[Gate-users] Can't launch Gate v6.0.0 after compiling
Didier Benoit
benoit at cppm.in2p3.fr
Tue Mar 2 20:55:44 CET 2010
Hi Uwe and Marc,
Yes, the problem is in the physical processes. It' a bug in the
"GateVProcess" and "GatePhysicsList" classes. I hope I could fix this
bug the next week, and surely there will be a new patch (gate_v6.0.1).
Kind Regards,
Didier
Le 02/03/2010 20:41, Marc Chamberland a écrit :
> 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
>>>>>>>
>>>>>> /----------------------------------------------------------------------
>>>>>> 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
>>>>>> ----------------------------------------------------------------------/
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------------------------
>>>>>> ------------------------------------------------------------------------------------------------
>>>>>> Forschungszentrum Juelich GmbH
>>>>>> 52425 Juelich
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>>>>>> Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
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>>>>>>
>>>>> _______________________________________________
>>>>> Gate-users mailing list
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>>>>>
>>>> ----------------------------------------------------------------
>>>> Didier BENOIT, Ingénieur GATE
>>>> Imagerie et Modélisation en Neurobiologie et Cancérologie (IMNC)
>>>> IMNC - UMR 8165 CNRS - Université Paris 7 - Université Paris 11
>>>> Campus d'Orsay
>>>> Bâtiment 440
>>>> 91406 ORSAY Cedex
>>>>
>>>> Tél: (33) 1 69 15 36 46
>>>> E-mail: benoit at imnc.in2p3.fr
>>>> benoit at cppm.in2p3.fr
>>>> http://www.imnc.in2p3.fr
>>>> ----------------------------------------------------------------
>>>>
>>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>> /----------------------------------------------------------------------
>> 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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--
*/----------------------------------------------------------------/*
*/Didier BENOIT, Ingénieur GATE/*
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