[Gate-users] Can't launch Gate v6.0.0 after compiling
Marc Chamberland
mchamber at connect.carleton.ca
Tue Mar 2 20:41:12 CET 2010
Hi Uwe,
I had the same problem as you, but disabling the LMF libraries (which I don't expect to use for now) solved it.
However, Didier pointed out that there are problems with certain processes on Mac OS X. Indeed, when I tried running the benchmark for PET, Gate didn't recognize any of the physical processes. I'll wait for the coming fix in the meantime.
Cheers!
Marc
Le 2010-03-02 à 14:26, Uwe Pietrzyk a écrit :
>
> Hi Didier, hi Marc,
>
> it didn't work in my case. I recompiled Geant4 and Gate and starting
> Gate without any .mac file runs into the idle prompt, which looks fine, I thought.
> But starting the the benchmark gives me:
>
> medmac37.ime.kfa-juelich.de 75 /Applications/gate_v6.0.0/benchmarks/benchPET --> Gate benchPET.mac
> [G4]
> [G4] *************************************************************
> [G4] Geant4 version Name: geant4-09-02-patch-03 (29-January-2010)
> [G4] Copyright : Geant4 Collaboration
> [G4] Reference : NIM A 506 (2003), 250-303
> [G4] WWW : http://cern.ch/geant4
> [G4] *************************************************************
> [G4]
> [Core-0] Initialization of geometry
> [Core-0] Initialization of physics
> [Core-0] Initialization of actors
> [Core-0]
> [Core-0] **********************************************************************
> [Core-0] GATE version name: gate_v6
> [Core-0] Copyright : OpenGATE Collaboration
> [Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
> [Core-0] WWW : http://www.opengatecollaboration.org/
> [Core-0] **********************************************************************
> [Core-0]
> [Core-0] Starting macro benchPET.mac
> dyld: lazy symbol binding failed: Symbol not found: _fillEHforGATE
> Referenced from: /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
> Expected in: flat namespace
>
> dyld: Symbol not found: _fillEHforGATE
> Referenced from: /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
> Expected in: flat namespace
>
> Trace/BPT trap
>
> In rebuilding Geant4 I have created shared and static libraries at the same time.
> This was an option, but could this cause a problem?
> Would it be useful to go back to the static solution Mac OS X again?
>
> Marc, did you change anything else?
>
> Kind regards,
>
> Uwe
>
> On 02.03.2010, at 17:45, Marc Chamberland wrote:
>
>> Thank you very much for your help, Didier. Compiling Geant4 with shared libraries worked to fix my problem. If anything else comes up, I'll let the mailing list know.
>>
>> Thanks again!
>> Marc
>>
>>
>> Le 2010-03-02 à 03:57, Didier BENOIT a écrit :
>>
>>> Hi Marc,
>>>
>>> Actually GATE 6 has some problems on Mac OS (concerning the processes), We are tracking the problems encountered by the Mac users and should be able to provide a solution soon.
>>>
>>> But I can launch GATE:
>>> [Mar mar 02 09:30:32 dbenoit at Ixtl ~]$ Gate
>>> [G4]
>>> [G4] *************************************************************
>>> [G4] Geant4 version Name: geant4-09-02-patch-03 (29-January-2010)
>>> [G4] Copyright : Geant4 Collaboration
>>> [G4] Reference : NIM A 506 (2003), 250-303
>>> [G4] WWW : http://cern.ch/geant4
>>> [G4] *************************************************************
>>> [G4]
>>> [Core-0] Initialization of geometry
>>> [Core-0] Initialization of physics
>>> [Core-0] Initialization of actors
>>> [Core-0]
>>> [Core-0] **********************************************************************
>>> [Core-0] GATE version name: gate_v6
>>> [Core-0] Copyright : OpenGATE Collaboration
>>> [Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
>>> [Core-0] WWW : http://www.opengatecollaboration.org/
>>> [Core-0] **********************************************************************
>>> [Core-0]
>>> Idle>
>>>
>>> Could you check if your GEANT is installed with the shared libraries?
>>> To check this, source your file env_gate.sh and check this line:
>>>
>>> .......
>>> On this machine the G4LIB_BUILD_SHARED=1
>>> .......
>>>
>>> If you are "On this machine the G4LIB_BUILD_SHARED=0" you have to reinstall GEANT4 :(.
>>>
>>> There the line to build the shared libraries in GEANT4:
>>> Do you want to build 'shared' (.so) libraries?[n] y
>>> You selected to build 'shared' (.so) libraries.
>>>
>>> Hope this help,
>>> Kind regards,
>>> Didier
>>>
>>> Le 2 mars 2010 à 02:31, Marc Chamberland a écrit :
>>>
>>>> Thanks for the reply, Uwe. Unfortunately, I haven't found any solution yet since my C++ skills are quite limited. For those having the same problem, it seems related to the PostStepDoIt( const G4Track&, const G4Step&) function, from the G4VEmProcess class in Geant4. This function is referred to from only 3 places in Gate:
>>>>
>>>> 1) In GateFictitiousFastSimulationModel.cc on line 240.
>>>>
>>>> 2 & 3) In the GateGenericWrapperProcess and GateTotalDiscreteProcess classes. They each define a PostStepDoIt function, but it looks like they're also using the G4VEmProcess version of the function in their definition.
>>>>
>>>> I'm not sure if this information is useful to solve the issue or not, but it can't hurt to put it out there.
>>>>
>>>> Cheers!
>>>> Marc
>>>>
>>>> Le 2010-03-01 à 03:52, Uwe Pietrzyk a écrit :
>>>>
>>>>>
>>>>> Hi Marc,
>>>>>
>>>>> I am facing exactly the same problem, except that my setting is slightly different:
>>>>> Mac OS X 10.6.2, Geant4.9.2.p02, CLHEP 2.0.3.2, gcc 4.2.1, root 5.24 and like
>>>>> in your case Gate_v5.0.0_p01 is working fine.
>>>>>
>>>>> Since I use the c-shell and could not find the env_gate.csh in Gate 6, I took the one from
>>>>> Gate 5 and modified it slightly.
>>>>> I also compared the file GateCommon.gmk which obviously is the former variables.gmk
>>>>> and found that LDFLAGS have been modified in GateCOmmon.gmk. In Mac OS X, there
>>>>> is no /usr/X11R6/lib64, only /usr/X11R6/lib, hence I adjusted this too, but it did not
>>>>> solve the problem we both experienced.
>>>>> Something fundamental must have been changed during the transition to Gate 6.
>>>>>
>>>>> Kind regards,
>>>>>
>>>>> Uwe
>>>>>
>>>>> On 28.02.2010, at 21:42, Marc Chamberland wrote:
>>>>>
>>>>>> Hi Gate Users!
>>>>>>
>>>>>> I've compiled Gate v6.0.0. Everything seemed fine during compilation, but when I try to launch Gate, I get the following error:
>>>>>>
>>>>>> Compiling Gate.cc ...
>>>>>> Using granular libraries ...
>>>>>> Linking Gate
>>>>>> ... Done!
>>>>>> [/Applications/gate_v6.0.0] Marc$ Gate
>>>>>> dyld: Symbol not found: __ZN12G4VEmProcess12PostStepDoItERK7G4TrackRK6G4Step
>>>>>> Referenced from: /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
>>>>>> Expected in: flat namespace
>>>>>> in /Applications/gate_v6.0.0/tmp/Darwin-g++/Gate/libGate.dylib
>>>>>> Trace/BPT trap
>>>>>> [/Applications/gate_v6.0.0] Marc$
>>>>>>
>>>>>> I'm on Mac OS X 10.6.2, with Geant4 9.2.p03, clhep 2.0.4.2, and gcc version 4.2.1 (Apple Inc. build 5646). For the record, I recently (two weeks ago) installed Gate v5.0.0 and didn't encounter this problem.
>>>>>>
>>>>>> Can anyone help me with this? Thank you in advance!
>>>>>>
>>>>>> Marc
>>>>>> _______________________________________________
>>>>>> Gate-users mailing list
>>>>>> Gate-users at lists.opengatecollaboration.org
>>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>
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>>>
>>> ----------------------------------------------------------------
>>> Didier BENOIT, Ingénieur GATE
>>> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
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>>> http://www.imnc.in2p3.fr
>>> ----------------------------------------------------------------
>>>
>>
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>
> /----------------------------------------------------------------------
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-1
> Forschungszentrum Jülich GmbH
> 52425 Jülich
> Tel: +49-2461-61 4763
> Fax: +49-2461-61 2820 + 8229
> Mobil: +49-162-103-4871
> eMail: U.Pietrzyk at fz-juelich.de
> http://www.fz-juelich.de/inm
> &
> Bergische Universität Wuppertal
> Fachbereich C - Physik / D.08.01
> Gaußstr. 20
> 42097 Wuppertal
> Tel: +49-(0)202-439-3523
> Fax: +49-(0)202-439-2811
> eMail: Uwe.Pietrzyk at physik.uni-wuppertal.de
> http://www.medizinphysik.uni-wuppertal.de
> ----------------------------------------------------------------------/
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