[Gate-users] Gate v6.0.0 on Mac OS X >> OK

Wed Mar 3 00:01:43 CET 2010

Hi Marc, hi Didier,

omitting the lmf-library was the key! On 64-bit-systems, I found the lmf
not working anymore and you are right to disable it, in case you are not
interested in.
According to Didier, I will not start any production on my Mac until the
bugs are fixed.

Many thanks and kind regards,

Uwe

-----
On 02.03.2010, at 20:55, Didier Benoit wrote:

> 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
>>>>>>> ----------------------------------------------------------------------/
>>>>>>> 
>>>>>>> 
>>>>>>> ------------------------------------------------------------------------------------------------
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>>>>>>>             
>>>>>> _______________________________________________
>>>>>> Gate-users mailing list
>>>>>> Gate-users at lists.opengatecollaboration.org
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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
>>> ----------------------------------------------------------------------/
>>> 
>>>     
>> _______________________________________________
>> 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
> http://www.imnc.in2p3.fr
> ----------------------------------------------------------------
>  
> 

/----------------------------------------------------------------------
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
----------------------------------------------------------------------/