Molecular_dna Root File Generation Error

Getting Started
1

When running a slightly edited version of the molecular_dna’s human_cell.mac example, I have been consistently running into a problem whereby the application stops running when it generates some of the molecular_dna threads (just gets stuck at generating one of them). This is happening regardless of the number of threads or the number of events being run. The executable file being built is the exact same as the one in the molecular_dna example and works for all macro examples provided out of the box.

I am currently running this Geant4 11.2.2 on a Windows 11 System with 8GB of RAM and
Intel Core i5-1035G1 CPU.

My macro file that I am attempting to run is:

/process/dna/e-SolvationSubType Meesungnoen2002

# print macro commands on screen and save run history for all runs
/control/verbose 1
/control/saveHistory

/chem/activate true

# setting up world with cells
/world/worldSize 1000 um
/cell/radiusSize 500 500 500 um
/scheduler/endTime 5.0 ns
/scheduler/maxNullTimeSteps 10000000
/dnageom/radicalKillDistance 9 nm
/dnageom/interactionDirectRange 3.5 angstrom

# DNA Geometry Model 
/dnageom/definitionFile geometries/cube-centred-X-8.txt
/dnageom/placementVolume turn geometries/turned_solenoid_750_withHistone.txt
/dnageom/placementVolume turntwist geometries/turned_twisted_solenoid_750_withHistone.txt true
/dnageom/placementVolume straight geometries/straight_solenoid_750_withHistone.txt

# DNA Damage Model
/dnadamage/directDamageLower 5 eV
/dnadamage/directDamageUpper 37.5 eV

/dnadamage/indirectOHBaseChance 1.0
/dnadamage/indirectOHStrandChance 0.405
/dnadamage/inductionOHChance 0.00

/dnadamage/indirectHBaseChance 1.0
/dnadamage/indirectHStrandChance 0.0
/dnadamage/inductionHChance 0.00

/dnadamage/indirectEaqBaseChance 1.0
/dnadamage/indirectEaqStrandChance 0.0
/dnadamage/inductionEaqChance 0.00

# Add the dna to the cell 
/chromosome/add cell ellipse 7005 2500 5300 112061.6 0 0 nm 0 0 0

/run/initialize 

# source conditions, spherical output:
/gps/particle alpha
/gps/pos/type Volume
/gps/pos/shape Sphere
/gps/pos/centre 0 0 0 um
/gps/pos/radius 0.1 um
/gps/ang/type iso

# Gaussian energy distribution 
/gps/ene/type Gauss
/gps/ene/mono 7.1 MeV
/gps/ene/sigma 0.43333 MeV

/run/beamOn 100

Is there anything that I am missing?

2

I’m having a similar problem.

3

This might be related to the issue reported in this thread: Download geant4.11.2

@ngoc could you take a look please?

4

Thanks @bmorgan ! we are testing on this. Let me ping @mdjordje @sincerti !

5

Im not sure how long a sim should take but, typically, I get stuck here:

Adding task 0 to task-group…
G4WT1 > ### Run 0 starts on worker thread 1.
G4WT1 > AnalysisManager::Initialize() GetRunID : 0
G4WT1 > … set ntuple merging row mode : row-wise - done
G4WT1 > … create file : molecular-dna_t1.root - done
G4WT1 > … open analysis file : molecular-dna.root - done
G4WT1 > … open analysis file : molecular-dna_t1.root - done
G4WT1 > → Event 0 starts with initial seeds (13049039,61775110).

6

Hello,

I tested the example with your macro on my MacBookPro, and it went ok fine for the first trial, then it crashed twice with the Fatal exception:

G4WT1 > 
-------- EEEE ------- G4Exception-START -------- EEEE -------
*** G4Exception : ConstructTimeStepModel
      issued by : ChemistryListConstructTimeStepModel
This example uses only IRT_syn
*** Fatal Exception *** core dump ***
G4WT1 > G4Track (0x15985c020) - track ID = 2, parent ID = 1

Also, when monitoring memory usage, the used memory increased up to > 8 GB.

Could you try to change your configuration to be less memory requiring ?

Best regards,

7

Hi Ivana

I’m not sure whom you’re replying to but my run seems to have completed successfully (I’m not sure what I’m looking for but it hasn’t raised any fatal errors). Total time for run for one alpha particle with energy 0.5 MeV approx. 36 hours

See attached file for console output subsequent to that which I posted above.

Regards

Tim

Console_Output_Successful_Run.txt (5.8 KB)

8

Hi @ivana
I believe that you are using the G4.11.3 beta version. I am checking this issue.

9

At hight LET, this application is not efficient.

10

I was testing with the current Geant4 development version.

11

Thanks @ivana ! can add this commande line in macro ? This new commande to choose chemistry models

Chemistry: selection of IRT_syn

/process/chem/TimeStepModel IRT_syn

12

Dear,

Can you give more info about the stop ? Because, i am running the example using your macro. It works even the simulation time is long.

13

Thanks Hoang.

Regards

Tim

14

Ok, this fixed the exception, however the user’s macro did not finish in 3 hours of running, so I stopped the process. The memory usegae was about 16 GB.

15

Thanks @ivana ! I will update the chemsitry model to improve the performance

16

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