[Gate-users] very different computation times while runing simulations in parallel

[Sarah Blind]

Dear Dimitrios, 

The simulations in parallel have all auto engine seed. 

Thank you, 

Sarah 

Ps: thank you for your remark, the duplicate command setEngineName is a mistake. 

----- Le 3 Avr 22, à 23:23, Dimitrios Thanasas <dthanas at uoa.gr> a écrit : 

> Dear Sarah,

> You have the command "/gate/random/setEngineName MersenneTwister " in two
> lines. In file main.mac and in file physcis.mac.
> You do not need it in physics.mac.
> The two simulations have "auto" engine seed or you have set a specific
> number?
> If you have set a specific number, try a different one (eg 123456789) at
> the second simulation.
> Running two different simulations does not cause a problem.

> Best regards,
> Dimitris Thanasas

> > Dear Gate users,

> > I'm analysing the deposited dose in Gy of the irradiation simulation of a
> > cell with in its inside a certain number of nanoparticles composed of 16%
> > bismuth.
> > Looking at the deposited dose on the nanoparticles focci, for several
> > simulations I obtain very different results and computation times:


> > * Simulation 1 : 105,545 Gy with a computation time of ~10h,
> > * Simulation 2 : 10.07 Gy with a computation time of ~ 2h.

> > I run these two simulations in parallel, each in a different file and a
> > different number for setEngineSeed.

> > I have a gamma beam and I send 300 000 Bq for a 60 secondes irradiation
> > simulation on 35^3 nanoparticles.
> > I think the simulation 2 failed ; can the fact that I run several
> > simulations at the same time be a problem ?

> > If this speak to anyone, thank your for your advices!

> > Sarah Blind




> > PS: Here is my code:

> > MAIN.MAC




> > /gate/geometry/setMaterialDatabase ../data/GateMaterials.db

> > /control/execute world.mac
> > /control/execute physics.mac
> > /control/execute detectors.mac

> > /gate/run/initialize

> > /control/execute 5sourceSpectrumMeV.mac

> > /gate/application/setTimeSlice 60. s
> > /gate/application/setTimeStart 0. s
> > /gate/application/setTimeStop 60. s

> > /gate/random/setEngineName MersenneTwister
> > /gate/random/setEngineSeed auto
> > /gate/application/start




> > WORLD.MAC


> > BQ_BEGIN

> > /gate/world/geometry/setXLength 30 um
> > /gate/world/geometry/setYLength 30 um
> > /gate/world/geometry/setZLength 30 um
> > /gate/world/setMaterial Air

> > /gate/world/daughters/name cell
> > /gate/world/daughters/insert sphere
> > /gate/cell/geometry/setRmin 0.0 mm
> > /gate/cell/geometry/setRmax 10 um
> > /gate/cell/placement/setTranslation 0 0 0 um
> > /gate/cell/setMaterial G4_WATER
> > /gate/cell/vis/setVisible 1
> > /gate/cell/vis/setColor blue
> > /gate/cell/vis/forceSolid false


> > /gate/cell/daughters/name NP
> > /gate/cell/daughters/insert sphere
> > /gate/NP/geometry/setRmin 0 mm
> > /gate/NP/geometry/setRmax 0.5 um
> > /gate/NP/placement/setTranslation 0 0 0 mm
> > /gate/NP/setMaterial AGuIX_bis

> > /gate/NP/repeaters/insert cubicArray
> > /gate/NP/cubicArray/setRepeatNumberX 30
> > /gate/NP/cubicArray/setRepeatNumberY 30
> > /gate/NP/cubicArray/setRepeatNumberZ 30
> > /gate/NP/cubicArray/setRepeatVector 5 5 5 nm

> > BQ_END


> > PHYSICS.MAC

> > BQ_BEGIN


> > /gate/physics/addPhysicsList QGSP_BERT_EMV

> > /gate/physics/Gamma/SetCutInRegion world 50 nm
> > /gate/physics/Electron/SetCutInRegion world 50 nm

> > /gate/physics/Gamma/SetCutInRegion cell 20 nm
> > /gate/physics/Electron/SetCutInRegion cell 20 nm

> > /gate/physics/Gamma/SetCutInRegion NP 0.5 nm
> > /gate/physics/Electron/SetCutInRegion NP 0.5 nm

> > /gate/random/setEngineName MersenneTwister

> > /gate/physics/addAtomDeexcitation

> > /gate/physics/addProcess PhotoElectric gamma
> > /gate/physics/processes/PhotoElectric/setModel LivermoreModel
> > /gate/physics/processes/PhotoElectric/setAugerElectron true
> > /gate/physics/processes/PhotoElectric/setDeltaRayCut 10 eV
> > /gate/physics/processes/PhotoElectric/setXRayCut 10 eV
> > /gate/physics/processes/PhotoElectric/setStepFunction e- 0.2 0.1 nm

> > /gate/physics/addProcess Compton gamma
> > /gate/physics/processes/Compton/setModel LivermoreModel
> > /gate/physics/processes/Compton/setStepFunction e- 0.2 0.1 nm

> > /gate/physics/addProcess RayleighScattering
> > /gate/physics/processes/RayleighScattering/setModel LivermoreModel

> > /gate/physics/addProcess GammaConversion
> > /gate/physics/processes/GammaConversion/setModel LivermoreModel

> > /gate/physics/addProcess ElectronIonisation
> > /gate/physics/processes/ElectronIonisation/setModel LivermoreModel e-
> > /gate/physics/processes/ElectronIonisation/setModel PenelopeModel e+
> > /gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 nm

> > /gate/physics/addProcess Bremsstrahlung e-
> > /gate/physics/addProcess Bremsstrahlung e+
> > /gate/physics/processes/Bremsstrahlung/setModel LivermoreModel e-
> > /gate/physics/processes/Bremsstrahlung/setModel PenelopeModel e+

> > /gate/physics/addProcess eMultipleScattering e-
> > /gate/physics/addProcess eMultipleScattering e+
> > /gate/physics/processes/eMultipleScattering/setModel UrbanModel e-
> > /gate/physics/processes/eMultipleScattering/setModel UrbanModel e+

> > /gate/physics/SetMinKineticEnergyInRegion world 1 eV
> > /gate/physics/SetMinKineticEnergyInRegion cell 1 eV
> > /gate/physics/ActivateSpecialCuts gamma

> > BQ_END


> > DETECTOR.MAC


> > BQ_BEGIN

> > /gate/actor/addActor DoseActor dose
> > /gate/actor/dose/save output/dose1.hdr
> > /gate/actor/dose/attachTo cell
> > /gate/actor/dose/stepHitType random
> > /gate/actor/dose/setPosition 0.0 0.0 0.0 mm
> > /gate/actor/dose/setSize 20 20 20 um
> > /gate/actor/dose/setResolution 400 400 400
> > /gate/actor/dose/saveEveryNSeconds 30

> > BQ_END


> > SOURCE.MAC


> > BQ_BEGIN

> > /gate/source/addSource mybeam gps
> > /gate/source/mybeam/gps/particle gamma
> > /gate/source/mybeam/gps/ene/type User
> > /gate/source/mybeam/gps/hist/type energy
> > /gate/source/mybeam/setActivity 300000. becquerel


> > [histogram]

> > /gate/source/mybeam/gps/position 0 0 15 um
> > /gate/source/mybeam/gps/pos/type Volume
> > /gate/source/mybeam/gps/pos/shape Cylinder
> > /gate/source/mybeam/gps/pos/inner_radius 0 mm
> > /gate/source/mybeam/gps/pos/radius 10 um
> > /gate/source/mybeam/gps/pos/halfz 0.01 um
> > /gate/source/mybeam/gps/ang/type beam2d









> > BQ_END


> > _______________________________________________
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> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

-- 
Sarah Blind 
Ingénieure de recherche - CNRS 
Centre de Recherche en Automatique de Nancy (CRAN) 
Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS) 
Site de la faculté de médecine 
9, Avenue de la Forêt de Haye 
54505 Vandoeuvre les Nancy 
Tél : 03.72.74.61.13 
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