[Gate-users] Problem running GATE and ROOT with regularMatrix argument
shahrokh nasseri
shahrokh.nasseri at gmail.com
Sun Aug 22 11:50:50 CEST 2010
Dear all users,
I am having about regularMatrix argument in GATE4.0.0. I installed
sucessfully clhep-2.0.3.2, gate.4.0.0, geant4.9.1.p03 and
root_v5.27.04.Linux-slc5-gcc3.4 (binary root). Also I add the following
variables to env_gate.sh in my computer (scientific linux 5 and gcc (GCC)
4.1.2 20080704 (Red Hat 4.1.2-46)):
export GATEHOME=/home/sn2/simulation/gate4.0.0/gate_v4.0.0
export G4INSTALL=/home/sn2/simulation/geant4.9.1.p03/geant4.9.1.p03
export G4INSTALL=/home/sn2/simulation/geant4.9.1.p03/geant4.9.1.p03
export G4VERSION=9.1
export ROOTSYS=/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root
export PATH=$PATH:$ROOTSYS/bin:$GATEHOME/bin/Linux-g++
export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib:/home/sn2/simulation/clhep-2.0.3.2/InstallFolder/lib
when I used compressedMatrix in the following command, all things are good.
/gate/world/daughters/insert compressedMatrix
When I used regularMatrix (/gate/world/daughters/insert regularMatrix), I
get the following error messages:
...
========= Table of registered couples ==============================
Index : 0 used in the geometry : Yes recalculation needed : No
Material : Air
Range cuts : gamma 0.000e+00 fm e- 1.000e+03 km e+
1.000e+00 mm
Energy thresholds : gamma 9.900e+02 eV e- 2.880e+295 J e+
9.900e+02 eV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 1 used in the geometry : Yes recalculation needed : No
Material : Lead
Range cuts : gamma 0.000e+00 fm e- 1.000e+03 km e+
1.000e+00 mm
Energy thresholds : gamma 9.900e+02 eV e- 2.880e+295 J e+
1.280e+00 MeV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 2 used in the geometry : Yes recalculation needed : No
Material : Al_Pb
Range cuts : gamma 0.000e+00 fm e- 1.000e+03 km e+
1.000e+00 mm
Energy thresholds : gamma 9.900e+02 eV e- 2.880e+295 J e+
3.106e+00 MeV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 3 used in the geometry : Yes recalculation needed : No
Material : NaI
Range cuts : gamma 0.000e+00 fm e- 1.000e+03 km e+
1.000e+00 mm
Energy thresholds : gamma 9.900e+02 eV e- 2.880e+295 J e+
5.894e+02 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 4 used in the geometry : Yes recalculation needed : No
Material : Quartz
Range cuts : gamma 0.000e+00 fm e- 1.000e+03 km e+
1.000e+00 mm
Energy thresholds : gamma 9.900e+02 eV e- 2.880e+295 J e+
5.147e+02 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
Index : 5 used in the geometry : Yes recalculation needed : No
Material : Glass
Range cuts : gamma 0.000e+00 fm e- 1.000e+03 km e+
1.000e+00 mm
Energy thresholds : gamma 9.900e+02 eV e- 2.880e+295 J e+
5.680e+02 keV
Region(s) which use this couple :
DefaultRegionForTheWorld
====================================================================
WARNING: The scene, "scene-0", of viewer "viewer-0 (G4HepRepFile)"
of scene handler "scene-handler-0" has changed. To see effect,
"/vis/viewer/select viewer-0" and "/vis/viewer/rebuild".
*** Break *** segmentation violation
===========================================================
There was a crash (#7 0x0031dc40 in SigHandler () from
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so).
This is the entire stack trace of all threads:
===========================================================
#0 0x00dd2402 in __kernel_vsyscall ()
#1 0x02fd3613 in __waitpid_nocancel () from /lib/i686/nosegneg/libc.so.6
#2 0x02f774fb in do_system () from /lib/i686/nosegneg/libc.so.6
#3 0x00dbcd1d in system () from /lib/i686/nosegneg/libpthread.so.0
#4 0x0031b433 in TUnixSystem::Exec () from
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
#5 0x0032142b in TUnixSystem::StackTrace () from
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
#6 0x0031dbb2 in TUnixSystem::DispatchSignals () from
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
#7 0x0031dc40 in SigHandler () from
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
#8 0x0031cebd in sighandler () from
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
#9 <signal handler called>
#10 0x0892a418 in G4VEmModel::CrossSectionPerVolume ()
#11 0x0892d014 in G4VEmProcess::PostStepGetPhysicalInteractionLength ()
#12 0x08900615 in G4SteppingManager::DefinePhysicalStepLength ()
#13 0x08901d91 in G4SteppingManager::Stepping ()
#14 0x088f152d in G4TrackingManager::ProcessOneTrack ()
#15 0x088e224e in G4EventManager::DoProcessing ()
#16 0x0854895f in G4RunManager::DoEventLoop ()
#17 0x08547d55 in G4RunManager::BeamOn ()
#18 0x081e958f in GateApplicationMgr::StartDAQ ()
#19 0x082393dd in GateApplicationMgrMessenger::SetNewValue ()
#20 0x08a824b1 in G4UIcommand::DoIt ()
#21 0x08a8a266 in G4UImanager::ApplyCommand ()
#22 0x08a95ed4 in G4UIbatch::ExecCommand ()
#23 0x08a97774 in G4UIbatch::SessionStart ()
#24 0x08a878f1 in G4UImanager::ExecuteMacroFile ()
#25 0x08a980d2 in G4UIcontrolMessenger::SetNewValue ()
#26 0x08a824b1 in G4UIcommand::DoIt ()
#27 0x08a8a266 in G4UImanager::ApplyCommand ()
#28 0x085217eb in G4UIterminal::ExecuteCommand ()
#29 0x08521330 in G4UIterminal::SessionStart ()
#30 0x081e756c in main ()
===========================================================
The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#10 0x0892a418 in G4VEmModel::CrossSectionPerVolume ()
#11 0x0892d014 in G4VEmProcess::PostStepGetPhysicalInteractionLength ()
#12 0x08900615 in G4SteppingManager::DefinePhysicalStepLength ()
#13 0x08901d91 in G4SteppingManager::Stepping ()
#14 0x088f152d in G4TrackingManager::ProcessOneTrack ()
#15 0x088e224e in G4EventManager::DoProcessing ()
#16 0x0854895f in G4RunManager::DoEventLoop ()
#17 0x08547d55 in G4RunManager::BeamOn ()
#18 0x081e958f in GateApplicationMgr::StartDAQ ()
#19 0x082393dd in GateApplicationMgrMessenger::SetNewValue ()
#20 0x08a824b1 in G4UIcommand::DoIt ()
#21 0x08a8a266 in G4UImanager::ApplyCommand ()
#22 0x08a95ed4 in G4UIbatch::ExecCommand ()
#23 0x08a97774 in G4UIbatch::SessionStart ()
#24 0x08a878f1 in G4UImanager::ExecuteMacroFile ()
#25 0x08a980d2 in G4UIcontrolMessenger::SetNewValue ()
#26 0x08a824b1 in G4UIcommand::DoIt ()
#27 0x08a8a266 in G4UImanager::ApplyCommand ()
#28 0x085217eb in G4UIterminal::ExecuteCommand ()
#29 0x08521330 in G4UIterminal::SessionStart ()
#30 0x081e756c in main ()
===========================================================
WARNING - Attempt to delete the physical volume store while geometry closed
!
WARNING - Attempt to delete the logical volume store while geometry closed !
WARNING - Attempt to delete the solid store while geometry closed !
WARNING - Attempt to delete the region store while geometry closed !
*** glibc detected *** ./Gate: double free or corruption (!prev): 0x0a858e20
***
======= Backtrace: =========
/lib/i686/nosegneg/libc.so.6[0x2fab1d5]
/lib/i686/nosegneg/libc.so.6(cfree+0x59)[0x2fab619]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0x7d46581]
./Gate(_ZN18G4LossTableManagerD1Ev+0x2d)[0x892950d]
/lib/i686/nosegneg/libc.so.6(exit+0xe9)[0x2f6d0f9]
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so(_ZN11TUnixSystem4ExitEib+0x97)[0x31b52f]
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so(_ZN11TUnixSystem15DispatchSignalsE8ESignals+0x159)[0x31dc05]
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so[0x31dc40]
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so[0x31cebd]
[0xdd2420]
./Gate(_ZN12G4VEmProcess36PostStepGetPhysicalInteractionLengthERK7G4TrackdP16G4ForceCondition+0x714)[0x892d014]
./Gate(_ZN17G4SteppingManager24DefinePhysicalStepLengthEv+0x75)[0x8900615]
./Gate(_ZN17G4SteppingManager8SteppingEv+0x1e1)[0x8901d91]
./Gate(_ZN17G4TrackingManager15ProcessOneTrackEP7G4Track+0x11d)[0x88f152d]
./Gate(_ZN14G4EventManager12DoProcessingEP7G4Event+0x4ce)[0x88e224e]
./Gate(_ZN12G4RunManager11DoEventLoopEiPKci+0xaf)[0x854895f]
./Gate(_ZN12G4RunManager6BeamOnEiPKci+0x65)[0x8547d55]
./Gate(_ZN18GateApplicationMgr8StartDAQEv+0x1bf)[0x81e958f]
./Gate(_ZN27GateApplicationMgrMessenger11SetNewValueEP11G4UIcommand8G4String+0x11d)[0x82393dd]
./Gate(_ZN11G4UIcommand4DoItE8G4String+0x8f1)[0x8a824b1]
./Gate(_ZN11G4UImanager12ApplyCommandEPKc+0x4d6)[0x8a8a266]
./Gate(_ZN9G4UIbatch11ExecCommandERK8G4String+0x34)[0x8a95ed4]
./Gate(_ZN9G4UIbatch12SessionStartEv+0xf4)[0x8a97774]
./Gate(_ZN11G4UImanager16ExecuteMacroFileEPKc+0x41)[0x8a878f1]
./Gate(_ZN20G4UIcontrolMessenger11SetNewValueEP11G4UIcommand8G4String+0xf2)[0x8a980d2]
./Gate(_ZN11G4UIcommand4DoItE8G4String+0x8f1)[0x8a824b1]
./Gate(_ZN11G4UImanager12ApplyCommandEPKc+0x4d6)[0x8a8a266]
./Gate(_ZN12G4UIterminal14ExecuteCommandE8G4String+0x3b)[0x85217eb]
./Gate(_ZN12G4UIterminal12SessionStartEv+0x50)[0x8521330]
./Gate(main+0x46c)[0x81e756c]
/lib/i686/nosegneg/libc.so.6(__libc_start_main+0xdc)[0x2f56e9c]
./Gate(_ZN10TCanvasImp8StreamerER7TBuffer+0x39)[0x81e6301]
======= Memory map: ========
00110000-00733000 r-xp 00000000 08:09 29363634
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
00733000-00751000 rw-p 00622000 08:09 29363634
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCore.so
00751000-007c8000 rw-p 00751000 00:00 0
007c8000-00908000 r-xp 00000000 08:09 29363675
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libGraf.so
00908000-00910000 rw-p 00140000 08:09 29363675
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libGraf.so
00910000-00918000 rw-p 00910000 00:00 0
00918000-0093f000 r-xp 00000000 08:09 29363766
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libRint.so
0093f000-00940000 rw-p 00027000 08:09 29363766
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libRint.so
00940000-00941000 rw-p 00940000 00:00 0
00941000-00943000 r-xp 00000000 08:09 3572564 /lib/libdl-2.5.so
00943000-00944000 r--p 00001000 08:09 3572564 /lib/libdl-2.5.so
00944000-00945000 rw-p 00002000 08:09 3572564 /lib/libdl-2.5.so
00945000-0094d000 r-xp 00000000 08:09 15991280 /usr/lib/libSM.so.6.0.0
0094d000-0094e000 rw-p 00007000 08:09 15991280 /usr/lib/libSM.so.6.0.0
0094e000-00968000 r-xp 00000000 08:09 3572526 /lib/ld-2.5.so
00968000-00969000 r--p 00019000 08:09 3572526 /lib/ld-2.5.so
00969000-0096a000 rw-p 0001a000 08:09 3572526 /lib/ld-2.5.so
0096a000-00cdf000 r-xp 00000000 08:09 29363695
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libHist.so
00cdf000-00cf2000 rw-p 00374000 08:09 29363695
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libHist.so
00cf2000-00cf5000 rw-p 00cf2000 00:00 0
00cf5000-00da7000 r-xp 00000000 08:09 29363669
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libGpad.so
00da7000-00dad000 rw-p 000b1000 08:09 29363669
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libGpad.so
00dad000-00daf000 rw-p 00dad000 00:00 0
00daf000-00dc3000 r-xp 00000000 08:09 3572565 /lib/i686/nosegneg/
libpthread-2.5.so
00dc3000-00dc4000 r--p 00013000 08:09 3572565 /lib/i686/nosegneg/
libpthread-2.5.so
00dc4000-00dc5000 rw-p 00014000 08:09 3572565 /lib/i686/nosegneg/
libpthread-2.5.so
00dc5000-00dc7000 rw-p 00dc5000 00:00 0
00dc7000-00dce000 r-xp 00000000 08:09 24816295 /usr/lib/libdrm.so.2.0.0
00dce000-00dcf000 rw-p 00006000 08:09 24816295 /usr/lib/libdrm.so.2.0.0
00dcf000-00dd1000 r-xp 00000000 08:09 15991263 /usr/lib/libXau.so.6.0.0
00dd1000-00dd2000 rw-p 00001000 08:09 15991263 /usr/lib/libXau.so.6.0.0
00dd2000-00dd3000 r-xp 00dd2000 00:00 0 [vdso]
00dd3000-00fed000 r-xp 00000000 08:09 29363630
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCint.so
00fed000-00ff1000 rw-p 0021a000 08:09 29363630
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libCint.so
00ff1000-0138c000 rw-p 00ff1000 00:00 0
0138c000-0148b000 r-xp 00000000 08:09 15991265 /usr/lib/libX11.so.6.2.0
0148b000-0148f000 rw-p 000ff000 08:09 15991265 /usr/lib/libX11.so.6.2.0
0148f000-014a6000 r-xp 00000000 08:09 15991279 /usr/lib/libICE.so.6.3.0
014a6000-014a7000 rw-p 00016000 08:09 15991279 /usr/lib/libICE.so.6.3.0
014a7000-014a9000 rw-p 014a7000 00:00 0
014a9000-01664000 r-xp 00000000 08:09 29363707
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libMathCore.so
01664000-0166e000 rw-p 001ba000 08:09 29363707
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libMathCore.so
0166e000-01671000 rw-p 0166e000 00:00 0
01671000-01765000 r-xp 00000000 08:09 29363728
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libNet.so
01765000-0176c000 rw-p 000f4000 08:09 29363728
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libNet.so
0176c000-0176d000 rw-p 0176c000 00:00 0
0176d000-017ad000 r-xp 00000000 08:09 29363799
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libThread.so
017ad000-017b0000 rw-p 0003f000 08:09 29363799
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libThread.so
01b36000-01d34000 r-xp 00000000 08:09 29363711
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libMatrix.so
01d34000-01d3b000 rw-p 001fe000 08:09 29363711
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libMatrix.so
01d3b000-01d3d000 rw-p 01d3b000 00:00 0
02254000-022be000 r-xp 00000000 08:09 15991350 /usr/lib/libGL.so.1.2
022be000-022c1000 rw-p 00069000 08:09 15991350 /usr/lib/libGL.so.1.2
022c1000-022c2000 rw-p 022c1000 00:00 0
0271e000-0275e000 r-xp 00000000 08:09 15991346 /usr/lib/libncurses.so.5.5
0275e000-02766000 rw-p 00040000 08:09 15991346 /usr/lib/libncurses.so.5.5
02766000-02767000 rw-p 02766000 00:00 0
02792000-0290d000 r-xp 00000000 08:09 29363768
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libRIO.so
0290d000-02911000 rw-p 0017b000 08:09 29363768
/home/sn2/simulation/root_v5.27.04.Linux-slc5-gcc3.4/root/lib/libRIO.so
02911000-02913000 rw-p 02911000 00:00 0
02a14000-02a2a000 r-xp 00000000 08:09 24815724 /Aborted
[sn2 at localhost Linux-g++]$
Please help me,
thanks a lot
Shahrokh
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