Difference between revisions of "2010 Summer Project Week Breakout Session:GWE"

From NAMIC Wiki
Jump to: navigation, search
 
(5 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
   Back to [[2010 Summer Project Week]]
+
   Back to [[2010 Summer Project Week#Agenda| Project Week Agenda]]
  
−
  Owner: Marco Ruiz
+
'''Session Leader: Marco Ruiz'''
  
 +
==Objective==
  
−
  Agenda
+
Introduce researchers to [[Engineering:UCSD|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).
 +
 
 +
[[image:Wcp-queue-1.png|thumb|left|300px|GWE: Queueing a parameter exploration experiment (order)]]
 +
 
 +
[[image:Rse-gwe-exp.gif|thumb|left|300px|RSE: Exploring the results of a GWE parameter exploration experiment]]
 +
 
 +
 
 +
==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>
 +
 
 +
 
 +
 
 +
==References==
 +
 
 +
* [[Engineering:UCSD|Systems Wiki Page]]
 +
* [http://www.gridwizardenterprise.org GWE Project Site]
 +
* [http://www.gridwizardenterprise.org/rse RSE Project Site]

Latest revision as of 06:20, 24 June 2010

Home < 2010 Summer Project Week Breakout Session:GWE
 Back to  Project Week Agenda

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

Retrieved from "https://www.na-mic.org/w/index.php?title=2010_Summer_Project_Week_Breakout_Session:GWE&oldid=55043"