national alliance for medical image computing grid computing with batchmake julien jomier kitware...
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National Alliance for Medical Image Computing http://na-mic.org
Grid Computing with BatchMake
Julien JomierKitware Inc.
National Alliance for Medical Image Computing http://na-mic.org
Motivation
Algorithm Design & Implementation
Data Processing
Reports & Analysis
National Alliance for Medical Image Computing http://na-mic.org
Outline
• Introduction to BatchMake
• Grid Computing with BatchMake
• Reporting with the BatchBoards
• BatchMake with Slicer
National Alliance for Medical Image Computing http://na-mic.org
Introduction to BatchMake
• Batch script generator• Open-Source BSD license • Common Language (CMake-like)• Generation for:
- Shell script - Condor - KWGrid
• Run locally or on grid• Cross platform command line and GUI tool• C++ with ITK and FTLK
National Alliance for Medical Image Computing http://na-mic.org
BatchMake Workflow
CommandLine Executable
ApplicationWrapper
BatchMake
Script
Local Execution
Condor Script
KWGrid Script
Shell Script
National Alliance for Medical Image Computing http://na-mic.org
Application Wrapper
• Describe command line arguments- Manually (GUI)- Automatically using itkMetaCommand
• Internal XML format
• .bmm files (BatchMake Modules)
• Compatible with Slicer execution modules
National Alliance for Medical Image Computing http://na-mic.org
MetaCommand
• C++ class for command line parsing
• Output recognized by- BatchMake (-vxml)- Slicer (--xml)
• command.SetOption("compileScript","c",false,"Compile a script");
command.AddOptionField("compileScript","filename", MetaCommand::STRING,true);
• http://www.itk.org/Wiki/MetaIO
• Insight/Utilities/MetaIO
National Alliance for Medical Image Computing http://na-mic.org
Example Script
1 - SetApp(imSeg @ImageSegmentation)2 - SetAppOption(imSeg.threshold 10)3 - 4 - Set(workdir '/BatchMake/Demo/Ellipse_Images')5 - ListFileInDir(files ${workdir} '*.mha')6 -7 - Foreach(file ${files})8 - Set(filename '${workdir}/${file}')9 - Set(outfile '${workdir}/out_${file}')10- SetAppOption(imSeg.inputFilename ${filename})11- SetAppOption(imSeg.outputFilename ${outfile})12- Run(output ${imSeg})13- EndForeach(file)
National Alliance for Medical Image Computing http://na-mic.org
Condor
• Specialized workload management system for compute-intensive jobs
• Created by UW-Madison• Free for use• Provides job queuing mechanism,
scheduling policy, priority scheme, resource monitoring, and resource management.
• Unix and Windows
National Alliance for Medical Image Computing http://na-mic.org
Condor Example Script
Universe = vanillaExecutable = EMSegmenterArguments = ‘brain.mha segmentation.mha --brain’Output = emsegmentation.out Error = emsegmentation.error Log = emsegmentation.logRequirements = (OpSys =="LINUX" && Arch=="INTEL")Should_transfer_files = YES When_to_transfer_output = ON_EXIT_OR_EVICTTransfer_input_files = brain.mhaQueue
National Alliance for Medical Image Computing http://na-mic.org
Condor Workflow (Vanilla)
Submit Machine
Central Manager
Execute Machines
Condor Pool
Submit job
Issue job
Idle Workstation
Busy Workstation
Available Execute Machine
Push out job to machine
Central Manager
Central ManagerUnavailable Execute Machine
Dispatch to Central manager
= Available
Dispatch to Central manager
= Unavailable
National Alliance for Medical Image Computing http://na-mic.org
BatchMake Condor Generation
National Alliance for Medical Image Computing http://na-mic.org
BatchMake Condor Generation
• Application/Module description - Inputs/Outputs - Data to transfer to nodes
• Loop unrolling
• Scope definition
• Directed Acyclic Graph (DAG)
• Ensure order of execution of jobs
National Alliance for Medical Image Computing http://na-mic.org
Monitoring Condor Jobs
• Flock Monitor (Condor)• Condor Watcher (FLTK)• Condor Web Watcher (Ajax/PHP)
National Alliance for Medical Image Computing http://na-mic.org
Reporting with BatchMake
CVS/SVN
CVS/SVN
Results posted on web(i.e., the batchboard)
CTest/DART compilessource code
Developers review results
Developers check-in
code
MIDASXNat
MIDASXNat
BatchMake validateson datasets
+
National Alliance for Medical Image Computing http://na-mic.org
Reporting with BatchMake
National Alliance for Medical Image Computing http://na-mic.org
BatchMake Server
• PHP Scripts with MySQL database
• Simple C++ HTTP post
• Statistical Analysis (Factor analysis: Taguchi).
• Dashboard creation capability
• User management
National Alliance for Medical Image Computing http://na-mic.org
BatchBoard Script
DashboardHost(http://www.insight-journal.org/batchmake)
DashboardUser(‘Julien Jomier')
DashboardKey('FKH3BPM1y11VXsMf')
CreateExperiment(exp ‘Liver Project‘ ‘Segmentation Experiment' '')
CreateMethod(Meth exp 'Registration' 'Register a T1 with noise to a translated T1')
AddMethodInput(noiseImageName Meth 'Fixed Image')
Set(fixedSlice '${fixedImage}Slice.png')
ExtractSlice('${fixedImage}' '${fixedSlice}' 2 1)
AddMethodInput(fixedSlice Meth 'Fixed Slice with noise' png)
DashboardSend(Meth)
National Alliance for Medical Image Computing http://na-mic.org
BatchMake and Slicer
• BatchMake distributed with Slicer• Some modules can be run on a
collection of data- EMSegment- GaussianBlur
• Generic way to run moduleson a collection
• Support for XNat
National Alliance for Medical Image Computing http://na-mic.org
GridWizard
• Open-Source• Written in Java• BIRN and Na-Mic • Support for Sun Grid Engine and
Condor• Shell-like scripts
National Alliance for Medical Image Computing http://na-mic.org
GridWizard Example
bin/gwiz-run prog -t 1:3
prog -t 1 prog -t 2prog -t 3
bin/gwiz-run prog -i sftp://host.com/opt/mri/subjects/*.img
prog -i sftp://host.com/opt/mri/subjects/s1.img prog -i sftp://host.com/opt/mri/subjects/s2.img
prog -i sftp://host.com/opt/mri/subjects/s3.img
National Alliance for Medical Image Computing http://na-mic.org
References
• www.batchmake.org
• www.insight-journal.org/batchmake
• http://forums.gridsphere.org/index.shtml
National Alliance for Medical Image Computing http://na-mic.org
Condor Job Submission Workflow
Collector
Submit Machine
Scheduler
Starter
Negociator
Central Manager Execute Machine
MasterClassAd
MasterMatch
ClassAd
Job
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