[Simulation question]: source rundemos.csh problem // libG4Tree.so problem // unsure about how to use the nrtest for qc-topas-nbio #18

cecilianw01 · 2024-07-02T06:12:56Z

cecilianw01
Jul 2, 2024

Simulation question

Hello!

Problem that I encountered

I have finished installing the TOPAS-nBio via this guideline. But I am experiencing in some problem in running the source rundemos.csh

This is the error message I received

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/OpenTopas/OpenTOPAS-install$ source ~/.bashrc
(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/OpenTopas/OpenTOPAS-install$ source rundemos.csh
../../bin/topas: error while loading shared libraries: libG4Tree.so: cannot open shared object file: No such file or directory
.
.
.
Archive:  Abdomen.zip
  inflating: Abdomen/1.dcm           
  inflating: Abdomen/2.dcm           
  inflating: Abdomen/3.dcm           
  inflating: Abdomen/README.txt      
  inflating: Abdomen/rtdose.dcm      
../../bin/topas: error while loading shared libraries: libG4Tree.so: cannot open shared object file: No such file or directory

gzip: stdin: not in gzip format
tar: Child returned status 1
tar: Error is not recoverable: exiting now
../../bin/topas: error while loading shared libraries: libG4Tree.so: cannot open shared object file: No such file or directory
Archive:  DICOM_Box.zip
   creating: DICOM_Box/
  inflating: DICOM_Box/image000.dcm  
replace __MACOSX/DICOM_Box/._image000.dcm? [y]es, [n]o, [A]ll, [N]one, [r]ename: A
  inflating: __MACOSX/DICOM_Box/._image000.dcm  
  inflating: DICOM_Box/image001.dcm  
.
.
.
../../bin/topas: error while loading shared libraries: libG4Tree.so: cannot open shared object file: No such file or directory
../../bin/topas: error while loading shared libraries: libG4Tree.so: cannot open shared object file: No such file or directory
rm: cannot remove '*.csv': No such file or directory
../../bin/topas: error while loading shared libraries: libG4Tree.so: cannot open shared object file: No such file or directory
rm: cannot remove 'examples/*/NbParticlesInTime.txt': No such file or directory

Previous libG4Tree.so problem

I actually have addressed similar libG4Tree.so problem in the OpenTOPAS forum and the solution was to either run ~/shellScripts/topas QtShapeTest.txt or directly topas QtShapeTest.txt
However I am not sure how to use it with this issue

Previous similar rundemos problem

I found similar problem discussed previously here and I have tried to implement the solution with the qc-topas-nbio

What I have tried to do

This is the OpenTOPAS.json file that I created

{
	"name": "topas",
	"QT_QPA_PLATFORM_PLUGIN_PATH":"$HOME/software/OpenTopas/OpenTOPAS-install/Frameworks",
	"TOPAS_G4_DATA_DIR":"$HOME/software/OpenTopas/G4DATA",
	"LD_LIBRARY_PATH":"$HOME/software/OpenTopas/OpenTOPAS-install/lib:$LD_LIBRARY_PATH",
	"LD_LIBRARY_PATH":"$HOME/software/geant4/geant4-v11.1.3-install/lib:$LD_LIBRARY_PATH",
	"exe" : "$HOME/software/OpenTopas/OpenTOPAS-install/bin/topas"
}

This is the result I received

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/OpenTopas/qc-testsuite$ source ~/software/OpenTopas/OpenTOPAS-install/rundemos.csh
bash: cd: examples/TimeFeature: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: cd: ../UCSFETF: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: cd: ../SpecialComponents: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: cd: ../Nozzle: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: ../../bin/topas: No such file or directory
bash: cd: ../Patient: No such file or directory
unzip:  cannot find or open Abdomen.zip, Abdomen.zip.zip or Abdomen.zip.ZIP.
bash: ../../bin/topas: No such file or directory
tar (child): synthetic_lung.tar.bz2: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
bash: ../../bin/topas: No such file or directory
unzip:  cannot find or open DICOM_Box, DICOM_Box.zip or DICOM_Box.ZIP.
bash: ../../bin/topas: No such file or directory
bash: cd: ../TimeFeature: No such file or directory
bash: ../../bin/topas: No such file or directory
rm: cannot remove '*.csv': No such file or directory
bash: ../../bin/topas: No such file or directory
rm: cannot remove 'examples/*/NbParticlesInTime.txt': No such file or directory
(base) cecilia@cecilia-X570-AORUS-ELITE:~/software$ nrtest execute apps/OpenTOPAS.json tests/ -o benchmarks/today
ERROR: Could not find path: "tests/"
ERROR: Could not find path: "apps/OpenTOPAS.json"
Traceback (most recent call last):
  File "/home/cecilia/anaconda3/bin/nrtest", line 109, in <module>
    args.func(args)
  File "/home/cecilia/anaconda3/bin/nrtest", line 29, in execute
    ts = TestSuite.read_config(args.app, test_files, args.output)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/cecilia/anaconda3/lib/python3.11/site-packages/nrtest/testsuite.py", line 43, in read_config
    with open(app_config_path) as f:
         ^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'apps/OpenTOPAS.json'

Can anyone please help me how to solve this? I apologize for the long question. I am trying to provide as much detail as possible.

Thank you for your attention!

TOPAS-nBio category

Examples

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.

cecilianw01 · 2024-07-03T04:40:58Z

cecilianw01
Jul 3, 2024
Author

Hello!

I have found the solution to my initial problem, but I encountered a new issue.

Solution

Here's how I fixed the initial problem:

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software$ cd /home/cecilia/software/TOPAS-nBio
(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio$ source rundemos.sh

Turns out I was running the wrong file and I should make sure I am in the correct directory while executing the file. Actually I think the previous problem was related to rundemos.csh for OpenTOPAS instead of for TOPAS-nBio.

New Problem

After successfully running rundemos.sh for TOPAS-nBio, I encountered the following messages:

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio$ source rundemos.sh 
Topas quitting, unable to open parameter file:../../scorers/DNAScorerStepByStep.txt
--failed -- dna/CharltonDNA.txt
.
.
. **[ Several messages about TOPAS quitting due to unable to open parameter file ]**
.
.
.
Checking overlaps for volume MyCell/Mitochondria12:12 (G4Ellipsoid) ... 
-------- WWWW ------- G4Exception-START -------- WWWW -------
*** G4Exception : GeomVol1002
      issued by : G4PVPlacement::CheckOverlaps()
Overlap with volume already placed !
          Overlap is detected for volume MyCell/Mitochondria12:12 (G4Ellipsoid) with MyCell/Nucleus:0 (G4Orb)
          overlap at local point (0.00670083,-0.00276325,0.00237275) by 373.296 nm  (max of 319 cases)
NOTE: Reached maximum fixed number -1- of overlaps reports for this volume !
*** This is just a warning message. ***
-------- WWWW -------- G4Exception-END --------- WWWW -------
.
.
. **[ A very long series of messages about detected overlaps ]**
.
.
.
Topas quitting, unable to open parameter file:DBSCAN.txt
--failed -- DBSCAN.txt
.
.
. **[ Several messages about TOPAS quitting due to unable to open parameter file ]**
.
.
.
Topas quitting, unable to open parameter file:GvalueRevisedPhysicsChemistry.txt
--failed -- GvalueRevisedPhysicsChemistry.txt

I tried to run DNAScorerStepByStep.txt and it worked well, but when I tried to run DBSCAN.txt, it resulted in an error. Here is the terminal output:

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio/examples/scorers/DBSCAN$ ~/shellScripts/topas DBSCAN.txt

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: DBSCAN.txt

Geant4 Data directory has been specified by the
TOPAS_G4_DATA_DIR environment variable as /home/cecilia/software/OpenTopas/G4DATA

**************************************************************
 Geant4 version Name: geant4-11-01-patch-03 [MT]   (10-November-2023)
  << in Multi-threaded mode >> 
                       Copyright : Geant4 Collaboration
                      References : NIM A 506 (2003), 250-303
                                 : IEEE-TNS 53 (2006), 270-278
                                 : NIM A 835 (2016), 186-225
                             WWW : http://geant4.org/
**************************************************************

TOPAS is in MT mode, setting number of threads to: 1

TOPAS set the tolerances based on the World size to:
      Surface tolerance = 1e-08 nm, and radial tolerance = 1e-08 nm.
Checking overlaps for volume Detector:0 (G4Box) ... OK! 

Checking for Unused Components.
These are Components that were never built even though they were at least
partially defined in some parameters. This is not necessarily an error.
It may be an intentional choice to have these Component definitions handy for later use.
To turn off this check, set Ge/CheckForUnusedComponents to False
  No unused components were found.

/home/cecilia/shellScripts/topas: line 5:  4818 Segmentation fault      (core dumped) $HOME/software/OpenTopas/OpenTOPAS-install/bin/topas $1
(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio/examples/scorers/DBSCAN$

I have added the line b:Ge/CheckForUnusedComponents = "False" as recommended and a new error occurs

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio/examples/scorers/DBSCAN$ ~/shellScripts/topas DBSCAN.txt

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: DBSCAN.txt
.
.
.
/home/cecilia/shellScripts/topas: line 5: 10618 Segmentation fault      (core dumped) $HOME/software/OpenTopas/OpenTOPAS-install/bin/topas $1

Can anyone please help me resolve this issue? Thank you.

4 replies

JoseRamosMendez Jul 4, 2024
Maintainer

Regarding the rundemos see #10 (reply in thread).

Regarding DBSCAN, what is your OS? Also, have you run successfully any other TOPAS/example (not TOPAS-nBio)?

cecilianw01 Jul 5, 2024
Author

Hello Jose!

Thank you for your reply

Regarding the rundemos

I have seen the answer you provided here and have been trying to follow the instructions. However, I am not sure if what I did was correct. I have created the OpenTOPAS.json file, but I am not sure how to properly run it. Here is how my JSON file looks:

{
	"name": "topas",
	"QT_QPA_PLATFORM_PLUGIN_PATH":"$HOME/software/OpenTopas/OpenTOPAS-install/Frameworks",
	"TOPAS_G4_DATA_DIR":"$HOME/software/OpenTopas/G4DATA",
	"LD_LIBRARY_PATH":"$HOME/software/OpenTopas/OpenTOPAS-install/lib:$LD_LIBRARY_PATH",
	"LD_LIBRARY_PATH":"$HOME/software/geant4/geant4-v11.1.3-install/lib:$LD_LIBRARY_PATH",
	"exe" : "$HOME/software/OpenTopas/OpenTOPAS-install/bin/topas"
}

However, I feel like perhaps as long as my OpenTOPAS works well, maybe it is not a big problem and I can ignore problem this for now?

Regarding the DBSCAN

My OS is Ubuntu 18.04.6 LTS. I have run several codes with OpenTOPAS, and they worked well. Here is an example of my running result for QtShapeTest.txt

This is another example of me running TOPAS-nBio example Membrane.txt

This is the result when I try to run DBSCAN.txt and DBSCAN_VRT.txt

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio/examples/scorers/DBSCAN$ ~/shellScripts/topas DBSCAN.txt 

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: DBSCAN.txt

Geant4 Data directory has been specified by the
TOPAS_G4_DATA_DIR environment variable as /home/cecilia/software/OpenTopas/G4DATA

**************************************************************
 Geant4 version Name: geant4-11-01-patch-03 [MT]   (10-November-2023)
  << in Multi-threaded mode >> 
                       Copyright : Geant4 Collaboration
                      References : NIM A 506 (2003), 250-303
                                 : IEEE-TNS 53 (2006), 270-278
                                 : NIM A 835 (2016), 186-225
                             WWW : http://geant4.org/
**************************************************************

TOPAS is in MT mode, setting number of threads to: 1

TOPAS set the tolerances based on the World size to:
      Surface tolerance = 1e-08 nm, and radial tolerance = 1e-08 nm.
Checking overlaps for volume Detector:0 (G4Box) ... OK! 
/home/cecilia/shellScripts/topas: line 5:  6791 Segmentation fault      (core dumped) $HOME/software/OpenTopas/OpenTOPAS-install/bin/topas $1

For the file DBSCAN_VRT.txt, the geometry works well. However, when I tried to run it, it said Segmentation fault (core dumped):

(base) cecilia@cecilia-X570-AORUS-ELITE:~/software/TOPAS-nBio/examples/scorers/DBSCAN$ ~/shellScripts/topas DBSCAN_VRT.txt 

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: DBSCAN_VRT.txt

Geant4 Data directory has been specified by the
TOPAS_G4_DATA_DIR environment variable as /home/cecilia/software/OpenTopas/G4DATA

**************************************************************
 Geant4 version Name: geant4-11-01-patch-03 [MT]   (10-November-2023)
  << in Multi-threaded mode >> 
                       Copyright : Geant4 Collaboration
                      References : NIM A 506 (2003), 250-303
                                 : IEEE-TNS 53 (2006), 270-278
                                 : NIM A 835 (2016), 186-225
                             WWW : http://geant4.org/
**************************************************************

TOPAS is activating the Qt graphical user interface even though
you did not turn this feature on, as this is the only way to provide
your requested OpenGL graphics on your current operating system.
Available UI session types: [ Qt, tcsh, csh ]
TOPAS is in MT mode, setting number of threads to: 1

TOPAS set the tolerances based on the World size to:
      Surface tolerance = 1e-08 nm, and radial tolerance = 1e-08 nm.
Checking overlaps for volume Detector:0 (G4Box) ... OK! 

Checking for Unused Components.
These are Components that were never built even though they were at least
partially defined in some parameters. This is not necessarily an error.
It may be an intentional choice to have these Component definitions handy for later use.
To turn off this check, set Ge/CheckForUnusedComponents to False
  No unused components were found.

Default
### TsEmDNAPhysics Construct Processes 
Ts Rudd ionisation model is constructed 
This command is no longer relevant. There is no longer any limit on the
number of display lists - except, of course, the available memory in
your computer. Keep an eye on that. Good luck!
Pausing at Geant4 command line before starting run sequence.
Use Qt widgets to adjust TOPAS Parameters, Components, Scorers, etc.
Then hit the right arrow on the right side of the main menu to execute the TOPAS Run Sequence.
You can also enter Geant4 commands on this command line, but note that changes made
this way are outside of TOPAS control and can result in unreliable behavior.
 Changing export format to "jpg"
Checking overlaps for volume Detector:0 (G4Box) ... OK! 
/home/cecilia/shellScripts/topas: line 5:  6796 Segmentation fault      (core dumped) $HOME/software/OpenTopas/OpenTOPAS-install/bin/topas $1

Please let me know how to solve this. Thank you for your help and attention.

Best,
Cecilia

JoseRamosMendez Jul 13, 2024
Maintainer

Hi Cecilia.

It's a weird error. Your PC maybe running out of memory. But, would you try debugging it with e.g. valgrind? If you don't have, then you can install it with

sudo apt-get install valgrind

Then try, assuming you followed the same paths as shown in the QuickUser's guide for Ubuntu (it might take a while):

export TOPAS_G4_DATA_DIR=$HOME/Applications/GEANT4/G4DATA
export LD_LIBRARY_PATH=$HOME/Applications/TOPAS/OpenTOPAS-install/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$HOME/Applications/GEANT4/geant4-install/lib:$LD_LIBRARY_PATH

valgrind --leak-check=yes $HOME/Applications/TOPAS/OpenTOPAS-install/bin/topas DBSCAN.txt

Copy the terminal output and share it here.
Best!

cecilianw01 Jul 15, 2024
Author

Hello! Thank you for your answer. I have tried your suggestion and these are the terminal output. I have modified the directory path according to my computer directiory

(base) cecilia@cecilia-X570-AORUS-ELITE:~/topas_extensions/TOPAS-nBio/examples/scorers/DBSCAN$ export TOPAS_G4_DATA_DIR=$HOME/software/OpenTopas/G4DATA
(base) cecilia@cecilia-X570-AORUS-ELITE:~/topas_extensions/TOPAS-nBio/examples/scorers/DBSCAN$ export LD_LIBRARY_PATH=$HOME/software/OpenTopas/OpenTOPAS-install/lib:$LD_LIBRARY_PATH
(base) cecilia@cecilia-X570-AORUS-ELITE:~/topas_extensions/TOPAS-nBio/examples/scorers/DBSCAN$ export LD_LIBRARY_PATH=$HOME/software/geant4/geant4-v11.1.3-install/lib:$LD_LIBRARY_PATH

(base) cecilia@cecilia-X570-AORUS-ELITE:~/topas_extensions/TOPAS-nBio/examples/scorers/DBSCAN$ valgrind --leak-check=yes $HOME/software/OpenTopas/OpenTOPAS-install/bin/topas DBSCAN.txt
==8320== Memcheck, a memory error detector
==8320== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==8320== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==8320== Command: /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas DBSCAN.txt
==8320== 

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: DBSCAN.txt

Geant4 Data directory has been specified by the
TOPAS_G4_DATA_DIR environment variable as /home/cecilia/software/OpenTopas/G4DATA

**************************************************************
 Geant4 version Name: geant4-11-01-patch-03 [MT]   (10-November-2023)
  << in Multi-threaded mode >> 
                       Copyright : Geant4 Collaboration
                      References : NIM A 506 (2003), 250-303
                                 : IEEE-TNS 53 (2006), 270-278
                                 : NIM A 835 (2016), 186-225
                             WWW : http://geant4.org/
**************************************************************

TOPAS is in MT mode, setting number of threads to: 1

TOPAS set the tolerances based on the World size to:
      Surface tolerance = 1e-08 nm, and radial tolerance = 1e-08 nm.
Checking overlaps for volume Detector:0 (G4Box) ... OK! 

Checking for Unused Components.
These are Components that were never built even though they were at least
partially defined in some parameters. This is not necessarily an error.
It may be an intentional choice to have these Component definitions handy for later use.
To turn off this check, set Ge/CheckForUnusedComponents to False
  No unused components were found.

==8320== Invalid read of size 8
==8320==    at 0x6759A37: std::filesystem::__cxx11::path::~path() (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4vis_management.so)
==8320==    by 0xC357F1B: G4Analysis::GetBaseName(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC35AF97: G4BaseFileManager::GetFullFileName(G4String const&, bool) const (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC387006: G4RootFileManager::OpenFile(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC301C1B: G4ToolsAnalysisManager::OpenFileImpl(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC373B6F: G4VAnalysisManager::OpenFile(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0x54B56E: TsScoringManager::GetRootAnalysisManager() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x59E9CF: TsFileHub::InstantiateFile(TsParameterManager*, TsExtensionManager*, G4String, G4String, G4String, TsVFile*) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x553A3B: TsVNtupleScorer::TsVNtupleScorer(TsParameterManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, TsExtensionManager*, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x33760F: TsScoreDBSCAN::TsScoreDBSCAN(TsParameterManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, TsExtensionManager*, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x2F4684: TsExtensionManager::InstantiateScorer(TsParameterManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, G4String, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x55F91C: TsScoringHub::InstantiateScorer(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==  Address 0x2b is not stack'd, malloc'd or (recently) free'd
==8320== 
==8320== 
==8320== Process terminating with default action of signal 11 (SIGSEGV)
==8320==  Access not within mapped region at address 0x2B
==8320==    at 0x6759A37: std::filesystem::__cxx11::path::~path() (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4vis_management.so)
==8320==    by 0xC357F1B: G4Analysis::GetBaseName(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC35AF97: G4BaseFileManager::GetFullFileName(G4String const&, bool) const (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC387006: G4RootFileManager::OpenFile(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC301C1B: G4ToolsAnalysisManager::OpenFileImpl(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0xC373B6F: G4VAnalysisManager::OpenFile(G4String const&) (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4analysis.so)
==8320==    by 0x54B56E: TsScoringManager::GetRootAnalysisManager() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x59E9CF: TsFileHub::InstantiateFile(TsParameterManager*, TsExtensionManager*, G4String, G4String, G4String, TsVFile*) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x553A3B: TsVNtupleScorer::TsVNtupleScorer(TsParameterManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, TsExtensionManager*, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x33760F: TsScoreDBSCAN::TsScoreDBSCAN(TsParameterManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, TsExtensionManager*, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x2F4684: TsExtensionManager::InstantiateScorer(TsParameterManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, G4String, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x55F91C: TsScoringHub::InstantiateScorer(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsScoringManager*, G4String, G4String, G4String, bool) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==  If you believe this happened as a result of a stack
==8320==  overflow in your program's main thread (unlikely but
==8320==  possible), you can try to increase the size of the
==8320==  main thread stack using the --main-stacksize= flag.
==8320==  The main thread stack size used in this run was 8388608.
==8320== 
==8320== HEAP SUMMARY:
==8320==     in use at exit: 13,487,661 bytes in 149,049 blocks
==8320==   total heap usage: 301,489 allocs, 152,440 frees, 20,568,550 bytes allocated
==8320== 
==8320== 24 bytes in 1 blocks are definitely lost in loss record 2,405 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x4CE6D2: TsGraphicsManager::TsGraphicsManager(TsParameterManager*, TsGeometryManager*) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F5193: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 24 bytes in 1 blocks are definitely lost in loss record 2,406 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x4FCE49: TsModularPhysicsList::ActiveG4EmModelPerRegion(G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x4FE9E3: TsModularPhysicsList::AddModule(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x4F53CC: TsPhysicsManager::GetPhysicsList() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07CE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 24 bytes in 1 blocks are definitely lost in loss record 2,407 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x4FBA12: TsModularPhysicsList::SetCuts() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x7319DF1: G4RunManagerKernel::InitializePhysics() (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4run.so)
==8320==    by 0x72FAEA2: G4RunManager::InitializePhysics() (in /home/cecilia/software/geant4/geant4-v11.1.3-install/lib/libG4run.so)
==8320==    by 0x5B081E: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 24 bytes in 1 blocks are definitely lost in loss record 2,408 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x4CEDA5: TsGraphicsManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B08B8: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 24 bytes in 1 blocks are definitely lost in loss record 2,409 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x54C546: TsScoringManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5AEAA7: TsSequenceManager::Sequence() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B0A30: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 40 bytes in 1 blocks are definitely lost in loss record 6,643 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x2D594C: TsGenericComponent::Construct() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x27FB9D: TsVGeometryComponent::InstantiateAndConstructChild(G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x281049: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x26EA81: TsGeometryManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 40 bytes in 1 blocks are definitely lost in loss record 6,644 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x21281D: TsParameterFile::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x200920: TsParameterManager::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x4F524F: TsPhysicsManager::GetPhysicsList() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07CE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 40 bytes in 1 blocks are definitely lost in loss record 6,645 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x21281D: TsParameterFile::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x2128C9: TsParameterFile::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x200920: TsParameterManager::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x4F524F: TsPhysicsManager::GetPhysicsList() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07CE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 40 bytes in 1 blocks are definitely lost in loss record 6,646 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x223E30: TsStringVectorFromValue::GetStringVector() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x21287D: TsParameterFile::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x2128C9: TsParameterFile::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x200920: TsParameterManager::GetStringVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x4F524F: TsPhysicsManager::GetPhysicsList() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07CE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 48 bytes in 2 blocks are definitely lost in loss record 7,146 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x27C68E: TsVGeometryComponent::AddOpticalSurfaces() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x27FBEC: TsVGeometryComponent::InstantiateAndConstructChild(G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x281049: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x26EA81: TsGeometryManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 56 (24 direct, 32 indirect) bytes in 1 blocks are definitely lost in loss record 7,334 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x5C9BC6: TsSourceManager::Initialize(TsSequenceManager*) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5AEA9B: TsSequenceManager::Sequence() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B0A30: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 80 bytes in 1 blocks are possibly lost in loss record 9,343 of 14,882
==8320==    at 0x4C31B0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x1266ED36: ??? (in /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0.0.0)
==8320==    by 0x1266EF6A: __glDispatchInit (in /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0.0.0)
==8320==    by 0x12402018: ??? (in /usr/lib/x86_64-linux-gnu/libGLX.so.0.0.0)
==8320==    by 0x40108D2: call_init (dl-init.c:72)
==8320==    by 0x40108D2: _dl_init (dl-init.c:119)
==8320==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==8320==    by 0x1: ???
==8320==    by 0x1FFEFFFD22: ???
==8320==    by 0x1FFEFFFD5F: ???
==8320== 
==8320== 80 bytes in 1 blocks are possibly lost in loss record 9,344 of 14,882
==8320==    at 0x4C31B0F: malloc (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x1266ED36: ??? (in /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0.0.0)
==8320==    by 0x1266F13B: __glDispatchRegisterStubCallbacks (in /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0.0.0)
==8320==    by 0xFE2A40A: ??? (in /usr/lib/x86_64-linux-gnu/libGL.so.1.0.0)
==8320==    by 0x40108D2: call_init (dl-init.c:72)
==8320==    by 0x40108D2: _dl_init (dl-init.c:119)
==8320==    by 0x40010C9: ??? (in /lib/x86_64-linux-gnu/ld-2.27.so)
==8320==    by 0x1: ???
==8320==    by 0x1FFEFFFD22: ???
==8320==    by 0x1FFEFFFD5F: ???
==8320== 
==8320== 130 (24 direct, 106 indirect) bytes in 1 blocks are definitely lost in loss record 10,509 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x26985C: TsGeometryManager::GetChildComponentsOf(G4String&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x28100D: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x26EA81: TsGeometryManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 130 (24 direct, 106 indirect) bytes in 1 blocks are definitely lost in loss record 10,510 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x26985C: TsGeometryManager::GetChildComponentsOf(G4String&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x28100D: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x28A089: TsBox::Construct() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x27FB9D: TsVGeometryComponent::InstantiateAndConstructChild(G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x281049: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x26EA81: TsGeometryManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 130 (24 direct, 106 indirect) bytes in 1 blocks are definitely lost in loss record 10,511 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x26985C: TsGeometryManager::GetChildComponentsOf(G4String&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x28100D: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x2D6013: TsGenericComponent::Construct() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x27FB9D: TsVGeometryComponent::InstantiateAndConstructChild(G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x281049: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x26EA81: TsGeometryManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 150 (48 direct, 102 indirect) bytes in 2 blocks are definitely lost in loss record 10,680 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x27FC04: TsVGeometryComponent::InstantiateAndConstructChild(G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x281049: TsVGeometryComponent::InstantiateChildren() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x26EA81: TsGeometryManager::Initialize() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 152 bytes in 38 blocks are definitely lost in loss record 10,723 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x21049D: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FE790: TsParameterManager::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FF56C: TsParameterManager::TsParameterManager(int, char**, G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F485C: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 152 bytes in 38 blocks are definitely lost in loss record 10,724 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x21049D: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x210521: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FE790: TsParameterManager::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FF56C: TsParameterManager::TsParameterManager(int, char**, G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F485C: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 152 bytes in 38 blocks are definitely lost in loss record 10,725 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x21049D: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x210521: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x210521: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FE790: TsParameterManager::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FF56C: TsParameterManager::TsParameterManager(int, char**, G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F485C: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 456 bytes in 38 blocks are definitely lost in loss record 13,674 of 14,882
==8320==    at 0x4C3289F: operator new[](unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x26005C: TsIntegerVectorFromValue::GetIntegerVector() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x2104D1: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x210521: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x210521: TsParameterFile::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FE790: TsParameterManager::GetIntegerVector(G4String const&) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1FF56C: TsParameterManager::TsParameterManager(int, char**, G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F485C: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 906 (24 direct, 882 indirect) bytes in 1 blocks are definitely lost in loss record 14,046 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x4CDE8D: TsGraphicsManager::TsGraphicsManager(TsParameterManager*, TsGeometryManager*) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F5193: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 2,346 (24 direct, 2,322 indirect) bytes in 1 blocks are definitely lost in loss record 14,657 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x1FF3E7: TsParameterManager::TsParameterManager(int, char**, G4String) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F485C: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== 3,155 (24 direct, 3,131 indirect) bytes in 1 blocks are definitely lost in loss record 14,715 of 14,882
==8320==    at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)
==8320==    by 0x26DE72: TsGeometryManager::CheckForUnusedComponents() (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x5B07AE: TsSequenceManager::TsSequenceManager(TsParameterManager*, TsExtensionManager*, TsMaterialManager*, TsGeometryManager*, TsPhysicsManager*, TsVarianceManager*, TsFilterManager*, TsScoringManager*, TsGraphicsManager*, TsChemistryManager*, TsSourceManager*, int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1F522E: TsMain::TsMain(int, char**) (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320==    by 0x1D8862: main (in /home/cecilia/software/OpenTopas/OpenTOPAS-install/bin/topas)
==8320== 
==8320== LEAK SUMMARY:
==8320==    definitely lost: 1,456 bytes in 172 blocks
==8320==    indirectly lost: 6,787 bytes in 88 blocks
==8320==      possibly lost: 160 bytes in 2 blocks
==8320==    still reachable: 13,479,258 bytes in 148,787 blocks
==8320==                       of which reachable via heuristic:
==8320==                         newarray           : 17,168 bytes in 150 blocks
==8320==                         multipleinheritance: 280 bytes in 1 blocks
==8320==         suppressed: 0 bytes in 0 blocks
==8320== Reachable blocks (those to which a pointer was found) are not shown.
==8320== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==8320== 
==8320== For counts of detected and suppressed errors, rerun with: -v
==8320== ERROR SUMMARY: 25 errors from 25 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)

Since I usually run topas by using the shellScripts file, so I tried your suggestion as well but with the shellScripts.

(base) cecilia@cecilia-X570-AORUS-ELITE:~/topas_extensions/TOPAS-nBio/examples/scorers/DBSCAN$ valgrind --leak-check=yes $HOME/shellScripts/topas DBSCAN.txt
==8738== Memcheck, a memory error detector
==8738== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==8738== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info
==8738== Command: /home/cecilia/shellScripts/topas DBSCAN.txt
==8738== 

Welcome to TOPAS, Tool for Particle Simulation (Version 4.0)
Loading parameters starting from: DBSCAN.txt

Geant4 Data directory has been specified by the
TOPAS_G4_DATA_DIR environment variable as /home/cecilia/software/OpenTopas/G4DATA

**************************************************************
 Geant4 version Name: geant4-11-01-patch-03 [MT]   (10-November-2023)
  << in Multi-threaded mode >> 
                       Copyright : Geant4 Collaboration
                      References : NIM A 506 (2003), 250-303
                                 : IEEE-TNS 53 (2006), 270-278
                                 : NIM A 835 (2016), 186-225
                             WWW : http://geant4.org/
**************************************************************

TOPAS is in MT mode, setting number of threads to: 1

TOPAS set the tolerances based on the World size to:
      Surface tolerance = 1e-08 nm, and radial tolerance = 1e-08 nm.
Checking overlaps for volume Detector:0 (G4Box) ... OK! 

Checking for Unused Components.
These are Components that were never built even though they were at least
partially defined in some parameters. This is not necessarily an error.
It may be an intentional choice to have these Component definitions handy for later use.
To turn off this check, set Ge/CheckForUnusedComponents to False
  No unused components were found.

Segmentation fault (core dumped)
==8738== 
==8738== HEAP SUMMARY:
==8738==     in use at exit: 3,595 bytes in 90 blocks
==8738==   total heap usage: 102 allocs, 12 frees, 7,634 bytes allocated
==8738== 
==8738== LEAK SUMMARY:
==8738==    definitely lost: 0 bytes in 0 blocks
==8738==    indirectly lost: 0 bytes in 0 blocks
==8738==      possibly lost: 0 bytes in 0 blocks
==8738==    still reachable: 3,595 bytes in 90 blocks
==8738==         suppressed: 0 bytes in 0 blocks
==8738== Reachable blocks (those to which a pointer was found) are not shown.
==8738== To see them, rerun with: --leak-check=full --show-leak-kinds=all
==8738== 
==8738== For counts of detected and suppressed errors, rerun with: -v
==8738== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)

Thank you for your attention.

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[Simulation question]: source rundemos.csh problem // libG4Tree.so problem // unsure about how to use the nrtest for qc-topas-nbio #18

{{title}}

Replies: 1 comment 4 replies

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

[Simulation question]: source rundemos.csh problem // libG4Tree.so problem // unsure about how to use the nrtest for qc-topas-nbio #18

cecilianw01 Jul 2, 2024