[Gate-users] installing Gate 4.0.0 on Mac OS X 10.4.11
Dendooven Peter
dendooven at kvi.nl
Thu Jun 18 16:58:53 CEST 2009
Below the procedure I follow. This is partially based on input from a
colleague running GATE under Linux.
1) Open "Terminal" application to start with a fresh terminal window.
2) Go to the GATE directory: /Applications/gate_v4.0.0
3) set the following environment variables (given are the values
confirmed by echo):
ROOTSYS = /Applications/root
G4INSTALL = /Applications/geant4.9.1.p03
G4WORKDIR = /Applications/g4work
G4VERSION = 9.1
GATEHOME = /Applications/gate_v4.0.0
PATH = /sw/bin:/sw/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/
usr/texbin:/usr/X11R6/bin:/Applications/root/bin:/Applications/root/
lib:/Applications/root/include:/Applications/gate_v4.0.0/bin/Darwin-g+
+:/Applications/g4work/bin/Darwin-g++:/Applications/g4work/bin/Darwin-
g++:/Applications/root/bin:/Applications/root/lib:/Applications/root/
include:/Applications/gate_v4.0.0/bin/Darwin-g++
LD_LIBRARY_PATH = /Applications/root/lib
DYLD_LIBRARY_PATH = /Applications/root/lib
4) Launching GATE configuration script /Applications/gate_v4.0.0/
env_gate.csh
This produces the following output, of which the first part comes
from the geant configuration script:
The current value of G4INSTALL is: /Applications/geant4.9.1.p03
The current value of G4VERSION is: 9.1
Launching Geant4 configuration script /Applications/geant4.9.1.p03/
env.csh
On this machine the G4SYSTEM=Darwin-g++
On this machine the G4INSTALL=/Applications/geant4.9.1.p03
On this machine the G4LIB=/Applications/geant4.9.1.p03/lib
On this machine the G4LEVELGAMMADATA=/Applications/geant4.9.1.p03/
data/PhotonEvaporation2.0
On this machine the G4RADIOACTIVEDATA=/Applications/geant4.9.1.p03/
data/RadioactiveDecay3.2
On this machine the G4LEDATA=/Applications/geant4.9.1.p03/data/
G4EMLOW5.1
On this machine the G4NEUTRONHPDATA=/Applications/geant4.9.1.p03/data/
G4NDL3.12
On this machine the G4ABLADATA=/Applications/geant4.9.1.p03/data/
G4ABLA3.0
On this machine the CLHEP_BASE_DIR=/Applications/CLHEP
On this machine the CLHEP_INCLUDE_DIR=/Applications/CLHEP/include
On this machine the CLHEP_LIB_DIR=/Applications/CLHEP/lib
On this machine the CLHEP_LIB=CLHEP
On this machine the G4VIS_BUILD_OPENGLX_DRIVER=1
On this machine the G4VIS_BUILD_RAYTRACERX_DRIVER=1
On this machine the G4VIS_USE_OPENGLX=1
On this machine the G4VIS_USE_RAYTRACERX=1
On this machine the XMFLAGS=
On this machine the XMLIBS=
On this machine the XMFLAGS=
On this machine the XMLIBS=
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
In your environment you have the G4WORKDIR=/Applications/g4work
Configuring GATE options
G4WORKDIR set to .
G4TMP set to ./tmp
G4BIN set to ./bin
Data analysis and output features enabled
Ascii data output enabled
Transport and generation of optical photons is enabled
Checking your LD_LIBRARY_PATH variable...
==> OK: /Applications/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 /Applications/gate_v4.0.0
Checking your path variable...
==> OK: /Applications/gate_v4.0.0/bin/Darwin-g++ is already in your
path variable
GATEHOME = /Applications/gate_v4.0.0
G4VERSION9 is set: GATE is compatible with the geant4 version 9.1
Done
5) Making sure there is no /tmp or /bin directory in the GATEHOME
directory.
6) Give the following command:
make >&make.log
The make.log file is attached.
All seems to go well up to:
Compiling Gate.cc ...
Using granular libraries ...
Linking Gate ...
i686-apple-darwin8-g++-4.0.1: unrecognized option '-rdynamic'
/usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
libMathCore.dylib referenced from: /Applications/root/lib/
libHist.dylib (checking for undefined symbols may be affected) (No
such file or directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
libRIO.dylib referenced from: /Applications/root/lib/libGraf.dylib
(checking for undefined symbols may be affected) (No such file or
directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
libNet.dylib referenced from: /Applications/root/lib/libTree.dylib
(checking for undefined symbols may be affected) (No such file or
directory, errno = 2)
/usr/bin/ld: warning can't open dynamic library: /Users/brun/root/lib/
libThread.dylib referenced from: /Applications/root/lib/libTree.dylib
(checking for undefined symbols may be affected) (No such file or
directory, errno = 2)
/usr/bin/ld: Undefined symbols:
TFile::TFile(char const*, char const*, char const*, int)
TVirtualFitter::GetFitter() referenced from libHist expected to
be defined in /Users/brun/root/lib/libMathCore.dylib
TVirtualFitter::SetFitter(TVirtualFitter*, int)referenced from
libHist expected to be defined in /Users/brun/root/lib/libMathCore.dylib
ROOT::Fit::Fitter::SetFunction
(ROOT::Math::IParametricFunctionMultiDim const&)referenced from
libHist expected to be defined in /Users/brun/root/lib/libMathCore.dylib
ROOT::Fit::Fitter::SetFunction
(ROOT::Math::IParametricGradFunctionOneDim const&)referenced from
libHist expected to be defined in /Users/brun/root/lib/libMathCore.dylib
(a long list of similar messages follows, ending with:)
TSQLRow::ShowMembers(TMemberInspector&, char*) referenced from
libTree expected to be defined in /Users/brun/root/lib/libNet.dylib
collect2: ld returned 1 exit status
make: *** [bin/Darwin-g++/Gate] Error 1
So a lot of things are not where they are expected or are expected in
directories that do not exist (such as /Users/brun).
Also, i686-apple-darwin8-g++-4.0. is asked to do something is does
not recognize.
At this point, echo $DYLD_LIBRARY_PATH gives:
/Applications/root/lib
I hope this information helps.
Cheers,
Peter
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On 18 Jun 2009, at 16:15, THIAM Cheick 219838 wrote:
> Ok,
>
> So I do not see any reason for which you have not executable....
> Can you send if possible the make.log of your compilation? And
> result of "echo $DYLD_LIBRARY_PATH" in your env ?
>
> Cheick
>
>
> -----Message d'origine-----
> De : Dendooven Peter [mailto:dendooven at kvi.nl]
> Envoy? : jeudi 18 juin 2009 15:53
> ? : THIAM Cheick 219838
> Objet : Re: [Gate-users] installing Gate 4.0.0 on Mac OS X 10.4.11
>
> Hi,
>
> the commands you show are in the env.csh file in the geant directory
> and are thus called from within the env_gate.csh file.
>
>
>
> Cheers,
> Peter
>
> On 18 Jun 2009, at 15:04, THIAM Cheick 219838 wrote:
>
>> Hi
>>
>> If the environments for G4 are fixed correctly and compilation is
>> OK, normally Gate executable is created in /bin/Darwin-g++/Gate ;
>> with *.d and *.o in /tmp/Darwin-g++/Gate; but for execution on Mac-
>> OS, the DYLD_LIBRARY_PATH must be shared for the lib(ROOTLIB,
>> CLHEPLIB...) directories, instead of LD_LIBRARY_PATH
>>
>> Please add in your env_gate.sh file, the following lines:
>>
>> ------------------------------------------
>> # Shared libraries for Mac
>> #
>> if test "X$G4SYSTEM" = "XDarwin-g++" ; then
>> if [ $G4LIB_BUILD_SHARED ] ; then
>> if [ $DYLD_LIBRARY_PATH ] ; then
>> DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${G4LIB}/${G4SYSTEM}
>> DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${CLHEP_LIB_DIR}
>> if [ $G4LIB_BUILD_GDML ] ; then
>> DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${XERCESCROOT}/lib
>> fi
>> export DYLD_LIBRARY_PATH
>> else
>> DYLD_LIBRARY_PATH=${G4LIB}/${G4SYSTEM}
>> DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${CLHEP_LIB_DIR}
>> if [ $G4LIB_BUILD_GDML ] ; then
>> DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${XERCESCROOT}/lib
>> fi
>> export DYLD_LIBRARY_PATH
>> fi
>> fi
>> fi
>> -----------------------
>>
>> That should work's compiling with this try...
>>
>> Cheers,
>> Cheick
>>
>>
>>
>> -----Message d'origine-----
>> De : gate-users-bounces at lists.healthgrid.org [mailto:gate-users-
>> bounces at lists.healthgrid.org] De la part de Dendooven Peter
>> Envoy? : jeudi 18 juin 2009 11:40
>> ? : gate-users at lists.healthgrid.org
>> Objet : Re: [Gate-users] installing Gate 4.0.0 on Mac OS X 10.4.11
>>
>> Dear Cheick,
>>
>> thanks for the input. Following your suggestion, the lib64 related
>> problem has gone away. Also, the lmf-related comments have
>> mysteriously disappeared. The make now runs without any messages.
>> However, typing "Gate" results in "Command not found".
>>
>> The make process creates a /tmp/Darwin-g++/Gate directory with 758
>> items. In it is an exe directory containing Gate.d, Gate.o and
>> obj.last . I cannot see an executable called Gate on the whole of my
>> computer.
>> Do you have any idea of the present problem ?
>>
>> Best wishes,
>> Peter
>>
>> On 17 Jun 2009, at 16:21, THIAM Cheick 219838 wrote:
>>
>>> Hello,
>>>
>>> I think that X11 installation on Mac-OS (10.4 or 10.5) does not
>>> contain lib64... Are you sure /usr/X11R6/lib64 dir exist in your
>>> installation? if it is not case, I suggest to comment line 99 in
>>> your variables.gmk file
>>>
>>> # LDFLAGS :=-L/usr/X11R6/lib64 $(LDFLAGS) ; and try again
>>>
>>> Hope this helps,
>>>
>>> Cheick
>>>
>>>
>>>
>>> -----Message d'origine-----
>>> De : gate-users-bounces at lists.healthgrid.org [mailto:gate-users-
>>> bounces at lists.healthgrid.org] De la part de Dendooven Peter
>>> Envoy? : mercredi 17 juin 2009 15:25
>>> ? : gate-users at lists.healthgrid.org
>>> Objet : [Gate-users] installing Gate 4.0.0 on Mac OS X 10.4.11
>>>
>>> Dear all,
>>>
>>> after some trouble installing Gate 4.0.0 with Geant4.9.1.p03 on Mac
>>> OS X 10.4.11 (on an Intel-based MacBook), the make process seems to
>>> run fine until the following messages appear:
>>>
>>> Compiling Gate.cc ...
>>> Using granular libraries ...
>>> Linking Gate ...
>>> i686-apple-darwin8-g++-4.0.1: unrecognized option '-rdynamic'
>>> /usr/bin/ld: warning -L: directory name (/usr/X11R6/lib64) does not
>>> exist
>>> /lib) does not exist -L: directory name (/Applications/lmf_v3.0
>>> /lib) does not exist -L: directory name (/Applications/lmf_v3.0
>>> /usr/bin/ld: can't locate file for: -lLMF
>>> collect2: ld returned 1 exit status
>>> make: *** [bin/Darwin-g++/Gate] Error 1
>>>
>>> X11 was installed from the original Mac OS installation CD using the
>>> default installation process.
>>>
>>> Geant4.9.1.p03 and Root run fine on their own.
>>>
>>> Any help in solving this problem is appreciated. The GATE
>>> installation guide (version 3.1.2) is not clear to me in this
>>> respect.
>>>
>>> Best wishes,
>>> Peter Dendooven
>>>
>>> -----------------------------------
>>> Dr. Peter Dendooven
>>> KVI
>>> University of Groningen
>>> Zernikelaan 25
>>> 9747 AA Groningen
>>> the Netherlands
>>> tel.: +31 50 363 3615/3600
>>> fax: +31 50 363 4003
>>> e-mail: dendooven at kvi.nl
>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.healthgrid.org
>>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>>
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>
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