Slicer3:Grid Integration

Project: Integration of NAMIC Kit and the 'Grid'

Goals:

• Supply Grid execution components to Slicer3 Execution Model
• Clearly define expectations and dependencies for grid execution

Current Status:

• Validation as primary use case for grid

1. Create JSON-aware Grid component to interface with NAMIC executables
2. parameter sweep through quality / contrast space using NonRigidRegistrationForEchoPlanarImaging

Current Tools

• condor_submission page can be found here

namic-submit [--save-submit-file <submitfile>] [--job-directory <jobdir>] <cmd> [<args>...]

where:

• submitfile is a condor job submit file; if not specified a temp file is generated
• jobdir is a working state directory for a set of submissions that you want to later observe with namic-wait or manually inspect
• cmd is a shell script or executable that can be run on the remote environment
• args are arguments to the cmd

functionality: namic-submit takes the given command and args and runs the job on a condor-determined external compute node. By default stdin, stdout, and stderr of the cmd are mapped to the corresponding files of namic-submit.

If srb proxy is not set up, namic-submit prompts you for srb user id and password and sets up proxy.

namic-wait [--job-directory <jobdir>] [<groupid>]

where:

• jobdir is a directory that corresponds to the state for jobs submitted by namic-submit

functionality: namic-wait blocks until all jobs submitted with the given groupid have completed running

Team Members:

• Jeff Grethe- UCSD
• Brendan Faherty - UCSD
• Steve Pieper - BWH
• Daniel Blezek - GE