[Gate-users] The question about the speed of calculation

[Grevillot Loic]

Hi!
Indeed, the number of primaries/s/core for carbon ions is small (between 3 and 40 roughly for some cases I checked).
You do not need to simulate 109 primaries, but only 105 or 106 and scale the output according to the intended number of primaries.
Maybe this paper (online<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.frontiersin.org%2Farticles%2F10.3389%2Ffphy.2021.704760%2Ffull%3F%26utm_source%3DEmail_to_authors_%26utm_medium%3DEmail%26utm_content%3DT1_11.5e1_author%26utm_campaign%3DEmail_publication%26field%3D%26journalName%3DFrontiers_in_Physics%26id%3D704760&data=04%7C01%7Cloic.grevillot%40medaustron.at%7C07fa8c2caa564886d97708d96610f425%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637653046166665780%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=fHO06zpL1LitWFfX19dGNbWz2I5GgTpMnBtiDQIzv%2B4%3D&reserved=0>) can give you some hints on computation time and cluster capacity for clinical conditions (the impact of the physics-list on computation time is also discussed).

Best,
Loïc



From: Gate-users [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf Of hao qiushi
Sent: Sunday, August 22, 2021 4:09 AM
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] The question about the speed of calculation

Dear Gate Expert,
I have simulated the radiotherapy of carbon ion beam to hit the mouse model,but the simulation speed is only a few particles per second,and my project needs to simulate 10E9 particles,I do not know if I'm the only one that's so slow,could someone help me to check my macro file? If possible ,please help me to  verify the calculation speed ,thanks in advance, the macro file is attached below


/control/execute mac/verbose.mac
#/control/execute mac/visu.mac

/gate/geometry/setMaterialDatabase /home/gate/Downloads/vgate/dosimetry/data/GateMaterials.db

# World=======================

/gate/world/geometry/setXLength 2 m
/gate/world/geometry/setYLength 2 m
/gate/world/geometry/setZLength 2 m
/gate/world/setMaterial Vacuum

# digimouse ==================

/gate/HounsfieldMaterialGenerator/SetMaterialTable                  /home/gate/Downloads/vgate/dosimetry/data/Schneider2000MaterialsTable.txt
/gate/HounsfieldMaterialGenerator/SetDensityTable                   /home/gate/Downloads/vgate/dosimetry/data/Schneider2000DensitiesTable.txt
/gate/HounsfieldMaterialGenerator/SetDensityTolerance               0.1 g/cm3
/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename /home/gate/Downloads/vgate/dosimetry/data/patient-HUmaterials.db
/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename       /home/gate/Downloads/vgate/dosimetry/data/patient-HU2mat.txt
/gate/HounsfieldMaterialGenerator/Generate

/gate/world/daughters/name                        pmma
/gate/world/daughters/insert                      ImageNestedParametrisedVolume
/gate/geometry/setMaterialDatabase                /home/gate/Downloads/vgate/dosimetry/data/patient-HUmaterials.db
/gate/pmma/geometry/setHUToMaterialFile           /home/gate/Downloads/vgate/dosimetry/data/patient-HU2mat.dat
/gate/pmma/geometry/setImage                      /home/gate/Downloads/vgate/dosimetry/data/ct_data/ct_380x992x208.hdr

/gate/pmma/placement/setTranslation               0 0 500 mm
/gate/pmma/placement/setRotationAxis              1 0 0
/gate/pmma/placement/setRotationAngle             -90 deg

# PHYSICS=========

/gate/physics/addPhysicsList QGSP_BERT_EMV

/gate/physics/addPhysicsList QGSP_BERT_HP

/gate/physics/Gamma/SetCutInRegion      world 0.1 mm
/gate/physics/Electron/SetCutInRegion   world 0.1 mm
/gate/physics/Positron/SetCutInRegion   world 0.1 mm

/gate/physics/Gamma/SetCutInRegion      pmma 0.1 mm
/gate/physics/Electron/SetCutInRegion   pmma 0.1 mm
/gate/physics/Positron/SetCutInRegion   pmma 0.1 mm

# output===================

/gate/actor/addActor                               DoseActor  doseDistribution
/gate/actor/doseDistribution/save                  /home/gate/Downloads/vgate/dosimetry/output_txt/output-C100.mhd
/gate/actor/doseDistribution/attachTo         pmma
#/gate/actor/doseDistribution/setSize              38 99.2 20.8 mm
/gate/actor/doseDistribution/stepHitType           random
/gate/actor/doseDistribution/setPosition           0 0 0 cm
/gate/actor/doseDistribution/setResolution         380 992 208
/gate/actor/doseDistribution/enableEdep            true
/gate/actor/doseDistribution/enableDose            true
/gate/actor/doseDistribution/enableNumberOfHits    true

/gate/actor/addActor                               DoseActor  doseDistribution_txt
/gate/actor/doseDistribution_txt/save                  /home/gate/Downloads/vgate/dosimetry/output_txt/output-C100.txt
/gate/actor/doseDistribution_txt/attachTo         pmma
#/gate/actor/doseDistribution_txt/setSize               38 99.2 20.8 mm
/gate/actor/doseDistribution_txt/stepHitType           random
/gate/actor/doseDistribution_txt/setPosition           0 0 0 cm
/gate/actor/doseDistribution_txt/setResolution         1 992 1
/gate/actor/doseDistribution_txt/enableEdep            true
/gate/actor/doseDistribution_txt/enableDose            true
/gate/actor/doseDistribution_txt/enableNumberOfHits    true



# ProductionAndStoppingActor==================

/gate/actor/addActor                     ProductionAndStoppingActor    prdandstp_11
/gate/actor/prdandstp_11/save               /home/gate/Downloads/vgate/dosimetry/output_txt/product_stop11.mhd
/gate/actor/prdandstp_11/attachTo           pmma
/gate/actor/prdandstp_11/setResolution      380 992 208
/gate/actor/prdandstp_11/stepHitType        random

/gate/actor/addActor                     ProductionAndStoppingActor    prdandstp_10
/gate/actor/prdandstp_10/save               /home/gate/Downloads/vgate/dosimetry/output_txt/product_stop10.mhd
/gate/actor/prdandstp_10/attachTo           pmma
/gate/actor/prdandstp_10/setResolution      380 992 208
/gate/actor/prdandstp_10/stepHitType        random

/gate/actor/addActor                     ProductionAndStoppingActor    prdandstp_15
/gate/actor/prdandstp_15/save               /home/gate/Downloads/vgate/dosimetry/output_txt/product_stop15.mhd
/gate/actor/prdandstp_15/attachTo           pmma
/gate/actor/prdandstp_15/setResolution      380 992 208
/gate/actor/prdandstp_15/stepHitType        random

/gate/actor/addActor                     ProductionAndStoppingActor    prdandstp_11_txt
/gate/actor/prdandstp_11_txt/save               /home/gate/Downloads/vgate/dosimetry/output_txt/product_stop11.txt
/gate/actor/prdandstp_11_txt/attachTo           pmma
/gate/actor/prdandstp_11_txt/setResolution      1 992 1
/gate/actor/prdandstp_11_txt/stepHitType        random

/gate/actor/addActor                     ProductionAndStoppingActor    prdandstp_10_txt
/gate/actor/prdandstp_10_txt/save               /home/gate/Downloads/vgate/dosimetry/output_txt/product_stop10.txt
/gate/actor/prdandstp_10_txt/attachTo           pmma
/gate/actor/prdandstp_10_txt/setResolution      1 992 1
/gate/actor/prdandstp_10_txt/stepHitType        random

/gate/actor/addActor                     ProductionAndStoppingActor    prdandstp_15_txt
/gate/actor/prdandstp_15_txt/save               /home/gate/Downloads/vgate/dosimetry/output_txt/product_stop15.txt
/gate/actor/prdandstp_15_txt/attachTo           pmma
/gate/actor/prdandstp_15_txt/setResolution      1 992 1
/gate/actor/prdandstp_15_txt/stepHitType        random

/gate/actor/addActor               SimulationStatisticActor stat
/gate/actor/stat/save              /home/gate/Downloads/vgate/dosimetry/output_txt/stat-C100.txt
/gate/actor/stat/saveEveryNSeconds 10

# filtter====================

/gate/actor/prdandstp_11/addFilter                     particleFilter
/gate/actor/prdandstp_11/particleFilter/addParticleZ      6
/gate/actor/prdandstp_11/particleFilter/addParticleA      11

/gate/actor/prdandstp_10/addFilter                     particleFilter
/gate/actor/prdandstp_10/particleFilter/addParticleZ      6
/gate/actor/prdandstp_10/particleFilter/addParticleA      10

/gate/actor/prdandstp_15/addFilter                     particleFilter
/gate/actor/prdandstp_15/particleFilter/addParticleZ      8
/gate/actor/prdandstp_15/particleFilter/addParticleA      15

/gate/actor/prdandstp_11_txt/addFilter                     particleFilter
/gate/actor/prdandstp_11_txt/particleFilter/addParticleZ      6
/gate/actor/prdandstp_11_txt/particleFilter/addParticleA      11

/gate/actor/prdandstp_10_txt/addFilter                     particleFilter
/gate/actor/prdandstp_10_txt/particleFilter/addParticleZ      6
/gate/actor/prdandstp_10_txt/particleFilter/addParticleA      10

/gate/actor/prdandstp_15_txt/addFilter                     particleFilter
/gate/actor/prdandstp_15_txt/particleFilter/addParticleZ      8
/gate/actor/prdandstp_15_txt/particleFilter/addParticleA      15
# INITIALISATION============

/gate/run/initialize
#/gate/physics/processList Available
#/gate/physics/processList Enabled


# BEAMS==================

/gate/source/addSource     mybeam  PencilBeam
/gate/source/mybeam/setParticleType GenericIon
/gate/source/mybeam/setIonProperties 6 12 6 0
/gate/source/mybeam/setEnergy 2400 MeV
/gate/source/mybeam/setSigmaEnergy 2 MeV
/gate/source/mybeam/setPosition 0 0 0 mm
/gate/source/mybeam/setSigmaX 2 mm
/gate/source/mybeam/setSigmaY 2 mm
/gate/source/mybeam/setSigmaTheta  0.01 mrad
/gate/source/mybeam/setSigmaPhi    0.01 mrad
/gate/source/mybeam/setEllipseXThetaEmittance 0.01 mm*mrad
/gate/source/mybeam/setEllipseYPhiEmittance   0.01 mm*mrad
#/gate/source/mybeam/setIntensity 100000000


# JamesRandom Ranlux64 MersenneTwister
/gate/random/setEngineName MersenneTwister
/gate/random/setEngineSeed auto

/gate/application/noGlobalOutput
#/gate/application/readTimeSlicesIn               data/timeslice.dat
#/gate/application/readNumberOfPrimariesInAFile   data/primary.dat
/gate/application/setTotalNumberOfPrimaries 500000
/gate/application/start
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