[Gate-users] Building gate_v6.0_p01

Andinet Enquobahrie andinet.enqu at kitware.com
Fri Oct 15 15:41:29 CEST 2010 

Hi Alexandre-

I poked around a little bit and found out that  the problem was gate
envt variables were not correctly set in my terminal. I was just
running env_gate.sh shell instead of "sourcing it ". Hence, variables
like G4WORKDIR were not set in the shell environment. After I did,


Entering source/arf ...
source/arf finished
Entering source/geometry ...
source/geometry finished
Entering source/general ...
source/general finished
Entering source/digits_hits ...
source/digits_hits finished
Entering source/physics ...
source/physics finished
Using granular libraries ...
Linking Gate ...
/home/andinet/Projects/GATE/gate_v6.0_p01/tmp/Linux-g++/Gate/exe/Gate.o:
In function `Welcome()':
Gate.cc:(.text+0x13dd): undefined reference to
`GateMessageManager::GetMessageLevel(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >)'
Gate.cc:(.text+0x140c): undefined reference to
`GateMessageManager::GetSpace(int)'
Gate.cc:(.text+0x14ec): undefined reference to
`GateMessageManager::GetMessageLevel(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >)'
Gate.cc:(.text+0x151b): undefined reference to
`GateMessageManager::GetSpace(int)'
Gate.cc:(.text+0x1617): undefined reference to
`GateMessageManager::GetMessageLevel(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >)'
Gate.cc:(.text+0x1646): undefined reference to
`GateMessageManager::GetSpace(int)'
Gate.cc:(.text+0x1742): undefined reference to
`GateMessageManager::GetMessageLevel(std::basic_string<char,
std::char_traits<char>, std::allocator<char> >)'

At least now, it started the linking stage. I am getting linking
errors though. I will look into it further and report back.

Thanks,
Andinet


On Fri, Oct 15, 2010 at 9:25 AM, Andinet Enquobahrie
<andinet.enqu at kitware.com> wrote:
> Hi Alexandre-
>
> Thanks for your help.
>
> I tried what you suggested ( run the make command twice in a row ) but
> got the same result. See below.
>
>
> Trillian gate_v6.0_p01]$ make
> Entering source/arf ...
> source/arf finished
> Entering source/geometry ...
> source/geometry finished
> Entering source/general ...
> source/general finished
> Entering source/digits_hits ...
> source/digits_hits finished
> Entering source/physics ...
> source/physics finished
> [Trillian gate_v6.0_p01]$ make
> Entering source/arf ...
> source/arf finished
> Entering source/geometry ...
> source/geometry finished
> Entering source/general ...
> source/general finished
> Entering source/digits_hits ...
> source/digits_hits finished
> Entering source/physics ...
> source/physics finished
> [Trillian gate_v6.0_p01]$
>
> It is still not entering the linking stage.
>
>
> On Fri, Oct 15, 2010 at 3:25 AM, Alexandre Dupas
> <alexandre.dupas at gmail.com> wrote:
>> Dear Andinet,
>>
>> In your settings, the Gate makefile do not enter the linking stage. I
>> had a quite similar issue with Gate 5 and since the makefiles are
>> similar, my workaround should work.
>>
>> Try to run the make command twice in a row. In the first pass, you
>> should see all the "Entering dir/dir finished" lines and at the end of
>> the second run, you should see something like "linking Gate/linking
>> done".
>>
>> The issue, in Gate 5, comes from a missing dependency between the
>> library building and the processing of the subdirs. On mono-thread
>> compilation, this is not an issue since the declaration order is also
>> the processing order. The linking is done when all the subdirs are
>> done but using "make -j4" for instance does not work the same way
>> since the jobs are processed simultaneously and the object files
>> required to produce executable and library are not available.
>>
>> Your environment setup appears to be ok.
>>
>> Cheers,
>> Alexandre
>>
>> --
>> Alexandre Dupas
>> Postdoctoral Research Fellow
>> INSERM U698, Bichat Médecine Nucléaire
>>
>> 2010/10/15 Andinet Enquobahrie <andinet.enqu at kitware.com>:
>>> Hi all-
>>>
>>> I am trying to build gate_v6.0_p01 on my Linux machine. I am using the
>>> following version of the helper softwares as recommended in the README
>>> file
>>>
>>> - GEATN 4.9.1 patch 03
>>> - CLHEP 2.0.3.2
>>>  - ROOT v5.27.04
>>>
>>> I built and installed GEATN, CLHEP and ROOT succesfully as described in
>>>
>>> http://wiki.opengatecollaboration.org/index.php/InstallationGuide
>>>
>>> I had no problems.
>>>
>>> But, when I built gate , it is not generating the Gate executable.
>>> Here is how a make run looks like
>>>
>>>  > make
>>> Entering source/arf ...
>>> source/arf finished
>>> Entering source/geometry ...
>>> source/geometry finished
>>> Entering source/general ...
>>> source/general finished
>>> Entering source/digits_hits ...
>>> source/digits_hits finished
>>> Entering source/physics ...
>>> source/physics finished
>>>
>>> I don't get Gate executable in  my
>>>
>>> ${GATEHOME}/bin/${G4SYSTEM}
>>>
>>>
>>> My environment setup looks like the following.
>>>
>>> ./env_gate.sh
>>>
>>> The current value of G4INSTALL is: /home/andinet/Projects/GEANT/geant4.9.1.p03
>>> The current value of G4VERSION is: 9.1
>>>
>>> Launching Geant4 configuration script
>>> /home/andinet/Projects/GEANT/geant4.9.1.p03/env.sh
>>>
>>> On this machine the G4SYSTEM=Linux-g++
>>> On this machine the G4INSTALL=/home/andinet/Projects/GEANT/geant4.9.1.p03
>>> On this machine the
>>> G4INCLUDE=/home/andinet/Projects/GEANT/geant4.9.1.p03/include/
>>> On this machine the G4LIB=/home/andinet/Projects/GEANT/geant4.9.1.p03/lib
>>> On this machine the
>>> G4LEVELGAMMADATA=/home/andinet/Projects/GEANT/geant4.9.1.p03/data/PhotonEvaporation2.0
>>> On this machine the
>>> G4RADIOACTIVEDATA=/home/andinet/Projects/GEANT/geant4.9.1.p03/data/RadioactiveDecay3.2
>>> On this machine the
>>> G4LEDATA=/home/andinet/Projects/GEANT/geant4.9.1.p03/data/G4EMLOW5.1
>>> On this machine the
>>> G4NEUTRONHPDATA=/home/andinet/Projects/GEANT/geant4.9.1.p03/data/G4NDL3.12
>>> On this machine the
>>> G4ABLADATA=/home/andinet/Projects/GEANT/geant4.9.1.p03/data/G4ABLA3.0
>>> On this machine the CLHEP_BASE_DIR=/home/andinet/Projects/CLHEP
>>> On this machine the CLHEP_INCLUDE_DIR=/home/andinet/Projects/CLHEP/include
>>> On this machine the CLHEP_LIB_DIR=/home/andinet/Projects/CLHEP/lib
>>> On this machine the CLHEP_LIB=CLHEP
>>> On this machine the XMFLAGS=
>>> On this machine the XMLIBS=
>>> On this machine the XMFLAGS=
>>> On this machine the XAWFLAGS=
>>> On this machine the XAWLIBS=
>>> On this machine the G4LIB_BUILD_STATIC=1
>>> On this machine the G4LIB_USE_GRANULAR=1
>>> On this machine the G4UI_USE_TCSH=1
>>>
>>> Configuring GATE options
>>>
>>> G4WORKDIR set to /home/andinet/Projects/GATE/gate_v6.0_p01
>>> G4TMP set to /home/andinet/Projects/GATE/gate_v6.0_p01/tmp
>>> G4BIN set to /home/andinet/Projects/GATE/gate_v6.0_p01/bin
>>> Data analysis and output features enabled
>>> Ascii data output enabled
>>> Transport and generation of optical photons is disabled
>>> Checking your LD_LIBRARY_PATH variable...
>>>  ==> OK: /home/andinet/Projects/ROOT//lib is already in your LD_LIBRARY_PATH
>>> Use of ROOT enabled
>>> ROOT real-time plotter disabled
>>> LMF data output disabled
>>> ECAT7 data output disabled
>>> GATEHOME is set to /home/andinet/Projects/GATE/gate_v6.0_p01
>>> Checking your path variable...
>>>  ==> OK: /home/andinet/Projects/GATE/gate_v6.0_p01/bin/Linux-g++ added
>>> to your path variable
>>> Checking your LD_LIBRARY_PATH variable...
>>>  ==> OK: /home/andinet/Projects/GATE/gate_v6.0_p01/tmp/Linux-g++/Gate
>>> added to your path variable
>>> G4VERSION9_2 is not set
>>> This GATE version only works with Geant4.9.1
>>> Done
>>>
>>>
>>> Can anybody let me know what is wrong in my env't set up? I appreciate your help
>>>
>>> Thanks,
>>> Andinet
>>>
>>>
>>> --
>>> Andinet Enquobahrie, Ph.D.
>>> Technical Lead
>>> Kitware, Inc.
>>>
>>> http://www.kitware.com
>>> (919) 969-6990 x311
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
> --
> Andinet Enquobahrie, Ph.D.
> Technical Lead
> Kitware, Inc.
>
> http://www.kitware.com
> (919) 969-6990 x311
>



-- 
Andinet Enquobahrie, Ph.D.
Technical Lead
Kitware, Inc.

http://www.kitware.com
(919) 969-6990 x311

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