[Run issue]: run nuclues related model core

[nknanfeng]

Contact Details

1569911051@qq.com

What was the issue?

I am using the following TOPAS script to simulate a volume source placed in the cytoplasm. When I set RunInHistory to a level of 1,000,000, I encounter a segmentation fault. Based on the collected core dump information, the issue seems related to the physicochemical module.

Interestingly, when I replace the physicochemical module with the one from the nucleus example, the simulation runs smoothly for a 1,000,000-level RunInHistory. Additionally, increasing the cytoplasm's volume range also avoids the segmentation fault.

Could this issue be related to an incorrect use of the physicochemical module in this context? Or is it possible that the module is not compatible with the cytoplasm model in this example?

The TsEllipsoidalShell is a custom implementation I created for an ellipsoidal shell geometry model. The current shape of the cytoplasm is a spherical shell with an inner radius of 4.65 µm and an outer radius of 9.99 µm

I would greatly appreciate your insights on this matter.
cell_topas.txt

TOPAS-nBio category

Example

Version

3.0

What Operative System (OS) are you running on?

No response

Relevant log output

#0  0x00007f226c8fe7db in G4IT::operator[](int) const () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#1  0x000055e1c23fec54 in G4KDNode<G4IT>::operator[] (this=<optimized out>, i=<optimized out>) at /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/include/Geant4/G4KDNode.hh:149
#2  0x000055e1c240202c in G4KDNode_Base::FindParent<G4Molecule> (this=this@entry=0x7f22519e4688, x0=...) at /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/include/Geant4/G4KDNode.icc:80
#3  0x000055e1c2402063 in G4KDNode_Base::Insert<G4Molecule> (this=0x7f22519e4688, point=point@entry=0x7f2251b133e0)
    at /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/include/Geant4/G4KDNode.icc:93
#4  0x000055e1c2402112 in G4KDTree::Insert<G4Molecule> (this=0x7f22519decc0, pos=pos@entry=0x7f2251b133e0) at /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/include/Geant4/G4KDTree.icc:77
#5  0x000055e1c2402486 in G4ITFinder<G4Molecule>::Push (this=0x7f2251abd350, track=<optimized out>) at /usr/include/c++/9/bits/stl_tree.h:319
#6  0x00007f226c8587e3 in G4DNAMolecularReaction::MakeReaction(G4Track const&, G4Track const&) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#7  0x00007f226c857a16 in G4DNAMolecularReaction::FindReaction(G4ITReactionSet*, double, double, bool) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#8  0x00007f226c901486 in G4ITModelProcessor::ComputeTrackReaction(G4ITStepStatus, double, double, double, bool, double, G4UserTimeStepAction*, int) ()
   from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#9  0x00007f226c958638 in G4Scheduler::Stepping() () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#10 0x00007f226c959c39 in G4Scheduler::DoProcess() () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#11 0x00007f226c959f0f in G4Scheduler::SynchronizeTracks() () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#12 0x00007f226c95a0d9 in G4Scheduler::Process() () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#13 0x00007f226c8d235e in G4DNAChemistryManager::Run() () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4processes.so
#14 0x000055e1c25dbaca in TsStackingAction::NewStage (this=0x7f22501f4c40) at /home/tdw/OpenTOPAS/sequence/TsStackingAction.cc:99
#15 0x00007f226de4dbd6 in G4StackManager::PopNextTrack(G4VTrajectory**) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4event.so
#16 0x00007f226de0925c in G4EventManager::DoProcessing(G4Event*) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4event.so
#17 0x00007f226df1c1fc in G4WorkerRunManager::DoEventLoop(int, char const*, int) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4run.so
#18 0x00007f226dece902 in G4RunManager::BeamOn(int, char const*, int) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4run.so
#19 0x00007f226df1f7eb in G4WorkerRunManager::DoWork() () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4run.so
#20 0x00007f226dec505e in G4MTRunManagerKernel::StartThread(G4WorkerThread*) () from /home/tdw/Applications/GEANT4/geant4-v11.1.3/geant4-install/lib/libG4run.so
#21 0x00007f226a08adf4 in ?? () from /lib/x86_64-linux-gnu/libstdc++.so.6
#22 0x00007f2269e2d609 in start_thread (arg=<optimized out>) at pthread_create.c:477
#23 0x00007f2269d52353 in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95

Code of Conduct

• I agree to follow this project's Code of Conduct

Attestation

• I testify that I have fully read the bug reporting guideline beforehand.