Slicer3:Grid Integration

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Home < 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