Slicer3:Grid Integration
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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
- Create JSON-aware Grid component to interface with NAMIC executables
- 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