Difference between revisions of "2010 Summer Project Week Breakout Session:GWE"
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==Agenda== | ==Agenda== | ||
− | + | * ''[http://www.gridwizardenterprise.org GWE System (Grid Wizard Enterprise)]'' | |
+ | ** Installation and configuration. | ||
+ | ** Creating and running a parameter exploration experiment. | ||
+ | ** Reviewing results. | ||
+ | ** Project information and other resources. | ||
− | + | <pre> | |
− | + | 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 | ||
+ | </pre> | ||
− | + | * ''[http://www.gridwizardenterprise.org/rse RSE System (Record Set Explorer)]'' | |
+ | ** Installation and configuration. | ||
+ | ** Creating a record set. | ||
+ | ** Exploring a record set. | ||
+ | ** View management. | ||
+ | ** Project information and other resources. | ||
+ | |||
+ | <pre> | ||
+ | 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 | ||
+ | </pre> | ||
+ | |||
+ | * 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'' | ||
+ | <pre> | ||
+ | ${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} | ||
+ | </pre> | ||
+ | |||
+ | * ''Gradient anisotropic diffusion on a volume and take 3 representative slices of each run'' | ||
+ | <pre> | ||
+ | ${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} && ${SLICING_Z_CMD} | ||
+ | </pre> | ||
− | |||
− | |||
− | |||
− | |||
− | |||
Latest revision as of 06:20, 24 June 2010
Home < 2010 Summer Project Week Breakout Session:GWEBack to Project Week Agenda
Session Leader: Marco Ruiz
Contents
Objective
Introduce researchers to open source systems created to aid them, with the tasks of building and executing parameter exploration experiments and reviewing the results of such experiments. These solutions are tailored to run equally in a local environment (personal computer or local/remote supercomputer) or in a cluster environment (Condor, SGE, PBS. LSP, Torque, etc).
Agenda
- GWE System (Grid Wizard Enterprise)
- Installation and configuration.
- Creating and running a parameter exploration experiment.
- Reviewing results.
- Project information and other resources.
export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.5/Home/ export GWE_HOME=/demos/gwe/gwe-0.7.3.alpha export PATH=$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}