[Gate-users] GATE and GEANT Install

Thu Dec 18 13:51:22 CET 2008

Solved, thanks.

From: gjtian at hotmail.comTo: gate.stute at gmail.comSubject: RE: [Gate-users] GATE and GEANT InstallDate: Thu, 18 Dec 2008 19:42:03 +0800CC: gate-users at lists.healthgrid.org

Thank you for your help.This is the libxml2 install information. I can find the libxml2.alibxml2.la libxml2.so libxml2.so2 libxml2.so.2.6.3 in /usr/libgary at polyu-gary:~$ sudo apt-get install libxml2Reading package lists... DoneBuilding dependency tree       Reading state information... Donelibxml2 is already the newest version.The following packages were automatically installed and are no longer required:  kdelibs-data cvsUse 'apt-get autoremove' to remove them.0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded.But I still get the error like this:./source/digitizer/include/GateHitFileReader.hh:50:19: error: TROOT.h: No such file or directory./source/digitizer/include/GateHitFileReader.hh:51:19: error: TFile.h: No such file or directory./source/digitizer/include/GateHitFileReader.hh:52:19: error: TTree.h: No such file or directoryIt seems that I need these header files.Do I need to add /usr/lib into the LD_LIBRARY_PATH?

Date: Thu, 18 Dec 2008 12:01:08 +0100From: gate.stute at gmail.comTo: gjtian at hotmail.comSubject: Re: [Gate-users] GATE and GEANT InstallCC: gate-users at lists.healthgrid.orgHi,Just install the libxml2 library and its headers, recompile Gate and it will be ok, finally !Cheers,Simon
On Thu, Dec 18, 2008 at 2:50 AM, TienGarry <gjtian at hotmail.com> wrote:

Hi, ALLI installed geant, root, clhep, and lmf3.0 successfully. After the geant4 installation, I can find the env.sh script file in two paths in mysystem./home/gary/GATE4.0/geant4.9.1.p03/.config/bin/Linux-g++/home/gary/GATE4.0/geant4.9.1.p03/install/src/geant4/.config/bin/Linux-g++when I type gary at polyu-gary:~/GATE4.0/geant4.9.1.p03$ source /home/gary/GATE4.0/geant4.9.1.p03/.config/bin/Linux-g++or gary at polyu-gary:~/GATE4.0/geant4.9.1.p03$ source /home/gary/GATE4.0/geant4.9.1.p03/install/src/geant4/.config/bin/Linux-g++/env.shI can get the following information:On this machine the G4SYSTEM=Linux-g++On this machine the G4INSTALL=/home/gary/GATE4.0/geant4.9.1.p03/install/src/geant4On this machine the G4LIB=/home/gary/GATE4.0/geant4.9.1.p03/install/lib/geant4On this machine the G4LEVELGAMMADATA=/home/gary/GATE4.0/geant4.9.1.p03/data/PhotonEvaporation2.0On this machine the G4RADIOACTIVEDATA=/home/gary/GATE4.0/geant4.9.1.p03/data/RadioactiveDecay3.2On this machine the G4LEDATA=/home/gary/GATE4.0/geant4.9.1.p03/data/G4EMLOW5.1On this machine the G4NEUTRONHPDATA=/home/gary/GATE4.0/geant4.9.1.p03/data/G4NDL3.12On this machine the G4ABLADATA=/home/gary/GATE4.0/geant4.9.1.p03/data/G4ABLA3.0On this machine the CLHEP_BASE_DIR=/home/gary/GATE4.0/CLHEP/installOn this machine the CLHEP_INCLUDE_DIR=/home/gary/GATE4.0/CLHEP/install/includeOn this machine the CLHEP_LIB_DIR=/home/gary/GATE4.0/CLHEP/install/libOn this machine the CLHEP_LIB=CLHEPOn this machine the G4VIS_BUILD_RAYTRACERX_DRIVER=1On this machine the G4VIS_USE_RAYTRACERX=1On 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_SHARED=1On this machine the G4LIB_USE_GRANULAR=1On this machine the G4UI_USE_TCSH=1LD_LIBRARY_PATH is set to include CLHEP and Geant4 libraries. NOTE : verify that the correct path for the CLHEP library- $CLHEP_BASE_DIR/lib - is included in the $LD_LIBRARY_PATHvariable in your environment, and no other outdated installationsof CLHEP are by chance referenced through $LD_LIBRARY_PATH andpresent in your system !But for my gate4 installation, I follow the guide, gary at polyu-gary:~/GATE4.0/gate_v4.0.0$ exprot G4VERSION=9.1then copy geant env.sh file into path G4INSTALL=/home/gary/GATE4.0/geant4.9.1.p03/install/src/geant4,then typegary at polyu-gary:~/GATE4.0/gate_v4.0.0$ source env_gate.shI can get:G4WORKDIR set to .G4TMP set to ./tmpG4BIN set to ./binData analysis and output features enabledAscii data output enabledTransport and generation of optical photons is enabledUse of ROOT disabledROOT real-time plotter disabledLMF data output disabledECAT7 data output disabledGATEHOME is set to /home/gary/GATE4.0/gate_v4.0.0Checking your path variable... ==> OK: /home/gary/GATE4.0/gate_v4.0.0/bin/Linux-g++ is already in your path variableG4VERSION9 is set: GATE is compatible with the geant4 version 9.1Donegary at polyu-gary:~/GATE4.0/gate_v4.0.0$ make I get the following errors.Entering source/geometry ...Making dependency for file src/GateSurface.cc .../bin/sh: xml2-config: not foundIn file included from src/GateSurface.cc:18:../management/include/GateXMLDocument.hh:19:30: error: libxml/xmlmemory.h: No such file or directory../management/include/GateXMLDocument.hh:20:27: error: libxml/parser.h: No such file or directoryCompiling GateSurface.cc .../bin/sh: xml2-config: not foundIn file included from src/GateSurface.cc:18:../management/include/GateXMLDocument.hh:19:30: error: libxml/xmlmemory.h: No such file or directory../management/include/GateXMLDocument.hh:20:27: error: libxml/parser.h: No such file or directoryIn file included from src/GateSurface.cc:18:../management/include/GateXMLDocument.hh:28: error: 'xmlNodePtr' does not name a type../management/include/GateXMLDocument.hh:62: error: 'xmlDocPtr' does not name a type../management/include/GateXMLDocument.hh:63: error: 'xmlNodePtr' does not name a type/home/gary/GATE4.0/CLHEP/install/include/CLHEP/Units/PhysicalConstants.h:78: warning: 'CLHEP::electron_charge' defined but not usedmake[1]: *** [../../tmp/Linux-g++/Gate/GateSurface.o] Error 1source/geometry finishedEntering source/digitizer ...make[1]: Nothing to be done for `obj'.source/digitizer finishedEntering source/output ...make[1]: Nothing to be donIf I define $ROOT_SYS and $LMF_HOME, I still can not make gate sucessfully.Pls help me, guys, I spent a lot of time on it, but can not make it. This is the last step for me to become a real GATE USER.Thank you so much.

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