 |
|
|
|
|
|
|
 |
 |
|
||||
 |
|
|||||
 |
 |
 |
|
|||
 |
Convert LONI Pipeline XML to Condor FilesMy experience dealing with the processing and analysis of brain imaging data has lead me to recommend that users "batch script" as much as possible. Furthermore, I would like to recommend that users develop and manipulate their pipelines using the LONI Pipeline Processing Environment and execute their processes on multiple computers using Condor (a distributed job scheduler).For more information on these recommendations, you may check out my power-point presentation on Reasons to Batch, and the poster I presented at the 2005 Human Brain Mapping Conference entitled Condor: Managing Computationally Intensive Jobs from a Computer Science Perspective. (WARNING: This file is ~7MB). Feel free to download my loni2condor python conversion script at your own risk. Keep in mind that I am the only person who has used it so far, and it is likely to be riddled with errors. I am more than happy to help work them out if you contact me. In order to make use of this script you must first have LONI Pipeline Processing Environment (http://www.loni.ucla.edu/Software/), Condor (http://www.cs.wisc.edu/condor/) and Python (http://www.python.org) functioning on your system. I must note that the latter two steps are quite "non-trivial", I apologize In order to make use of it you will need to follow the steps below.
Create and Save a LONI Pipeline. Step 2: Convert the saved XML LONI Pipeline to a set of Condor Files.
>> loni2condor.py --input=FILENAME --output==DIR_NAME
-h, --help
show this help message and exit
-iFILENAME, --loniXML=FILENAME, --xml=FILENAME, --in=FILENAME, --input=FILENAME
The input LONI Pipeline XML File
-oDIR_NAME, --out=DIR_NAME, --condorDir=DIR_NAME, --output=DIR_NAME, --outDir=DIR_NAME
The output directory where condor_files will be created.
Step 3:
Submit the Master Condor File. >> condor_submit_dag DIR_NAME/condorFiles/MASTER_CONDOR_SCRIPT.dag Please feel free to contact me if you have any questions or comments. |
|
||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
 |
|
|||||
Copyright © 2005 Andrew S. Fox, All rights reserved. -- Last Modified | ||||||