VIP Workshop December 2012

voltaireblingData Management

Nov 20, 2013 (3 years and 6 months ago)

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The GATE
-
LAB system

Sorina

Camarasu
-
Pop, Pierre
Gueth
,

Tristan
Glatard
, Rafael Silva, David Sarrut


VIP Workshop

December 2012


1

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)


2

One example


GATE simulation of proton cancer treatment


Goal: study the dose distribution inside patient data

Protontherapy treatment room

CT patient data

3

One example


Proton beam (complex)


Track every particles inside biological material


Store deposited energy


Around 10
8

particles to track +
secondaries


About 7 days computing time


“brute
-
force”, reference

Proton beam



intensity, energy



position orientation

4

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

5

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

6

What is the GateLab ?

Design

your
simulations

Click to load
macro file
in
web browser

Monitor
simulation

Click to download
(merged)

results

Computing


(x 10
3

jobs)

GATE
-
LAB


Upload all files


Split simulation


Handle errors


Load balancing


Merge results

7

One example


From the GATE
-
LAB (VIP):


Specific input parser


Submission options: mode + GATE release


Specific job monitoring


Specific output merger


8

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


9

Launch simulation screen

Simulation name

Estimated time

Gate release

Type of submission

Go !

10

Monitor simulation screen

Total # of particles

Current # of particles

11

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


12


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

13

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






14

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)





15

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)

16

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