[Gate-users] speed up simulation

Michal Knap michal.knap at gmail.com
Thu Feb 12 16:32:05 CET 2015


*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

[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
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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 78knap.m at nukleomed.pl

michal.knap at gmail.comwww.nukleomed.pl
 <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!
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