[Gate-users] Couldnt run Gate command: v4.0.0 on Mac OS X 10.5.4

[Arda Konik]

Thanks Uwe, I replaced " variables.gmk" and Gate starts now. However,  
i got other errors when I ran   "benchmarkPET.mac " :
   1) *** Break *** bus error   at the beginning
   2) and later  many other errors like this:Gate(85275,0xa08b5fa0)  
malloc: *** error for object 0x5063bf8: Non-aligned pointer being  
freed *** set a breakpoint in malloc_error_break to debug
   3) finally  " segmentation fault "

  I copied the portion of the output starting with the error on the  
4th line here

G4VRangeToEnergyConverter::ConvertCutToKineticEnergy   for e-
The cut in range [300 (mm)]   is too big   for material  idx=5
The cut in energy is set1.79769e+305GeV

  *** Break *** bus error
/Applications/gate/gate_v4.0.0/85275: No such file or directory.
Attaching to process 85275.
Reading symbols for shared libraries . done
Reading symbols for shared  
libraries 
  ......................................................................................................................................................................................... done
0x96afaf69 in wait4 ()

========== STACKS OF ALL THREADS ==========

Thread 2 (process 85275 thread 0x2307):
#0  0x96a9468e in __semwait_signal ()
#1  0x96abf986 in _pthread_cond_wait ()
#2  0x96abf36d in pthread_cond_wait$UNIX2003 ()
#3  0x94aa9432 in glvmDoWork ()
#4  0x96abe6f5 in _pthread_start ()
#5  0x96abe5b2 in thread_start ()

Thread 1 (process 85275 thread 0x10b):
#0  0x96afaf69 in wait4 ()
#1  0x96af8abc in system$UNIX2003 ()
#2  0x00c7b0e1 in TUnixSystem::StackTrace ()
#3  0x00c7e435 in TUnixSystem::DispatchSignals ()
#4  0x00c7e5a8 in SigHandler ()
#5  <signal handler called>
#6  0x03ed7d8b in G4ProcessManager::GetProcessActivation ()
#7  0x03da0bef in G4LossTableManager::EnergyLossProcessIsInitialised ()
#8  0x03db18d5 in G4VEnergyLossProcess::PreparePhysicsTable ()
#9  0x02e40793 in G4VUserPhysicsList::PreparePhysicsTable ()
#10 0x02e412d5 in G4VUserPhysicsList::BuildPhysicsTable ()
#11 0x02e38e9b in G4RunManagerKernel::BuildPhysicsTables ()
#12 0x02e39000 in G4RunManagerKernel::RunInitialization ()
#13 0x02e36140 in G4RunManager::RunInitialization ()
#14 0x006eb312 in GateRunManager::RunInitialization ()
#15 0x02e36d63 in G4RunManager::BeamOn ()
#16 0x005e2df3 in GateApplicationMgr::StartDAQ ()
#17 0x005e337a in GateApplicationMgrMessenger::SetNewValue ()
#18 0x0446a901 in G4UIcommand::DoIt ()
#19 0x04472020 in G4UImanager::ApplyCommand ()
#20 0x0445e104 in G4UIbatch::ExecCommand ()
#21 0x0445e3cb in G4UIbatch::SessionStart ()
#22 0x04470a8d in G4UImanager::ExecuteMacroFile ()
#23 0x00748211 in GateUIcontrolMessenger::LaunchMacroFile ()
#24 0x0074832b in GateUIcontrolMessenger::SetNewValue ()
#25 0x0446a901 in G4UIcommand::DoIt ()
#26 0x04472020 in G4UImanager::ApplyCommand ()
#27 0x000058d8 in main ()
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x5063bf8: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x5063ef4: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50643d0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50646cc: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b16b54: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b17574: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b18094: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b18ab4: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b19ffc: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1aa1c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1d484: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1dea4: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1e8c4: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1f2e4: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b2072c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b2114c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b21b6c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b2258c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d1840: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d1d4c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d2768: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d3184: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d3ba0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x5063a14: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50641ec: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b16970: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b17390: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b17eb0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b188d0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b19e18: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1a838: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1d2a0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1dcc0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1e6e0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b1f100: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b20548: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b20f68: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b21988: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x4b223a8: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d165c: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d1b68: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d2584: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d2fa0: Non- 
aligned pointer being freed (2)
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50d39bc: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Gate(85275,0xa08b5fa0) malloc: *** error for object 0x50649c4: Non- 
aligned pointer being freed
*** set a breakpoint in malloc_error_break to debug
Segmentation fault





On Nov 21, 2008, at 2:59 AM, Uwe Pietrzyk wrote:

>
> Hi Arda,
>
> I nearly used an identical setup except for GEANT where I used  
> GEANT4.9.1.p02 and I have MacOS 10.5.5
> on MacBook and Mac Mini. But you could replace the variables.gmk in  
> the Gatev4..-directory by the one you
> find attached to this eMail and re-compile gate, after cleaning up  
> the tmp and bin folder in the gate directory.
>
> Best wishes and good luck
>
> Uwe Pietrzyk
>
>
>
>
>
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