[Gate-users] Problems with compiling GATE
Samuel BURG
samuel_burg at yahoo.fr
Tue Jul 29 12:07:51 CEST 2008
Hello,
first, </gate/output/ascii/setOutFileSinglesFlag 0> cannot work until </gate/digitizer/Singles/insert adder> do.
second, I use Geant 4.9.p01 (28-08-2007) as recommended, not 4.9.p02.
For me it work with 4.9.p01 (if I remember it also work for me with 4.8.p02)
Best regards,
Samuel Burg
----- Message d'origine ----
De : franklin pereira <pnicholasf at gmail.com>
À : Samuel BURG <samuel_burg at yahoo.fr>
Envoyé le : Lundi, 28 Juillet 2008, 20h54mn 37s
Objet : Re: Re : [Gate-users] Problems with compiling GATE
Hello,
I installed root-5.14, recompiled geant and gate using gcc-4.1.2
After that I tried the PET benchmark tests but it aborts. I have
included the std output here.
As you will notice, the commands that do not execute are:
***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesFlag 0> *****
Also, I set the flags for graphics output using openGL, but this does
not show in the available graphics system list detected by gate.
I checked for openGL libraries and they are there ( they come with the
ubuntu 8.04 distribution).
Also the geant configure script is able to detect it under the /usr directory.
I'd appreciate your feedback in this regard.
Thank you,
Franklin.
*************************************************************
Geant4 version Name: geant4-09-00-patch-02 (25-January-2008)
Copyright : Geant4 Collaboration
Reference : NIM A 506 (2003), 250-303
WWW : http://cern.ch/geant4
*************************************************************
Visualization Manager instantiating...
Visualization Manager initialising...
Registering graphics systems...
You have successfully registered the following graphics systems.
Current available graphics systems are:
ASCIITree (ATree)
DAWNFILE (DAWNFILE)
G4HepRep (HepRepXML)
G4HepRepFile (HepRepFile)
RayTracer (RayTracer)
VRML1FILE (VRML1FILE)
VRML2FILE (VRML2FILE)
Registering model factories...
You have successfully registered the following model factories.
Registered model factories:
generic
drawByCharge
drawByParticleID
drawByOriginVolume
drawByAttribute
Registered filter factories:
chargeFilter
particleFilter
originVolumeFilter
attributeFilter
Time set to (s) 0
[GateSystemListManager::CheckScannerAutoCreation:
Creating new system based on volume inserter 'cylindricalPET'
GATE object: 'systems/cylindricalPET'
Components:
GATE object: 'systems/cylindricalPET/base'
Attached to volume: cylindricalPET
Nb of children: 1
GATE object: 'systems/cylindricalPET/rsector'
Attached to volume: head
Nb of children: 1
GATE object: 'systems/cylindricalPET/module'
Attached to volume: module
Nb of children: 1
GATE object: 'systems/cylindricalPET/submodule'
Attached to volume: block
Nb of children: 1
GATE object: 'systems/cylindricalPET/crystal'
Attached to volume: crystal
Nb of children: 4
GATE object: 'systems/cylindricalPET/layer0'
Attached to volume: LSO
Nb of children: 0
GATE object: 'systems/cylindricalPET/layer1'
Attached to volume: BGO
Nb of children: 0
GATE object: 'systems/cylindricalPET/layer2'
Attached to volume: ---
Nb of children: 0
GATE object: 'systems/cylindricalPET/layer3'
Attached to volume: ---
Nb of children: 0
geometrical design type: 1
ring diameter: 86.5 cm
rsector axial pitch: 0 fm
rsector azimuthal pitch: 45 degree
rsector tangential size: 32 cm
rsector axial size: 40.2 cm
module axial size: 10 cm
module tangential size: 8 cm
module axial pitch: 10 cm
module tangential pitch: 8 cm
submodule axial size: 1.99 cm
submodule tangential size: 1.59 cm
submodule axial pitch: 2 cm
submodule tangential pitch: 1.6 cm
crystal radial size: 3 cm
crystal axial size: 3.8 mm
crystal tangential size: 3 mm
crystal axial pitch: 4 mm
crystal tangential pitch: 3.2 mm
layer0 radial size: 1.5 cm
in layer0 interaction length: 7.5 mm
layer1 radial size: 1.5 cm
in layer1 interaction length: 7.5 mm
Axial nb of rsectors: 1
Azimuthal nb of rsectors: 8
Axial nb of modules: 4
Tangential nb of modules: 4
Axial nb of submodules: 5
Tangential nb of submodules: 5
Axial nb of crystals: 5
Tangential nb of crystals: 5
Radial nb of layers: 2
WARNING !
SetCutValueForOthers became obsolete.
It is harmless to remove this invokation without any side effects.
This dummy method implementation will be removed soon.
***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
***** Batch is interupted!! *****
Ignoring confine condition
Ignoring confine condition
GateSourceMgr::ListSources: List of the sources in the source managaer
Source --------------> F18LineSource
ID : 0
type :
activity (Bq) : 100000
startTime (s) : 0
time (s) : 0
forcedUnstable : 1
forcedHalfLife (s) : 6586.2
verboseLevel : 0
----------------------
Source --------------> O15LineSource
ID : 1
type :
activity (Bq) : 100000
startTime (s) : 0
time (s) : 0
forcedUnstable : 1
forcedHalfLife (s) : 122.24
verboseLevel : 0
----------------------
***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesFlag 0> *****
***** Batch is interupted!! *****
Graphics systems deleted.
Visualization Manager deleting...
2008/7/28 Samuel BURG <samuel_burg at yahoo.fr>:
>
> The best solution is to downgarde GCC to 4.1.x.
> Then you can compil all the stuff for Gate without any error.
> It's better to use ROOT 5.14 for Gate 3.1.2
>
> I've allready do that on Ubuntu 8.04 TSL x64, so I know the relevent
> packadges are availaible.
>
> Best regards,
>
> Samuel Burg
>
>
> ----- Message d'origine ----
> De : Zhibin Huang <zxh6 at case.edu>
> À : franklin pereira <pnicholasf at gmail.com>
> Cc : gate-users at lists.healthgrid.org
> Envoyé le : Vendredi, 25 Juillet 2008, 21h06mn 36s
> Objet : Re: [Gate-users] Problems with compiling GATE
>
> Recently I successfully installed Gate under Ubuntu8.04 when I used
> ROOT5.19. It seems that in Ubntu8.04, ROOT5.14 can't be compiled
> successfully.
>
> Before you install GATE, you have to modify the GNUmake file. As a
> reference, please see the attachment and modify the path properly. My
> webpage may also be useful for both Gate installation and Ubuntu8.04
> configuration:
> please search for GATE under the link:
> https://filer.case.edu/~zxh6/data/daily-log
>
> Good luck!
>
> On Fri, Jul 25, 2008 at 1:43 PM, franklin pereira <pnicholasf at gmail.com>
> wrote:
>>
>> Hi,
>>
>> I have a Dell Vostro ( intel core duo processor) with Ubuntu 8.04
>> installed.
>> The default version of the gcc compiler is 4.2.3
>>
>> I recently downloaded Gate3.1.2, Geant4 (version 9.0), ROOT (5.14).
>>
>> Geant4 compiled without any problems.
>>
>> However, I am having problems with compiling ROOT-5.14.
>> I get tons of warnings and then the compilation aborts with the
>> following error message:
>>
>>
>> *************************************************************************************************************************
>> >> bin/rmkdepend -R -fcint/src/gcc3strm.d -Y -w 1000 -- -pipe -m32 -Wall
>> >> -W -Woverloaded-virtual -fPIC -Iinclude -DG__REGEXP -DG__UNIX
>> >> -DG__SHAREDLIB -DG__OSFDLL -DG__ROOT -DG__REDIRECTIO -DG__STD_EXCEPTION
>> >> -DG__HAVE_CONFIG -DG__NOMAKEINFO -DG__CINTBODY -Icint/src -pthread
>> >> -Icint/lib/gcc3strm -D__cplusplus -- cint/src/gcc3strm.cxx
>> g++ -O -pipe -m32 -Wall -W -Woverloaded-virtual -fPIC -Iinclude
>> -DG__REGEXP -DG__UNIX -DG__SHAREDLIB -DG__OSFDLL -DG__ROOT
>> -DG__REDIRECTIO -DG__STD_EXCEPTION -DG__HAVE_CONFIG -DG__NOMAKEINFO
>> -DG__CINTBODY -Icint/src -pthread -Icint/lib/gcc3strm -o
>> cint/src/gcc3strm.o -c cint/src/gcc3strm.cxx
>> cint/src/gcc3strm.cxx: In function 'int G__G__stream_7_7_0(G__value*,
>> const char*, G__param*, int)':
>> cint/src/gcc3strm.cxx:311: error: 'class std::fpos<__mbstate_t>' has
>> no member named 'operator=='
>> cint/src/gcc3strm.cxx: In function 'int G__G__stream_7_8_0(G__value*,
>> const char*, G__param*, int)':
>> cint/src/gcc3strm.cxx:317: error: 'class std::fpos<__mbstate_t>' has
>> no member named 'operator!='
>> make: *** [cint/src/gcc3strm.o] Error 1
>>
>> *************************************************************************************************************************
>>
>>
>> ROOT 5.20, however, compiles cleanly, but gate will not compile with
>> this version of ROOT as is cannot find the proper function
>> declarations for the various ROOT functions ( the header files are in
>> /root/include and this is passed on to the g++ compiler correctly
>> in the GATE makefile ).
>>
>>
>> A sample of these error messages are:
>>
>>
>> **************************************************************************************************************
>> >>Using global libraries ...
>> Linking Gate ...
>>
>> /opt/Geant4/geant4.9.0.p02/tmp/Linux-g++/Gate/libGate.a(GateHitFileReader.o):
>> In function `GateHitFileReader::PrepareAcquisition()':
>> GateHitFileReader.cc:(.text+0x102a): undefined reference to
>> `TFile::TFile(char const*, char const*, char const*, int)'
>> /opt/Geant4/geant4.9.0.p02/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o):
>> In function `GateToRoot::RecordVoxels(GateVGeometryVoxelStore*)':
>> GateToRoot.cc:(.text+0xe47): undefined reference to `TFile::TFile(char
>> const*, char const*, char const*, int)'
>> /opt/Geant4/geant4.9.0.p02/tmp/Linux-g++/Gate/libGate.a(GateToRoot.o):
>> In function `GateToRoot::RecordBeginOfAcquisition()':
>> GateToRoot.cc:(.text+0x3fd3): undefined reference to
>> `TFile::TFile(char const*, char const*, char const*, int)'
>> GateToRoot.cc:(.text+0x423b): undefined reference to
>> `TFile::TFile(char const*, char const*, char const*, int)'
>> /opt/root/lib/libTree.so: undefined reference to
>> `TFileCacheRead::TFileCacheRead(TFile*, int)'
>> /opt/root/lib/libTree.so: undefined reference to `TFile::GetCacheRead()
>> const'
>> /opt/root/lib/libTree.so: undefined reference to
>> `TBufferFile::WriteClones(TClonesArray*, int)'
>> /opt/root/lib/libTree.so: undefined reference to
>> `TBufferFile::WriteArray(float const*, int)'
>> /opt/root/lib/libTree.so: undefined reference to
>> `TSQLRow::Streamer(TBuffer&)'
>> /opt/root/lib/libTree.so: undefined reference to
>> `TBufferFile::WriteVersion(TClass const*, bool)'
>> /opt/root/lib/libHist.so: undefined reference to
>> `ROOT::Fit::BinData::Initialize(unsigned int, unsigned int,
>> ROOT::Fit::BinData::ErrorType)'
>> /opt/root/lib/libTree.so: undefined reference to `typeinfo for TSQLResult'
>> /opt/root/lib/libTree.so: undefined reference to
>> `TBufferFile::ReadObject(TClass const*)'
>> /opt/root/lib/libTree.so: undefined reference to `TKey::Create(int,
>> TFile*)'
>>
>> ********************************************************************************************************************
>>
>>
>> My guess is that the function declarations in ROOT5.20 have changed
>> from version 5.14, therefore the conflict.
>> However, I am clueless regarding the compilation errors generated
>> while trying to compile ROOT-5.14.
>> Is this due to the newer version of gcc that comes with the Ubuntu OS
>> ? I am at a loss and would appreciate help regarding this.
>>
>> Thanks a lot,
>> Franklin.
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.healthgrid.org
>> http://lists.healthgrid.org/mailman/listinfo/gate-users
>
>
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