The GATE-LAB system
Sorina Camarasu-Pop, Pierre Gueth,
Tristan Glatard, Rafael Silva, David Sarrut
VIP Workshop
December 2012
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GATE-LAB ?
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What is GATE-LAB ?
It is one module in VIP, dedicated to GATE
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What is GATE ?
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A software for Monte-Carlo simulations in medical physics
Particles tracking
Both for imaging (PET, SPECT, X/proton-radiography, …) and
radiation therapy (dose computation)
Based on the Geant4 library fro particles physic (CERN)
Open source
Developed by the OpenGate collaboration
http://www.opengatecollaboration.org
Community of users (estimated to 1000 worldwide)
First release of GATE in May 2004 ; 18 releases since
2 reference articles : [Phys Med Biol 2004 and 2011] (highly cited)
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One example
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GATE simulation of proton cancer treatment
Goal: study the dose distribution inside patient data
Protontherapy treatment room
CT patient data
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One example
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Proton beam (complex)
Track every particles inside biological material
Store deposited energy
Around 108 particles to track + secondaries
About 7 days computing time
“brute-force”, reference
Proton beam
• intensity, energy
• position orientation
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One example : results
Example of dose distribution
• Overlaid on the CT data
• Computed with GATE
• More than 1 month comp time
• Done in few hours VIP/GateLab
• Speed up = 290
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GATE-LAB specificities
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Why ?
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GATE-LAB started before VIP
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Started since 2008
Test version 2011-2012
Open to public since Feb 2012 (beta)
Tight integration between GATE and GATE-LAB
GATE code has been modified
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In general MC simulations can be very long (up to days)
Access to grid or cluster need skills, not straightforward
To provide easy and efficient access to Gate
to monitor the progress of the simulations
to stop simulation on demand
VIP-GATE-LAB has been adapted
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To manage all GATE output types
Very high performance computer
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What is the GateLab ?
Design your
simulations
Click to load
macro file in
web browser
Computing
(x 103 jobs)
Monitor
simulation
GATE-LAB
• Upload all files
• Split simulation
• Handle errors
• Load balancing
• Merge results
Click to download
(merged) results
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One example
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From the GATE-LAB (VIP):
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Specific input parser
Submission options: mode + GATE release
Specific job monitoring
Specific output merger
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One example
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Specific input parser
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Load the main macro file
Parse the macro file to find all needed files
Archive and zip together all files
Upload files on the GATE-LAB server
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Simulation name
Estimated time
Gate release
Type of submission
Go !
Launch simulation screen
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Total # of particles
Current # of particles
Monitor simulation screen
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One example
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Specific output merger
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GATE simulations can have multiple results
Each result is split into several files (nb of jobs)
The “merger” gather all files and merge them according to the file
types
One of the most critical point
Could be long
Incremental merger in development
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Static vs Dynamic mode
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N jobs, p particles.
Two modes
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Static
mode
Two
times: Each job simulates p/N particles
Dynamic
mode : Jobs simulate particles until the system stops them
faster
Static
Dynamic
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Submission modes
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Which mode to use ?
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Dynamic : each job & events must be strictly equivalent
If time is involved : use static mode
For radiation therapy applications
For PET/SPECT, one run
For PET/SPECT, multiple run
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: dynamic
: static
: not (yet) possible
Need to split according to time rather than Events, need
refactoring
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Limits of the GateLab
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No scripting possible (launch one simulation at a time)
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Difficult to manage large files
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Typically needed for “phase-space”
Either as input or output
Difficulty for simulation involving time
(with jobs not equivalent, not interruptible)
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Results - GateLab
 Currently, about 228 registered users
 About 25 active user/months
 Active user = launch at least 3 simulations
 About 200 simulations per months (except in summer ...)
 Global average speedup around 50 (increasing !)
 Max speedup of 350
(taking queuing & merging time into account)
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Conclusion
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GateLab allows easy and free high performance computation
for Gate simulations
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Work in progress
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New splitting procedure for PET simulations
New more robust merger
Improved interface
Feedback welcome !
http://gatelab.creatis.insa-lyon.fr
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Acknowledgments : Sorina Camarasu, Tristan Glatard, Rafael
Ferreira da Silva, Pierre Gueth, David Sarrut