
– Heterogeneous collection of arge scale compute resources are available to NA-MIC researchers and users of the NA-MIC kit (e.g. BIRN, TeraGrid, local clusters)
• Provide interface module (Grid Wizard Interface) for the NA-MIC kit to enable distributed execution of algorithms from Slicer and modules such as BatchMake
QuickTime™ and a decompressor
are needed to see this picture.
National Alliance for Medical Image Computing http://na-mic.org
• A researcher’s high performance computing resource is usually a collection of resources (i.e. clusters)
• To use this collection of resources, the “Client” is responsible to provide the logic to integrate the the disparate clusters within the logic of their specific applications
• Most of the times this effort is non-trivial, non-reusable, non-extensible, lacks robustness and is far from giving the end user all the desired functionality
GRID
...
Cluster Operating System
Network
HeadNode
ComputeNodes
FileSystem
Resource Manager
Cluster Operating System
Network
HeadNode
ComputeNodes
FileSystem
Resource Manager
Cluster Operating System
Network
HeadNode
ComputeNodes
FileSystem
Resource Manager
Grid AND/OR Cluster Client
A Researcher’s “Grid”
National Alliance for Medical Image Computing http://na-mic.org
• Tight integration with cluster internals and transparent access to them.
• Granular level of execution control: submission, pause, resume, abort.
• Real time monitoring and alerting capabilities.
• Granular reporting of historic, diagnostics and statistics data.
• Transparent environment translation for requests.
• Programmatic control with rich and simple API.
Cluster Operating System
Network
Head Node Compute Nodes File System
Resource Manager
“Grid Wizard Enterprise” Cluster Components
... ...
“Grid Wizard Enterprise” enabled Cluster
National Alliance for Medical Image Computing http://na-mic.org
Tool Integration - Generic: Slicer3
National Alliance for Medical Image Computing http://na-mic.org
Immediate Goals
Curre
nt
April 20
08
June
200
8
Pre-release. Alpha version of complete infrastructure including automatic deployment
Production Release - Stable version with drivers for most popular cluster components (including full transparent SRB support), full monitoring, alert capabilities and API bundles.
Febr
uary
200
8
Grid Interface prototype
On-Going:BatchMake Integration
Pre-release (Beta version) - Full Slicer 3 Integration