[Gate-users] !! Gate v6.0.0 on Mac OS X >>still not OK

Didier Benoit benoit at cppm.in2p3.fr
Wed Mar 3 00:28:33 CET 2010 

Hi Uwe,

Yes it's the "normal" bug :), the processes are not loaded in GATE6 on 
Mac Os X.

Kind regards,
Didier

Le 03/03/2010 00:25, Uwe Pietrzyk a écrit :
>
> Hi,
>
> I briefly tested the benchPET. I could start GATE, but there is nothing
> written to the root-file after 20 min. Also, the visualisation does 
> not work
> and crashes the X11-environment ...
>
> So I will wait until bugs are solved. Let me know, when I can continue
> testing Gate6 on Mac Os X ...
>
> Kind regards,
>
> Uwe
> -----
> On 03.03.2010, at 00:01, Pietrzyk, Uwe wrote:
>
>>
>> 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  <http://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
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>>>>>>>>> ------------------------------------------------------------------------------------------------
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>>>>>>>>>              
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>> ----------------------------------------------------------------------/
>>>>>
>>>>>      
>>>> _______________________________________________
>>>> 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 <mailto:benoit at imnc.in2p3.fr>/*
>>>
>>> */http://www.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 <mailto: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 
>> <mailto:Uwe.Pietrzyk at physik.uni-wuppertal.de>
>> http://www.medizinphysik.uni-wuppertal.de 
>> <http://www.medizinphysik.uni-wuppertal.de/>
>> ----------------------------------------------------------------------/
>>
>
> /----------------------------------------------------------------------
> 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 <mailto: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 
> <mailto:Uwe.Pietrzyk at physik.uni-wuppertal.de>
> http://www.medizinphysik.uni-wuppertal.de 
> <http://www.medizinphysik.uni-wuppertal.de/>
> ----------------------------------------------------------------------/
>


-- 

*/----------------------------------------------------------------/*

*/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 <mailto:benoit at imnc.in2p3.fr>/*

*/http://www.imnc.in2p3.fr/*

*/----------------------------------------------------------------/*

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