[Gate-users] Problem running GATE and ROOT with regularMatrix argument
shahrokh nasseri
shahrokh.nasseri at gmail.com
Sun Aug 22 16:34:24 CEST 2010
Hi,
Dear Simon
Thanks a lot for your help. Unfortunately I want to use visualization
option in GATE because I need to inquiry and tracking primary
particles into voxellized phantom and voxellized source(interfile).
I have some problem to get some projections from a Jaszcak phantom.
For this purpose, I use the following commands in my macro file to
initialize voxellized phantom .
/gate/world/daughters/name jaszcak_phantom
/gate/world/daughters/insert compressedMatrix
#
/gate/jaszcak_phantom/geometry/insertReader interfile
/gate/jaszcak_phantom/interfileReader/insertTranslator range
/gate/jaszcak_phantom/interfileReader/rangeTranslator/readTable range.dat
/gate/jaszcak_phantom/interfileReader/rangeTranslator/describe 1
/gate/jaszcak_phantom/interfileReader/readFile rods.h33
#
# off center Y-axis is +0 cm
/gate/jaszcak_phantom/placement/setTranslation 0 0 0 cm
/gate/jaszcak_phantom/placement/setRotationAxis 0 1 0
/gate/jaszcak_phantom/placement/setRotationAngle 180 deg
Unfortunately, when I track primary particles into Jaszcak phantom, I
notice that it mismatches between voxellized source and voxellized
phantom in the spatial coordinates. As you can see, I need to use
visualization option to inquiry this mismatch.
I hope you can help me to solve my problems.
Shahrokh
On 8/22/10, Simon Stute <gate.stute at gmail.com> wrote:
> Hi,
>
> If you are using visualization, try to disable it.
> There are possible incompatibilities between regular volumes and visu.
>
> You have this message :
>
> 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".
>
> So if you don't use visu (meening you don't create a visu window), you have
> to put the command /vis/disable at the beginning of your macro.
>
> Hope it works,
> SImon
>
>
> On Sun, Aug 22, 2010 at 11:50 AM, shahrokh nasseri <
> shahrokh.nasseri at gmail.com> wrote:
>
>> 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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>
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