[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[] =
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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 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.

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