2010 Summer Project Week Breakout Session:GWE

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Session Leader: Marco Ruiz

Objective

Introduce researchers to open source systems created to aid them, with the tasks of building and executing parameter exploration experiments and reviewing the results of such experiments. These solutions are tailored to run equally in a local environment (personal computer or local/remote supercomputer) or in a cluster environment (Condor, SGE, PBS. LSP, Torque, etc).

GWE: Queueing a parameter exploration experiment (order)
RSE: Exploring the results of a GWE parameter exploration experiment


Agenda

  • GWE System (Grid Wizard Enterprise)
    • Installation and configuration.
    • Creating and running a parameter exploration experiment.
    • Reviewing results.
    • Project information and other resources.
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Home/
export GWE_HOME=/demos/gwe/gwe-0.7.3.alpha
export PATH=$GWE_HOME/bin:$PATH
gwe-web.sh 
  • RSE System (Record Set Explorer)
    • Installation and configuration.
    • Creating a record set.
    • Exploring a record set.
    • View management.
    • Project information and other resources.
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Home/
export RSE_HOME=/demos/gwe/rse-0.6.2.alpha
export PATH=$RSE_HOME/bin:$PATH
rse.sh 
  • Q&A / Discussion


Case Studies (parameter exploration experiments expressed as P2EL statements)

  • Slice all volumes found under a directory all of the axis, multiple planes
${SLICER_HOME}=/demos/gwe/Slicer3
${volumes_files_dir}=/demos/gwe/data
${volumes_name_regexp}=.*[.](nrrd|nhdr)
${volumes_filenames}=$dir(${volumes_files_dir},${volumes_name_regexp})
${axis}=$const(0,1,2)
${plane}=$range(40,140,4)
${slicingCmd}=$sliceGen(${SLICER_HOME},${volumes_filenames},${axis},${plane})

${slicingCmd}
  • Gradient anisotropic diffusion on a volume and take 3 representative slices of each run
${SLICER_HOME}=/demos/gwe/Slicer3
${conductance}=$range(0,3,1)
${timeStep}=$const(0,0.07,0.5)
${iterations}=$const(1,5)
${output}=$const(/demos/gradient-out/out-${SYSTEM_JOB_NUM}.nrrd)
${gradient}=$slicer(${SLICER_HOME},GradientAnisotropicDiffusion)

${SLICING_X_CMD}=$sliceGen(${SLICER_HOME},${output},0,100)
${SLICING_Y_CMD}=$sliceGen(${SLICER_HOME},${output},1,100)
${SLICING_Z_CMD}=$sliceGen(${SLICER_HOME},${output},2,100)

${gradient} --conductance ${conductance} --timeStep ${timeStep} --iterations ${iterations} /demos/gwe/data/brain.nrrd ${output} 
&&
${SLICING_X_CMD} && ${SLICING_Y_CMD} && ${SLICING_Z_CMD}


References