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The GATE-LAB system

The GATE-LAB system. Sorina Camarasu -Pop, Pierre Gueth , Tristan Glatard , Rafael Silva, David Sarrut VIP Workshop December 2012. GATE-LAB ?. What is GATE-LAB ? It is one module in VIP, dedicated to GATE What is GATE ? A software for Monte-Carlo simulations in medical physics

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The GATE-LAB system

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  1. The GATE-LAB system SorinaCamarasu-Pop, Pierre Gueth, Tristan Glatard, Rafael Silva, David Sarrut VIP Workshop December 2012

  2. GATE-LAB ? • What is GATE-LAB ? • It is one module in VIP, dedicated to GATE • What is GATE ? • 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 OpenGatecollaboration 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)

  3. One example • GATE simulation of proton cancer treatment • Goal: study the dose distribution inside patient data Protontherapy treatment room CT patient data

  4. One example • 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

  5. 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

  6. GATE-LAB specificities • Why ? • 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 • GATE-LAB started before VIP • 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 • to monitor the progress of the simulations • to stop simulation on demand • VIP-GATE-LAB has been adapted • To manage all GATE output types Veryhigh performance computer

  7. What is the GateLab ? Design your simulations Click to load macro file in web browser • GATE-LAB • Upload all files • Split simulation • Handle errors • Load balancing • Merge results Computing (x 103 jobs) Monitor simulation Click to download (merged)results

  8. One example • From the GATE-LAB (VIP): • Specific input parser • Submission options: mode + GATE release • Specific job monitoring • Specific output merger

  9. One example • Specific input parser • 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

  10. Simulation name Estimated time Gate release Type of submission Go ! Launch simulation screen

  11. Total # of particles Current # of particles Monitor simulation screen

  12. One example • Specific output merger • 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

  13. Static vs Dynamic mode • N jobs, p particles. • Two modes • Static mode: Each job simulates p/N particles • Dynamic mode: Jobs simulate particles until the system stops them Two times faster Dynamic Static

  14. Submission modes • Which mode to use ? • Dynamic : each job & events must be strictly equivalent • If time is involved : use static mode • For radiation therapy applications : dynamic • For PET/SPECT, one run : static • For PET/SPECT, multiple run : not (yet) possible • Need to split according to time rather than Events, need refactoring

  15. Limits of the GateLab • No scripting possible (launch one simulation at a time) • Difficult to manage large files • Typically needed for “phase-space” • Either as input or output • Difficulty for simulation involving time(with jobs not equivalent, not interruptible)

  16. 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)

  17. Conclusion • GateLab allows easy and free high performance computation for Gate simulations • Work in progress • New splitting procedure for PET simulations • New more robust merger • Improved interface • Feedback welcome ! http://gatelab.creatis.insa-lyon.fr • Acknowledgments : SorinaCamarasu, Tristan Glatard, Rafael Ferreira da Silva, Pierre Gueth, David Sarrut

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