[Run issue]: Segmentation Fault in TOPAS-nBio with Chemistry Enabled at Higher Doses

[isabel24cl]

Contact Details

[email protected]

What was the issue?

Hello everyone! I am running a TOPAS-nBio simulation based on theTsNucleus example (TOPAS-nBio/examples/scorers/SBSDamageToDNANucleus/ExampleNucleusDNADamage.txt) within a few TsSphericalCells (10 cells). The simulation uses the Varian TrueBeam 6 MeV until the desired dose is reached, at which point I create a phase space file to save the scored electrons.

The issue I’m encountering is that for 1 or 2 Gy, the simulation sometimes runs successfully but other times results in a segmentation fault error. However, for 4 Gy and higher, it always crashes with a segmentation fault.

I have noticed that removing the chemistry allows the simulation to run without errors, but I need the chemistry enabled for my study.

Has anyone else encountered this issue, or does anyone have insights into what might be causing the segmentation fault? Below, I have attached the main TOPAS file I am running.

TOPAS-nBio category

Chemistry

Version

3.0

What Operative System (OS) are you running on?

Windows (WSL)

Relevant log output

i:Ts/ShowHistoryCountAtInterval = 195000
i:Ts/NumberOfThreads = 10
b:Ge/QuitIfOverlapDetected = "false"
b:Ge/CheckForUnusedComponents = "false"

## -- World ----------------------------------------------------------
d:Ge/World/HLX = 300.0 um
d:Ge/World/HLY = 300.0 um
d:Ge/World/HLZ = 300.0 um
b:Ge/World/Invisible = "false"

d:GE/Eppendorf/HLX = 300 um
d:GE/Eppendorf/HLY = 300 um
d:GE/Eppendorf/HLZ = 50 um
b:Ge/Eppendorf/Invisible = "false"
s:Ge/Eppendorf/Type = "TsBox"
s:Ge/Eppendorf/Material = "G4_WATER"
s:Ge/Eppendorf/Parent = "World"

includeFile = Cell_distribution.txt


# -- Materials ----------------------------------------------------------
s:Ma/G4_HistoneMaterial/CloneFromMaterial   = "G4_WATER"
d:Ma/G4_HistoneMaterial/CloneWithDensity    = 1.407 g/cm3
s:Ma/G4_BaseMaterial/CloneFromMaterial      = "G4_WATER"
d:Ma/G4_BaseMaterial/CloneWithDensity       = 1.0 g/cm3
s:Ma/G4_BackboneMaterial/CloneFromMaterial  = "G4_WATER"
d:Ma/G4_BackboneMaterial/CloneWithDensity   = 1.0 g/cm3
s:Ma/G4_WATER_MODIFIED/CloneFromMaterial    = "G4_WATER"
d:Ma/G4_WATER_MODIFIED/CloneWithDensity     = 1.0 g/cm3


# ## -- Beam Position ----------------------------------------------------------
s:Ge/BeamPosition/Parent = "World"
s:Ge/BeamPosition/Type = "Group"
d:Ge/BeamPosition/TransX = 0. um
d:Ge/BeamPosition/TransY = 0. um
d:Ge/BeamPosition/TransZ = -2 * Ge/Eppendorf/HLZ um
d:Ge/BeamPosition/RotX = 180. deg
d:Ge/BeamPosition/RotY = 0. deg
d:Ge/BeamPosition/RotZ = 0. deg

## -- Source (e-) ----------------------------------------------------------
s:So/MySource/Type = "PhaseSpace"
s:So/MySource/PhaseSpaceFileName = "ASCIIOutput_4gy"
s:So/MySource/Component = "BeamPosition"
#b:So/MySource/LimitedAssumeFirstParticleIsNewHistory = "true"
#b:So/MySource/LimitedAssumeEveryParticleIsNewHistory = "true"
#b:So/MySource/LimitedAssumePhotonIsNewHistory = "true"
i:So/MySource/PhaseSpaceMultipleUse = 0
i:So/MySource/NumberOfHistoriesInRun = 1950000    
b:So/MySource/PhaseSpacePreCheck = "false"

## -- Physics Models (per region) --------------------------------------------
sv:Ph/Default/Modules = 2 "g4em-standard_opt2" "g4em-dna-chemistry"  # "TsEmDNAChemistry"
s:Ph/Default/ForRegion/DetailedTransport/ActiveG4EmModelFromModule = "g4em-dna" 

## -- Chemistry (scorers/IRTGetGValues/TsIRTvalue.txt) -------------------------------
includeFile = supportFiles/TOPASDefaultReactions.txt
s:Ch/ChemistryName = "TOPASChemistry"
b:Ch/TOPASChemistry/ChemicalStageTransportActive = "True"
d:Ch/TOPASChemistry/ChemicalStageTimeEnd = 2.5 ns 

dv:Ch/TOPASChemistry/ChemicalStageTimeStepsHighEdges   = 2 1.0 2.5 ns 
dv:Ch/TOPASChemistry/ChemicalStageTimeStepsResolutions = 2 1.0 10  ps 

### What i ran to create the Phase Space file ###
## -- Source Varian ----------------------------------------------------------
# s:So/MySource/Type = "PhaseSpace"
# s:So/MySource/Component = "BeamPosition"
# s:So/MySource/PhaseSpaceFileName = "supportFiles/Varian_TrueBeam6MV_01"
# b:So/MySource/LimitedAssumeFirstParticleIsNewHistory = "true"
# b:So/MySource/LimitedAssumeEveryParticleIsNewHistory = "false"
# b:So/MySource/LimitedAssumePhotonIsNewHistory = "true"
# i:So/MySource/PhaseSpaceMultipleUse = 0
# i:So/MySource/NumberOfHistoriesInRun = 5000000
# b:So/MySource/PhaseSpacePreCheck = "false"
# u:So/MySource/PhaseSpaceScaleXPosBy = 0
# u:So/MySource/PhaseSpaceScaleYPosBy = 0
# u:So/MySource/PhaseSpaceScaleZPosBy = 0


# # ## -- Phase Space Scorer (e-) ----------------------------------------------------------
# s:Sc/eScorer/Quantity = "PhaseSpace"
# b:Sc/eScorer/OutputToConsole = "True"
# s:Sc/eScorer/OutputType = "ASCII" # "Binary", "ASCII," "Limited" or "ROOT"
# s:Sc/eScorer/Surface  = "Eppendorf/ZMinusSurface"
# s:Sc/eScorer/OutputFile = "ASCIIOutput_1gy_new"
# s:Sc/eScorer/IfOutputFileAlreadyExists   = "Overwrite"
# sv:Sc/eScorer/OnlyIncludeParticlesNamed = 2 "e-" "e+"
# #sv:Sc/MyScorer/OnlyIncludeParticlesCharged = 1 "Negative"
# s:Sc/eScorer/OnlyIncludeParticlesOfGeneration = "Secondary"
# b:Sc/eScorer/IncludeTOPASTime            = "True"
# b:Sc/eScorer/IncludeTimeOfFlight         = "True"
# b:Sc/eScorer/IncludeRunID                = "True"
# b:Sc/eScorer/IncludeEventID              = "True"
# b:Sc/eScorer/IncludeTrackID              = "True"
# b:Sc/eScorer/IncludeParentID             = "True"
# b:Sc/eScorer/IncludeCreatorProcess       = "True"
# b:Sc/eScorer/IncludeVertexInfo           = "True"
# b:Sc/eScorer/IncludeSeed                 = "True"
# #s:Sc/eScorer/OnlyIncludeParticlesGoing = "In"
# b:Sc/eScorer/PropagateToChildren = "True"

# s:Sc/Detetor/Component = "Eppendorf"
# s:Sc/Detetor/Quantity = "DoseToMedium"
# b:Sc/Detetor/OutputToConsole = "True"
# s:Sc/Detetor/OutputType = "CSV" # "Binary", "ASCII," "Limited" or "ROOT"
# s:Sc/Detetor/IfOutputFileAlreadyExists = "Overwrite"
# d:Sc/Detetor/RepeatSequenceUntilSumGreaterThan = 4 Gy
# b:Sc/Detetor/PropagateToChildren = "True"

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[jschuemann]

Hi Isabel,
there are some instances in chemistry that cause a seg fault. This is typically due to the underlying Geant4 code. We have added some functions to catch and reduce the seg faults, but not all.
I would suggest to use 4 runs of 1 Gy delivery and then add those up, if that is possible for your application.