[Gate-users] Can't launch Gate v6.0.0 after compiling

Tue Mar 2 20:26:58 CET 2010

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
>>>> Sitz der Gesellschaft: Juelich
>>>> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
>>>> Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe
>>>> Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
>>>> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
>>>> Prof. Dr. Sebastian M. Schmidt
>>>> ------------------------------------------------------------------------------------------------
>>>> ------------------------------------------------------------------------------------------------
>>> 
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>> 
>> ----------------------------------------------------------------
>> 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
----------------------------------------------------------------------/