[Gate-users] Can not run Gate 6.1

Fri May 4 16:45:19 CEST 2012

Dear Aleksandra,

please find below a couple of essential commands from my ".cshrc"-file
relevant for GATE including some add-on for DYLD_LIBRARY_PATH …

Hope this is helpful for you!

Kind regards and best wishes

Uwe

 -+-+-+-+-+-+-+-+-+-+-+-+-+

alias start_GATE	'source /Applications/gate_v6.1/env_gate.csh'

setenv LD_LIBRARY_PATH :.:/usr/X11R6/lib:/usr/lib:/opt/local/lib:
setenv PATH {$PATH}:/usr/bin:/usr/X11R6/bin:

setenv ROOTSYS "/Applications/root"
setenv PATH "${PATH}:${ROOTSYS}/bin"
setenv LD_LIBRARY_PATH {$LD_LIBRARY_PATH}:"${ROOTSYS}/lib"
setenv DYLD_LIBRARY_PATH "${ROOTSYS}/lib"
setenv PRESTO_PROJECT "/Users/upietrzyk/prog_dev/root_utils"

# also add CLHEP to DYLD ...
setenv DYLD_LIBRARY_PATH {$DYLD_LIBRARY_PATH}:/Applications/CLHEP_2045/lib:

setenv G4INSTALL "/Applications/geant4.9.3.p02"
setenv G4WORKDIR "${HOME}/g4work"
setenv G4VERSION "9.3"
setenv GATEHOME "/Applications/gate_v6.1"
setenv PATH "${PATH}:${GATEHOME}/bin/Darwin-g++"
setenv PATH {$PATH}:/Applications:/usr/local:/usr/local/bin:/usr/texbin:/Users/upietrzyk/bin:.
setenv PATH {$PATH}:/opt/local/bin:/opt/local/sbin:/opt/local:/opt/local/include:

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
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/inm-4/DE/Home/home_node.html
&
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
----------------------------------------------------------------------/

On 04.05.2012, at 15:16, Aleksandra Biegun wrote:

> Dear Uwe,
> 
> I did try your suggestion with the "GateCommon.gmk" file, namely I made the same changes as were in your file:
> 
> I changed:
> EXTRALIBS += -L$ROOTSYS/lib $(shell $(ROOTSYS)/bin/root-config --libs) -ldl
> 
> into: EXTRALIBS += -L${ROOTSYS}/lib $(shell $(ROOTSYS)/bin/root-config --libs) -ldl
> 
> and also used: LDFLAGS += -L/usr/X11R6/lib -lXt
> 
> instead of:LDFLAGS += -L/usr/X11R6/lib64 -lXt
> 
> but I got the same problem as at the beginning:
> 
> kviq21:gate_v6.1 dendoove$ echo $DYLD_LIBRARY_PATH 
> /Applications/root/lib:/Applications/CLHEP/lib:/Applications/root/lib:/Applications/CLHEP/lib:/Applications/gate6.1_withGeant492p2/gate_v6.1/tmp/Darwin-g++/Gate
> kviq21:gate_v6.1 dendoove$ Gate            
> dyld: Symbol not found: __ZN12G4VEmProcess12PostStepDoItERK7G4TrackRK6G4Step
>   Referenced from: /Applications/gate6.1_withGeant492p2/gate_v6.1/tmp/Darwin-g++/Gate/libGate.dylib
>   Expected in: flat namespace
>  in /Applications/gate6.1_withGeant492p2/gate_v6.1/tmp/Darwin-g++/Gate/libGate.dylib
> Trace/BPT trap: 5
> 
> So it looks like there is some object missing...
> 
> Just to clarify the situation: 
> echo $DYLD_LIBRARY_PATH 
> 
> /Applications/root/lib:/Applications/CLHEP/lib:/Applications/root/lib:/Applications/CLHEP/lib:/Applications/gate6.1_withGeant492p2/gate_v6.1/tmp/Darwin-g++/Gate
> 
> where: /Applications/CLHEP contain CLHEP 2.0.4.2, as recommended for Geant4 9.2.p02
> 
> As I mentioned, I could run Gate when Geant4 9.4.p03 is used 
> (with CLHEP 2.1.0.1), but I need to run Gate with Geant4 9.2.p02. 
> This fails so far.
> 
> If you have more suggestions I would be happy to try.
> 
> Kind regards,
> Aleksandra
> 
> 
> 
> 
> On Sun, Apr 22, 2012 at 9:47 PM, Pietrzyk, Uwe <u.pietrzyk at fz-juelich.de> wrote:
> 
> Hi Aleksandra,
> 
> I am not sure, if you know of some changes in the makefile for Mac/Lion.
> I have attached the file we use to this eMail. It concerns some libraries.
> You can see the differences with the command:
> 
> diff old-file new-file
> 
> Hope this is helpful.
> 
> Kind regards and best wishes
> 
> Uwe Pietrzyk
> /----------------------------------------------------------------------
> Prof. Dr. Uwe Pietrzyk
> Diplom-Physiker
> Institut für Neurowissenschaften und Medizin / INM-4
> 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
> ----------------------------------------------------------------------/
> 
> 
> 
> 
> 
> 
> 
> 
> On 22.04.2012, at 20:27, Aleksandra Biegun wrote:
> 
>> Hello Hermann,
>> 
>> thanks for your response.
>> 
>> I have already tried to add Gate libraries to $DYLD_LIBRARY_PATH, but it
>> did not work, and before compiling Gate I followed all the instructions
>> recommended by Gate people on the link you have sent me. Did not help.
>> I must admit that I have no problem with installing Gate together with
>> geant4 9.4.p03 on lion,
>> but I do have a problem with Geant4 9.2.p02. But I also know that other
>> people could compile Gate 6.1
>> with Geant 9.2.p02, but on linux machine.
>> 
>> If anyone still have any suggestions I will be more than happy to hear them.
>> 
>> If I will solve this problem, I will surely post it!
>> 
>> Kind regards,
>> Aleksandra
>> 
>> 
>> On Sun, Apr 22, 2012 at 6:49 PM, Hermann Fuchs <
>> hermann.fuchs at meduniwien.ac.at> wrote:
>> 
>>> Hello
>>> 
>>> I do not have much experience compiling GATE on Mac as I used mostly Linux.
>>> However, such an error message usually means that some path/library is not
>>> found.
>>> 
>>> Perhaps MacOS looks in the wrong place and/or you might need to set a
>>> different environment variable.
>>> 
>>> Try adding GATE to
>>> 
>>> $DYLD_LIBRARY_PATH
>>> 
>>> You might also have a look at the Mac Installation instructions. These can
>>> be found in the previous installation instructions
>>> http://wiki.**opengatecollaboration.org/**index.php/Current_Recommended_**
>>> Procedure<http://wiki.opengatecollaboration.org/index.php/Current_Recommended_Procedure>
>>> It is only for an old MacOs version, but perhaps it helps.
>>> When I tried it on my Mac some time ago it worked.
>>> 
>>> If you do find the error, please keep me posted.
>>> 
>>> Best regards,
>>> Hermann
>>> 
>>> 
>>> On 20.04.2012 16:17, Aleksandra Biegun wrote:
>>> 
>>>> 
>>>> Dear Gate-users,
>>>> 
>>>> I am trying to run Gate on mac (Lion, 10.7.3) and I can not jump over an
>>>> error message I have got:
>>>> 
>>>> $ Gate
>>>> dyld: Symbol not found: __**ZN12G4VEmProcess12PostStepDoIt**
>>>> ERK7G4TrackRK6G4Step
>>>> Referenced from: /Applications/gate_v6.1/tmp/**
>>>> Darwin-g++/Gate/libGate.dylib
>>>> Expected in: flat namespace
>>>> in /Applications/gate_v6.1/tmp/**Darwin-g++/Gate/libGate.dylib
>>>> Trace/BPT trap: 5
>>>> 
>>>> I installed geant4 9.2.p02 with CLHEP 2.0.4.2, ROOT 5.30 and Gate 6.1.
>>>> Geant4 works, ROOT works, Gate compiles, but when I try to run Gate
>>>> I have this problem I mentioned.
>>>> 
>>>> echo $DYLD_LIBRARY_PATH
>>>> /Applications/root/lib:/**Applications/root/lib/root:/**
>>>> Applications/CLHEP/lib:/**Applications/root/lib:/**
>>>> Applications/CLHEP/lib::/**Applications/geant4.9.2.p02/**lib/Darwin-g++
>>>> 
>>>> When I added Gate libraries, the problem remains.
>>>> 
>>>> I know that according the specification for Gate6.1 I should compile it
>>>> with newest version of Geant4,
>>>> e.g. 9.4.p03, but because of work purposes I need to have it compiled
>>>> with the older one 9.2.p02.
>>>> 
>>>> 
>>>> Could anyone help me with it?
>>>> 
>>>> Kind regards,
>>>> Aleksandra
>>>> 
>>>> ______________________________**_________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.**opengatecollaboration.org<Gate-users at lists.opengatecollaboration.org>
>>>> http://lists.**opengatecollaboration.org/**mailman/listinfo/gate-users<http://lists.opengatecollaboration.org/mailman/listinfo/gate-users>
>>>> 
>>> 
>>> ______________________________**_________________
>>> Gate-users mailing list
>>> Gate-users at lists.**opengatecollaboration.org<Gate-users at lists.opengatecollaboration.org>
>>> http://lists.**opengatecollaboration.org/**mailman/listinfo/gate-users<http://lists.opengatecollaboration.org/mailman/listinfo/gate-users>
>>> 
>> 
>> 
>> 
>> -- 
>> 
>> -- ^ ^ ----
>>   \/  Ola
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> 
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> 
> 
> 
> -- 
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> -- ^ ^ ----
>    \/  Ola

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