[Gate-users] Building gate_v6.0_p01

Andinet Enquobahrie andinet.enqu at kitware.com
Fri Oct 15 17:21:49 CEST 2010 

Just to close this thread:

With a clean make build, I was able to successfully build Gate.

Thanks all!
-Andinet

On Fri, Oct 15, 2010 at 9:41 AM, Andinet Enquobahrie
<andinet.enqu at kitware.com> wrote:
> 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
>



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

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

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