[Gate-users] GATE and GEANT Install

TienGarry gjtian at hotmail.com
Thu Dec 18 12:42:03 CET 2008

Thank you for your help.

This is the libxml2 install information. I can find the libxml2.a
libxml2.la libxml2.so libxml2.so2 libxml2.so.2.6.3 in /usr/lib

gary at polyu-gary:~$ sudo apt-get install libxml2
Reading package lists... Done
Building dependency tree       
Reading state information... Done
libxml2 is already the newest version.
The following packages were automatically installed and are no longer required:
  kdelibs-data cvs
Use '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 directory

It 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 +0100
From: gate.stute at gmail.com
To: gjtian at hotmail.com
Subject: Re: [Gate-users] GATE and GEANT Install
CC: gate-users at lists.healthgrid.org


Just install the libxml2 library and its headers, recompile Gate and it will be ok, finally !


On Thu, Dec 18, 2008 at 2:50 AM, TienGarry <gjtian at hotmail.com> wrote:


I installed geant, root, clhep, and lmf3.0 successfully. After the geant4 installation, I can find the env.sh script file in two paths in my


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++
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.sh

I 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/geant4
On this machine the G4LIB=/home/gary/GATE4.0/geant4.9.1.p03/install/lib/geant4

On this machine the G4LEVELGAMMADATA=/home/gary/GATE4.0/geant4.9.1.p03/data/PhotonEvaporation2.0
On this machine the G4RADIOACTIVEDATA=/home/gary/GATE4.0/geant4.9.1.p03/data/RadioactiveDecay3.2
On this machine the G4LEDATA=/home/gary/GATE4.0/geant4.9.1.p03/data/G4EMLOW5.1

On this machine the G4NEUTRONHPDATA=/home/gary/GATE4.0/geant4.9.1.p03/data/G4NDL3.12
On this machine the G4ABLADATA=/home/gary/GATE4.0/geant4.9.1.p03/data/G4ABLA3.0
On this machine the CLHEP_BASE_DIR=/home/gary/GATE4.0/CLHEP/install

On this machine the CLHEP_INCLUDE_DIR=/home/gary/GATE4.0/CLHEP/install/include
On this machine the CLHEP_LIB_DIR=/home/gary/GATE4.0/CLHEP/install/lib
On this machine the CLHEP_LIB=CLHEP

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 XAWFLAGS=
On this machine the XAWLIBS=
On this machine the G4LIB_BUILD_SHARED=1

On this machine the G4LIB_USE_GRANULAR=1
On this machine the G4UI_USE_TCSH=1

LD_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_PATH

variable in your environment, and no other outdated installations
of CLHEP are by chance referenced through $LD_LIBRARY_PATH and
present in your system !

But for my gate4 installation, I follow the guide, 

gary at polyu-gary:~/GATE4.0/gate_v4.0.0$ exprot G4VERSION=9.1
then copy geant env.sh file into path  G4INSTALL=/home/gary/GATE4.0/geant4.9.1.p03/install/src/geant4,
then type
gary at polyu-gary:~/GATE4.0/gate_v4.0.0$ source env_gate.sh

I can get:

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
Use of ROOT disabled

ROOT real-time plotter disabled
LMF data output disabled
ECAT7 data output disabled
GATEHOME is set to /home/gary/GATE4.0/gate_v4.0.0
Checking your path variable...
 ==> OK: /home/gary/GATE4.0/gate_v4.0.0/bin/Linux-g++ is already in your path variable

G4VERSION9 is set: GATE is compatible with the geant4 version 9.1


gary 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 found
In 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 directory

Compiling GateSurface.cc ...
/bin/sh: xml2-config: not found
In 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 directory

In 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 used

make[1]: *** [../../tmp/Linux-g++/Gate/GateSurface.o] Error 1
source/geometry finished
Entering source/digitizer ...
make[1]: Nothing to be done for `obj'.
source/digitizer finished
Entering source/output ...

make[1]: Nothing to be don

If 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.

MSN保护盾,十八般武艺保障MSN安全! 现在就下载!


Gate-users mailing list

Gate-users at lists.healthgrid.org


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20081218/4b8c08d5/attachment.htm>

More information about the Gate-users mailing list