Date post: | 11-Dec-2015 |
Category: |
Documents |
Upload: | abdiel-boyle |
View: | 215 times |
Download: | 1 times |
The GATE-LAB system
Sorina Camarasu-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 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)
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 Very high performance computer
7
What is the GateLab ?
Design your simulations
Click to load macro file in web
browser
Monitor simulation
Click to download (merged) results
Computing (x 103 jobs)
GATE-LAB• Upload all files• Split simulation• Handle errors• Load balancing• Merge 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
Launch simulation screen
Simulation name
Estimated time
Gate release
Type of submission
Go !
11
Monitor simulation screen
Total # of particles
Current # of particles
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
N jobs, p particles. Two modes
Static mode : Each job simulates p/N particles Dynamic mode : Jobs simulate particles until the system stops them
Static vs Dynamic mode
Static Dynamic
Two times faster
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 : Sorina Camarasu, Tristan Glatard, Rafael Ferreira da Silva, Pierre Gueth, David Sarrut