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

Uwe Pietrzyk u.pietrzyk at fz-juelich.de
Wed Mar 3 00:25:58 CET 2010


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 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
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>>>>>>>> Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
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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
>> 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
> ----------------------------------------------------------------------/
> 

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