Hi everyone!
This is my first post in the ROOT community and I want to thank you all for the help I get by reading the forum for years.
Now I success installing Garfieldpp on Archlinux from source, then when I run the example gem.c the simulation starts, it opens the ROOT visual interface too, but just after some seconds I got this strange C++ error:
/usr/include/c++/14.2.1/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>; reference = double&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
[1] 335004 IOT instruction (core dumped) ./gem
The previous lines contains - I think - the correct output of gem.c.
I tried searching online but I didn’t find anything helpful.
Do you know how I can solve this? Thank you!
Hello Mattia, probably @hschindl can help you with this.
Meanwhile, if you can provide a full stack trace that may help with debugging the issue.
Thank you @silverweed! The following are the output line of gem.c:
~/Documents/MC/Garfield Examples/Gem/build]$ ./gem
MediumMagboltz::SetComposition: Ar/CO2 (80/20)
MediumMagboltz::Mixer:
4000 linear energy steps between 0 and 40 eV.
ARGON ANISOTROPIC 2014
mass: 39.948 amu
ionisation threshold: 15.7596 eV
44 inelastic terms (44 excitations, 0 superelastic, 0 other)
CO2 2018 ANISOTROPIC
mass: 44.0095 amu
ionisation threshold: 13.776 eV
144 inelastic terms (0 excitations, 35 superelastic, 109 other)
MediumMagboltz::Mixer:
Lowest ionisation threshold in the mixture: 13.776 eV (CO2)
MediumMagboltz::Mixer:
Energy [eV] Collision Rate [ns-1]
2.50 1068.85
7.50 2892.41
12.50 5363.62
17.50 8777.02
22.50 11300.56
27.50 12660.82
32.50 12521.53
37.50 12101.91
MediumMagboltz::ComputePhotonCollisionTable:
Energy [eV] Mean free path [um]
1.00 ------------
3.00 ------------
5.00 ------------
7.00 288302.9619
9.00 3279.0615
11.00 23.1076
13.00 31.4118
15.00 145.1898
17.00 13.2429
19.00 11.1775
MediumMagboltz::EnablePenningTransfer:
Warning: present gas table has no ionisation rates.
Ignore this message if you are using microscopic tracking only.
MediumMagboltz::EnablePenningTransfer:
Penning transfer probability for 44 Ar excitation levels set to r = 0.51
MediumMagboltz::LoadMobility:
Read 36 values from file /home/okabe/garfield/install/share/Garfield/Data/IonMobility_Ar+_Ar.txt
ComponentAnsys123::Initialise:
Read properties of 3 materials from file MPLIST.lis.
Read 8758 elements from file ELIST.lis.
Highest node number: 14066
Background elements skipped: 0
Read 14066 nodes from file NLIST.lis.
Read 14066 potentials from file PRNSOL.lis.
ComponentAnsys123::Prepare:
Caching the bounding boxes of all elements... done.
Initialized tetrahedral tree.
ComponentAnsys123::PrintRange:
Dimensions of the elementary block
0 < x < 0.007 cm,
0 < y < 0.0121244 cm,
-0.1 < z < 0.1 cm,
-200 < V < 350 V.
Periodicities
x: mirror with length 0.007 cm
y: mirror with length 0.0121244 cm
z: none
ComponentAnsys123::SetGas: Associating material 1 with Ar/CO2.
ComponentAnsys123::PrintMaterials:
Currently 3 materials are defined.
Index Permittivity Resistivity Notes
0 1e+10 0
1 1 -1 Ar/CO2, drift medium, ionisable (drift medium)
2 4 -1
/usr/include/c++/14.2.1/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>; reference = double&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
[1] 468606 IOT instruction (core dumped) ./gem
I am using ArchLinux with KDE Plasma (Wayland, not X11 if ti has something to do with it) on a Dell laptop.
CPU: 11th Gen Intel(R) Core™ i7-11800H
GPU: NVIDIA RTX 3050Ti Laptop
I’ve used ROOT and Geant4 for months without any problem. Geant4 and Garifled are source installed, while ROOT by the AUR package (maybe I will change it to a source installation too).
The only one problem I have with ROOT is with the X11 (–web=off option) visualization that does not let me change the font format, so that I read nothing of the menu…
For Garfield I’ve just specified the installation folder to be:
-DCMAKE_INSTALL_PREFIX=$GARFIELD_HOME/install
I sourced the .sh file too.
Thank you for the help again!
EDIT: I forgot to say that I found the same C++ library problem on another software’s forum, I understand that - perhaps - there is a default CXXFLAGS option in conflict with Garfield.
Hi,
thanks for reporting this! The message seems to suggest that there is a bug somewhere in the code (trying to access an element greater than the size of the vector). Could you try to run gdb to see where this happens?
Hi,
if I did it correctly this is the only error:
/usr/include/c++/14.2.1/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>; reference = double&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
Program received signal SIGABRT, Aborted.
Downloading 4.06 K source file /usr/src/debug/glibc/glibc/nptl/pthread_kill.c
__pthread_kill_implementation (threadid=<optimized out>, signo=signo@entry=6,
no_tid=no_tid@entry=0) at pthread_kill.c:44
44 return INTERNAL_SYSCALL_ERROR_P (ret) ? INTERNAL_SYSCALL_ERRNO (ret) : 0;
Hi,
thanks a lot and sorry for my late reply! Could you rebuild the project in DEBUG mode and try again?
Hi,
I really appreciate your help. I’m quite a newbie about debugging. Do you mean running cmake in debug mode? How can I do it?
Hi,
yes, exactly; I meant add -DCMAKE_BUILD_TYPE=Debug or -DCMAKE_BUILD_TYPE= RelWithDebInfo when you run cmake to build Garfield++.
okay then I ran cmake -DCMAKE_BUILD_TYPE=Debug .., ran make and when I execute with gdb I get the exact same message I sent before:
/usr/include/c++/14.2.1/bits/stl_vector.h:1130: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = double; _Alloc = std::allocator<double>; reference = double&; size_type = long unsigned int]: Assertion '__n < this->size()' failed.
Program received signal SIGABRT, Aborted.
__pthread_kill_implementation (threadid=<optimized out>, signo=signo@entry=6, no_tid=no_tid@entry=0) at pthread_kill.c:44
44 return INTERNAL_SYSCALL_ERROR_P (ret) ? INTERNAL_SYSCALL_ERRNO (ret) : 0;
However, I noticed that if I set to false this boolean (that originally is true) around line 70 of the gem example:
meshView.SetFillMesh(false);
it works fine. The only difference is on the electric potential plot, since the gray trapezoids are not filled while they should be:
Thanks a lot! That’s already very helpful; I will take a look if I see something suspicious in this class…
Oh furthermore, my colleague has a Rocky Linux virtual machine with C++ version 11 (mine is 14.2.1), I help him installing garfield and it works perfectly fine! 
It could be a specific problem of my gcc version… I’ll try to install the v11 too to test this theory.
