[Gate-users] speed up simulation
Marc Chamberland
MarcChamberland at cmail.carleton.ca
Thu Feb 12 18:06:20 CET 2015
Hi Michał,
You should take a look at the cuts and variance reduction techniques offered in Gate: http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Cut_and_Variance_Reduction_Technics#Splitting_and_russian_roulette
Cuts will terminate the production of secondary particles when a particle's energy gets below a certain threshold (which is entered as a distance in a specific volume in Gate). Be careful, because this may change your results if you're too aggressive with the cuts.
Variance reduction techniques (splitting and Russian roulette) are guaranteed to give you the same results (within statistical fluctuations) and, possibly, increase the efficiency of the simulation. Since you're doing SPECT (I assume), maybe playing Russian roulette on electrons, then splitting the bremsstrahlung photons would be a good idea? I'm a bit rusty on this, so if someone else has a suggest, please let us know.
Of course, if you have access to a computer cluster, this really helps speed up things. If not, there's a possibility you could still split your simulation between your multi-core processor (if you have one).
Good luck!
Marc
__________________________
Marc Chamberland, MSc
PhD candidate
Department of Physics
Carleton University
Ottawa (ON)
On Feb 12, 2015, at 10:32, Michal Knap <michal.knap at gmail.com<mailto:michal.knap at gmail.com>> wrote:
Hi all,
I'm trying to simulate minigammacamera and my problem is that it takes too long time. I have 4 slices to do (37,5 s each) and i'm still on first one (16h!). Root file is now ~240 MB.
Is there any way to make it faster? Maybe i add to many parameters or something is too much in my simulation?
I have to get a spectrum, FWHM, spatial resolution, heterogeneity, sensitivity and count rate events.
With low activity everything wokrs fast, but i have to use 2 mCi and here are problems.
Here is my source:
/gate/source/addSource GammaSource
/gate/source/GammaSource/gps/type Volume
/gate/source/GammaSource/gps/shape Sphere
/gate/source/GammaSource/gps/radius 0.125 mm
/gate/source/GammaSource/gps/centre 0. 0. 0. cm
/gate/source/GammaSource/gps/particle gamma
/gate/source/GammaSource/gps/energytype Mono
/gate/source/GammaSource/gps/monoenergy 140 keV
/gate/source/GammaSource/setActivity 2 mCi
/gate/source/GammaSource/gps/mintheta 0. deg
/gate/source/GammaSource/gps/maxtheta 180. deg
/gate/source/GammaSource/gps/angtype iso
/gate/source/list
he is my digitizer:
/gate/physics/addPhysicsList emstandard
/gate/physics/addProcess RadioactiveDecay
/gate/digitizer/Singles/insert readout
/gate/digitizer/Singles/readout/setDepth 2
/gate/digitizer/Singles/insert adder
/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setResolution 0.26
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV
/gate/digitizer/Singles/insert spblurring
/gate/digitizer/Singles/spblurring/setSpresolution 2.0 mm
/gate/digitizer/Singles/spblurring/verbose 0
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 20. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 90. keV
Here is my phisics:
/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel StandardModel
/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel StandardModel
/gate/physics/addProcess RayleighScattering
/gate/physics/processes/RayleighScattering/setModel PenelopeModel
/gate/physics/addProcess ElectronIonisation
/gate/physics/processes/ElectronIonisation/setModel StandardModel e-
/gate/physics/processes/ElectronIonisation/setModel StandardModel e+
/gate/physics/addProcess Bremsstrahlung
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+
/gate/physics/processList Enabled
/gate/physics/processList Initialized
/gate/application/setTimeSlice 37.5 s
/gate/application/setTimeStart 0. s
/gate/application/setTimeStop 150. s
and this is what i get from terminal:
mknap at mknap-HP:~/Gate/Archive$ Gate main.mac
[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-09-06-patch-03 (14-March-2014)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Physic-0] WARNING: manual physic lists are being deprecated.
Please, use physic list builder mechanism instead. Related documentation can be found at:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics
[Core-0] Initialization of actors
[Core-0]
[Core-0] **********************************************************************
[Core-0] GATE version name: gate_v7.0
[Core-0] Copyright : OpenGATE Collaboration
[Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0] WWW : http://www.opengatecollaboration.org<http://www.opengatecollaboration.org/>
[Core-0] **********************************************************************
[Core-0]
[Core-0] You are using Geant4 version 9.6.3
[Core-0] Starting macro main.mac
GateDetectorConstruction::insertARFSD entered
created a ARF Sensivitive Detector
created command /gate/systems/SPECThead/arf/setARFStage
GATE object: 'systems/SPECThead'
Components:
GATE object: 'systems/SPECThead/base'
Attached to volume: SPECThead
Nb of children: 1
GATE object: 'systems/SPECThead/crystal'
Attached to volume: crystal
Nb of children: 1
GATE object: 'systems/SPECThead/pixel'
Attached to volume: ---
[Physic-0] The following Geant4's physic-list is enabled :emstandard
List of Enabled processes:
=== Process: RadioactiveDecay ===
Particle: GenericIon
=== Process: Bremsstrahlung ===
Particle: e+
* Model(s):
- StandardModel
Particle: e-
* Model(s):
- StandardModel
=== Process: ElectronIonisation ===
Particle: e+
* Model(s):
- StandardModel
Particle: e-
* Model(s):
- StandardModel
=== Process: PhotoElectric ===
Particle: gamma
* Model(s):
- StandardModel
=== Process: RayleighScattering ===
Particle: gamma
* Model(s):
- PenelopeModel
=== Process: Compton ===
Particle: gamma
* Model(s):
- StandardModel
List of initialized processes:
* B+
- msc
- hIoni
* B-
- msc
- hIoni
* D+
- msc
- hIoni
* D-
- msc
- hIoni
* Ds+
- msc
- hIoni
* Ds-
- msc
- hIoni
* GenericIon
- msc
- ionIoni
* He3
- msc
- ionIoni
* alpha
- msc
- ionIoni
* anti_He3
- msc
- hIoni
* anti_alpha
- msc
- hIoni
* anti_deuteron
- msc
- hIoni
* anti_lambda_c+
- msc
- hIoni
* anti_omega-
- msc
- hIoni
* anti_proton
- msc
- hIoni
- hBrems
- hPairProd
* anti_sigma+
- msc
- hIoni
* anti_sigma-
- msc
- hIoni
* anti_sigma_c+
- msc
- hIoni
* anti_sigma_c++
- msc
- hIoni
* anti_triton
- msc
- hIoni
* anti_xi-
- msc
- hIoni
* anti_xi_c+
- msc
- hIoni
* deuteron
- msc
- hIoni
* e+
- msc
- eIoni
- eBrem
- annihil
- CoulombScat
* e-
- msc
- eIoni
- eBrem
- CoulombScat
* gamma
- phot
- compt
- conv
* kaon+
- msc
- hIoni
- hBrems
- hPairProd
* kaon-
- msc
- hIoni
- hBrems
- hPairProd
* lambda_c+
- msc
- hIoni
* mu+
- msc
- muIoni
- muBrems
- muPairProd
- CoulombScat
* mu-
- msc
- muIoni
- muBrems
- muPairProd
- CoulombScat
* omega-
- msc
- hIoni
* pi+
- msc
- hIoni
- hBrems
- hPairProd
* pi-
- msc
- hIoni
- hBrems
- hPairProd
* proton
- msc
- hIoni
- hBrems
- hPairProd
* sigma+
- msc
- hIoni
* sigma-
- msc
- hIoni
* sigma_c+
- msc
- hIoni
* sigma_c++
- msc
- hIoni
* tau+
- msc
- hIoni
* tau-
- msc
- hIoni
* triton
- msc
- hIoni
* xi-
- msc
- hIoni
* xi_c+
- msc
- hIoni
Nb of children: 0
GateSourceMgr::ListSources: List of the sources in the source manager
Source --------------> GammaSource
ID : 0
type : gps
activity (Bq) : 7.4e+07
startTime (s) : 0
time (s) : 0
forcedUnstable : 0
forcedHalfLife (s) : -0.693147
verboseLevel : 0
relative to vol : World
----------------------
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Physic-0] WARNING: manual physic lists are being deprecated.
Please, use physic list builder mechanism instead. Related documentation can be found at:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics
[Core-0] Initialization of actors
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 150 sec
[Acquisition-0] Simulation will have = 4 run(s)
--------- MTwist engine status ---------
Initial seed = -1129822556
Current index = 131
Array status mt[] =
3165144740 1155098222 1449384873 1350476049 3031978104
3737374509 1043990768 3217161181 458851423 1489829086
1603455297 3651954705 3332747306 1911410228 975310931
1492748296 3631356825 4293153529 3060389848 2394838075
3396168141 2112471553 1354631130 1967447768 3666324241
96610137 1720728467 476186075 3907650783 498207727
3495909701 2481451107 523974721 2079684000 3832553603
1084056137 1511017040 3696059764 101932917 2697409674
1258328980 712035116 4120110634 289416274 4232559498
332484404 1588704470 1406809180 217333309 165072284
2025476546 3498781724 3528379819 3454464803 3257483162
1388563150 3222786527 4168090379 29534214 2448821343
1552881193 1960805291 397884948 3864519465 56379798
930669973 1982526791 1299872903 1073530566 882081289
1073344943 1107734572 395350501 1562783132 2357562007
3680708174 4109687433 1056730725 4283629571 2640940053
226517183 3606041318 1498385031 2595091703 3119059545
1083903894 3495912485 1104309019 253996222 2458637429
2580370057 3362348812 1487176995 1051237997 4089396571
3196176189 812599191 2503449646 1424898914 97543244
3543715332 1401066242 2019965585 2557344349 638638399
4186206622 1941167799 3627487583 718868188 3283412063
3344684510 2831813114 3380796492 2257685910 2126816506
639851220 1033116476 3118128167 2039087339 2810783343
1579541877 2706460739 793267227 3691498108 607401459
2171132598 666159238 1375822083 1475264494 170016166
877121188 1932216061 1305620244 4025827592 478830041
1560383102 1023371775 3086142846 3867641242 1899446050
656286039 1411243834 325096497 3596673854 1013079805
1191680444 3323220351 518658437 3629511657 3018163597
1445685757 267798025 3553523713 447314185 3423086339
1259386689 173227648 3886055619 3842914306 1638571774
694537879 2548535150 2302521826 487379369 865032237
3470121024 212109585 722948534 3670816922 682124864
1744974222 2280727568 4218346698 1775897588 3113960883
2584272606 1986131072 2044362640 4144651299 2896063257
762783159 2908878114 772773914 50375711 4111354927
4265454555 1265625622 3537069320 3227128303 1628012703
624471096 1164627965 2005527632 481027600 718970934
1348246839 2686084662 2117310031 2561140048 2535167783
551120477 12421332 1019113874 3193039467 3620091445
1161403169 3171182130 285723845 1844367461 3229690347
3977286942 1685118110 3403805387 4182290275 298074490
157473567 4145184591 1738151323 2056481696 2224610650
203384760 3486739355 334679290 2386856071 1179813205
1820795915 1105207960 3870802074 2389225117 436229370
2203955340 1334687411 887916070 825220493 2385023847
4148253118 3597421017 1363698965 2012327670 3864662460
897400455 1634783246 1638046425 788430161 4278833957
1331648185 794361522 2153901655 1194607581 4213376459
1740519046 3202156600 906012898 1768301005 1341637694
422123316 2166481800 2990731833 2184201093 442073376
2440721480 3790367229 2559343424 2649556951 1582368077
1249807275 3691431616 2263297524 470606398 92167305
3229995799 1423991577 811046540 1241820691 3675536720
875003916 3524625300 3245648098 1319929303 2352312203
3364491777 403344265 1109040643 60311435 1068357839
3544034978 2962822303 993883210 2606983190 545629195
1449409397 3934547693 2413018798 2545656487 3320701499
2907472965 872656647 1091922118 3904663945 209373251
3712448919 569681847 1782321085 3173152097 3322969403
3517283151 1774379506 3305493836 179896667 298533238
3211538888 3308218255 352951096 118536567 2087207529
3068589545 1511389391 548500521 932127047 1407086652
2783461005 1679793542 1510775649 4060143049 1789576122
2888260934 212170462 352575971 324423635 1542158530
3953065525 2570478527 1814106681 3405509739 1538360858
3085450064 2591600046 3586455027 1055658502 606776695
1991157379 2605964357 3246835541 3792163659 4247590500
1710874102 3333499657 535594003 766030903 2283985482
3574825322 3346862502 2542204277 3029429902 959907394
259605811 1911078367 1890013953 2614718986 1194664533
2358627760 3992158633 232024864 1751332561 1268137088
3204728364 594692440 3250201133 3863491930 1748349128
543698619 3784236180 3654288451 3293224571 1888514034
894675888 2501317356 4269068549 4245745820 3762673040
2513041367 1435940288 1993945759 675698427 2121384899
2429902033 813717533 1529387566 2449983467 3168218188
2760133136 379398567 3573908039 1673283075 1363553816
145870498 2535216954 2477770155 4220429111 3750747705
1022748054 4288745669 3224733556 3082825920 440802754
166811333 2623967531 1998899902 2269811247 2085882196
2905624959 437883174 965952350 3016746201 2766982465
2884963048 3201271734 3378995371 841496974 3586161231
1676430148 3397377496 835854921 55018062 2546671666
3396093375 2588138490 3863012745 3712068802 3122228652
3437340952 2143048368 2733315777 847953050 4086347160
1158841140 4271124729 800154493 1344453443 1495287399
1540651962 2573555162 4172288790 3629593694 2895461801
964716558 1593489640 487620998 3539514690 3429891136
3404749837 2551700719 2870476577 3010846830 2033771526
3451801700 21681735 1789391270 239127177 3793265106
759354525 3894819608 2925016273 1772392520 500463769
1425646952 3054314555 1101021066 2861504391 1840977704
1158197503 2454291763 1813041001 433728903 3799149081
617231651 3532736135 502993335 2956095565 821498084
3961372056 3558124354 741513827 46018252 4107582468
543705218 1992351476 1353470922 3608105723 4052492487
2952323810 4063263761 1810790922 187396158 3116783976
3952845927 1440748296 240939128 4251613262 3372419630
941425073 2527553540 1123152408 3174269198 2477735800
2867091489 3465706917 4150070335 4152357036 2026314466
4153402217 987113111 2792048335 3130134236 2655164604
1924093471 1256281342 451924986 2704863916 962812531
2963436707 3979839848 3176869181 927415072 272303472
2595138627 2029969295 1596178651 28288822 3397150565
1822242580 875677878 367631078 1707773081 1903548210
638584464 3861091820 3603702110 1940821255 3325045567
2928923596 805003785 913075079 3185428572 2399984730
2697316863 1583562287 3859710447 2630481892 2585138569
1397626361 577961477 3384126493 2026895621 710871650
568231067 233682575 3706090642 3111208127 463156762
1125486998 4108854302 3136173823 483710814 858271566
4161386913 3533780676 133031604 3029379648 1752078825
134677606 2901106751 4161203593 2508225397 98687853
2975884346 2483086716 3145543709 802408409 2970152506
3986081632 3046360622 612031302 2255489163 2049846865
724330239 1469510689 3042665137 3193707047 763421888
1767977938 552031176 4231670780 1559446822 2971924657
1125333036 2350136849 4021503246 2225595507 1334306854
3087964087 2666268700 2690819412 1766553679 2094900934
2228606682 2439776442 1299566109 1109900944 1596679920
317157587 2501819644 1145487806 2180164634 4036633314
1868969222 4045429767 2884854179 3263259339 1546886425
611012584 2129781435 1188876020 3173384818 131
----------------------------------------
[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final stop at 150 s.
Warning: the selected insertion name ('adder') was already in use.
Name 'adder2' will be used instead.
PhotoElectric: for gamma, applyCuts: 1 SubType= 12
LambdaPrime table from 200 keV to 10 TeV in 54 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PhotoElectric : Emin= 0 eV Emax= 10 TeV AngularGenSauterGavrila FluoActive
RayleighScattering: for gamma, applyCuts: 1 SubType= 11
Lambda table from 100 eV to 100 keV in 21 bins, spline: 0
LambdaPrime table from 100 keV to 10 TeV in 56 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
PenRayleigh : Emin= 0 eV Emax= 100 GeV
Compton: for gamma, applyCuts: 1 SubType= 13
Lambda table from 100 eV to 1 MeV in 28 bins, spline: 1
LambdaPrime table from 1 MeV to 10 TeV in 49 bins
===== EM models for the G4Region DefaultRegionForTheWorld ======
Klein-Nishina : Emin= 0 eV Emax= 10 TeV
### === Deexcitation model UAtomDeexcitation is activated for 9 regions:
Phantom
SPECThead
collimator
compartment
crystal
hole
movsource
shielding
DefaultRegionForTheWorld
### === G4UAtomicDeexcitation::InitialiseForNewRun()
### === PIXE model for hadrons: Empirical 1
### === PIXE model for e+-: Livermore 1
Bremsstrahlung: for e- SubType= 3
dE/dx and range tables from 100 eV to 10 TeV in 77 bins
Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
LPM flag: 1 for E > 1 GeV
===== EM models for the G4Region DefaultRegionForTheWorld ======
eBremSB : Emin= 0 eV Emax= 1 GeV DipBustGen
eBremLPM : Emin= 1 GeV Emax= 10 TeV DipBustGen
ElectronIonisation: for e- SubType= 2
dE/dx and range tables from 100 eV to 10 TeV in 77 bins
Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 10 TeV
Bremsstrahlung: for e+ SubType= 3
dE/dx and range tables from 100 eV to 10 TeV in 77 bins
Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
LPM flag: 1 for E > 1 GeV
===== EM models for the G4Region DefaultRegionForTheWorld ======
eBremSB : Emin= 0 eV Emax= 1 GeV DipBustGen
eBremLPM : Emin= 1 GeV Emax= 10 TeV DipBustGen
ElectronIonisation: for e+ SubType= 2
dE/dx and range tables from 100 eV to 10 TeV in 77 bins
Lambda tables from threshold to 10 TeV in 77 bins, spline: 1
finalRange(mm)= 1, dRoverRange= 0.2, integral: 1, fluct: 1, linLossLimit= 0.01
===== EM models for the G4Region DefaultRegionForTheWorld ======
MollerBhabha : Emin= 0 eV Emax= 10 TeV
### === Deexcitation model UAtomDeexcitation is activated for 9 regions:
Phantom
SPECThead
collimator
compartment
crystal
hole
movsource
shielding
DefaultRegionForTheWorld
### === G4UAtomicDeexcitation::InitialiseForNewRun()
### === PIXE model for hadrons: Empirical 1
### === PIXE model for e+-: Livermore 1
WARNING: Scene "none" not found.
/vis/scene/list to see scenes.
### === Deexcitation model UAtomDeexcitation is activated for 9 regions:
Phantom
SPECThead
collimator
compartment
crystal
hole
movsource
shielding
DefaultRegionForTheWorld
### === G4UAtomicDeexcitation::InitialiseForNewRun()
### === PIXE model for hadrons: Empirical 1
### === PIXE model for e+-: Livermore 1
I'll be very thankful for every help and opinion.
Best regards
Michał Knap
Nuclear technologist
ul. Żegańska 46A, 04-736 Warszawa
tel. 22 / 610 05 10 fax. 22 / 769 75 78
knap.m at nukleomed.pl<mailto:knap.m at nukleomed.pl>
michal.knap at gmail.com<mailto:michal.knap at gmail.com>
www.nukleomed.pl<http://www.nukleomed.pl/>
[http://www.nukleomed.pl/wp-content/uploads/2014/06/Nukleomed-logo-stopka.jpg]<http://www.nukleomed.pl/>
Treść tej wiadomości, wraz z ewentualnymi załącznikami, zawiera informacje przeznaczone tylko dla wymienionego w niej adresata i może zawierać informacje, które są poufne oraz prawnie chronione. Jeżeli nie są Państwo jej adresatem, bądź otrzymali ją przez pomyłkę należy: powiadomić niezwłocznie nadawcę poprzez odesłanie zwrotnej odpowiedzi na tą wiadomość, usunąć wiadomość w całości, nie ujawniać, nie rozpowszechniać, nie powielać i nie używać jej w jakikolwiek sposób w całości lub w części w jakiejkolwiek formie.
Think before You print!
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20150212/1f094e86/attachment-0001.html>
More information about the Gate-users
mailing list