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Grid Computing with BatchMake

Grid Computing with BatchMake. Julien Jomier Kitware Inc. Motivation. Data Processing. Reports & Analysis. Algorithm Design & Implementation. Outline. Introduction to BatchMake Grid Computing with BatchMake Reporting with the BatchBoards BatchMake with Slicer Future plans.

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Grid Computing with BatchMake

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  1. Grid Computing with BatchMake Julien JomierKitware Inc.

  2. Motivation Data Processing Reports & Analysis Algorithm Design & Implementation

  3. Outline • Introduction to BatchMake • Grid Computing with BatchMake • Reporting with the BatchBoards • BatchMake with Slicer • Future plans

  4. BatchMake Origins • Started in 2004 at UNC (CADDLab) • A2D2 from NLM • Kitware funds: KWGrid • BW-NAC: Batchboards • Na-Mic • STTR Kitware-UNC (Styner)

  5. Introduction to BatchMake • Batch script generator • Process of large number of datasets • 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

  6. BatchMake Workflow CommandLine Executable Local Execution ApplicationWrapper Shell Script BatchMake KWGrid Script Script Condor Script

  7. Application Wrapper • Describe command line arguments- Manually (GUI)- Automatically using itkMetaCommand • Currently using internal XML format • .bmm files (BatchMake Modules) • Switching to Slicer’s ModuleDescriptionParser- importing Slicer Module automatically

  8. 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

  9. 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 ${files}) • - Set(filename '${workdir}/${file}') • - Set(outfile '${workdir}/out_${file}') 10-SetAppOption(imSeg.inputFilename ${filename}) 11-SetAppOption(imSeg.outputFilename ${outfile}) 12- Run(output ${imSeg}) 13-EndForeach(file)

  10. Condor • Specialized workload management system for compute-intensive jobs • Created by UW-Madison • 15 Years of development • Provides job queueing mechanism, scheduling policy, priority scheme, resource monitoring, and resource management. • Unix and Windows

  11. Condor Universes • Standard Universe (checkpoint) • Vanilla • Parallel Virtual Machine • MPI • Globus • Java (JVM) • Scheduler (no matching)

  12. Condor Example Script Universe = vanilla Executable = EMSegmenter Arguments = ‘brain.mha segmentation.mha --brain’ Output = emsegmentation.out Error = emsegmentation.error Log = emsegmentation.log Requirements = (OpSys =="LINUX" && Arch=="INTEL") Should_transfer_files = YES When_to_transfer_output = ON_EXIT_OR_EVICT Transfer_input_files = brain.mha Queue

  13. Condor Pool Condor Workflow (Vanilla) Central Manager Central Manager Unavailable Execute Machine Dispatch to Central manager = Unavailable Submit job Submit Machine Issue job Busy Workstation Available Execute Machine Central Manager Dispatch to Central manager = Available Execute Machines Idle Workstation Push out job to machine

  14. ClassAd Job ClassAd Match Condor Job Submission Workflow Submit Machine Central Manager Execute Machine 1 Collector Master 3 Master 2 4 Scheduler Negociator 5 Starter

  15. BatchMake Condor Generation

  16. 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

  17. Monitoring Condor Jobs • Flock Monitor (Condor) • Condor Watcher (FLTK) • Condor Web Watcher (Ajax/PHP)

  18. Condor Summary • Pros:- Well supported- (Fairly) easy installation- Complete resources management • Cons:- Script can be complicated- Jobs don’t start right away- Hard to debug

  19. Reporting with BatchMake Developers check-in code CVS/SVN CTest/DART compilessource code Developers review results + MIDASXNat BatchMake validateson datasets Results posted on web(i.e., the batchboard)

  20. Reporting with BatchMake

  21. BatchMake Server • PHP Scripts with MySQL database • Simple C++ HTTP post • Statistical Analysis (Factor analysis: Taguchi). • Dashboard creation capability • User management

  22. 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)

  23. BatchMake and Slicer • BatchMake now distributed with Slicer • Some modules can be run on a collection of data- EMSegment- GaussianBlur • Generic way to run moduleson a collection

  24. BatchMake and MIDAS • STTR Kitware/UNC Martin Styner

  25. Future • Improve packaging • Improve documentation • Improve integration with Slicer • BatchMake and Xnat (discussion)

  26. References • www.batchmake.org • www.insight-journal.org/batchmake

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