[Gate-users] Installing GATE onto cluster - Error

Amy Meldrum ameldru at g.clemson.edu
Mon Apr 7 15:50:22 CEST 2014 

Hello Gate users,

I have been working with someone for the past few weeks to try and install
GATE onto the cluster at my university. However, errors seem to arise
during the installation of gate_v6_2. I have copied the installation
procedure we have been using, and the messages that come up for the error
during installation of GATE. Any help is appreciated, having GATE on a
cluster would make my simulations much easier.

Thank you,

-Amy


Following procedures from
http://wiki.opengatecollaboration.org/index.php/New_Compilation_ProcedureV6.2

##### ACQUIRE A CLUSTER NODE #####

qsub -I -l select=1:ngpus=1:gpu_model=k20,walltime=2:00:00


##### LOAD NEEDED MODULES #####

module add gcc/4.8.1 cmake/2.8.12 cuda-toolkit/5.5.22 fftw/2.1.5-double


##### INSTALLING CLHEP #####

cd /home/username

wget
http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/clhep-2.1.1.0.tgz
tar -zxf clhep-2.1.1.0.tgz
cd 2.1.1.0/CLHEP
./configure --prefix=$PWD
make -j 4
make install
export PATH=$PATH:/home/username/2.1.1.0/CLHEP/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/2.1.1.0/CLHEP/lib


##### INSTALLING ROOT #####

cd /home/username

wget ftp://root.cern.ch/root/root_v5.30.06.source.tar.gz
tar -zxf root_v5.30.06.source.tar.gz
mv root root_v5.30.06
./configure linuxx8664gcc --prefix=$PWD
make -j 4
make install
source /home/username/root_v5.30.06/bin/thisroot.sh


##### INSTALLING GEANT #####

cd /home/username

wget http://geant4.web.cern.ch/geant4/support/source/geant4.9.5.p01.tar.gz
tar -zxf geant4.9.5.p01.tar.gz
mkdir geant4.9.5.p01-build
mkdir geant4.9.5.p01-install
cd geant4.9.5.p01-build
ccmake ../geant4.9.5.p01
# Press c to configure
# Errors or warnings may pop-up on the 1st attempt
# Press e
CMAKE_INSTALL_PREFIX     /home/username/geant4.9.5.p01-install
GEANT4_INSTALL_DATA      ON
GEANT4_USE_SYSTEM_CLHEP  ON
# Press c to configure again
# Press e (ignore developer warnings)
# Press g to generate the Makefile
make -j 4
make install
source /home/username/geant4.9.5.p01-install/bin/geant4.sh


##### INSTALLING GATE #####

cd /home/username

wget
http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/gate_v6_2_tar_gz_15843.gz
tar -zxf gate_v6_2_tar_gz_15843.gz
mkdir gate.6.2-build
mkdir gate.6.2-install
cd gate.6.2-build
ccmake ../gate_v6.2
# Press c to configure
CMAKE_INSTALL_PREFIX     /home/username/gate_v6.2-install
GATE_USE_OPTICAL    ON
# Press c to configure
# Press c to configure again
# Press g to generate the Makefile
export
CPLUS_INCLUDE_PATH=/home/username/root_v5.30.06/include:$CPLUS_INCLUDE_PATH
make -j 4

[[ Stuck here
]]-------------------------------------------------------------

...
[  8%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateSurfaceList.cc.o
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CMakeFiles/Gate.dir/source/geometry/src/GateMDBCreators.cc.o
/home/username/gate_v6.2/source/geometry/src/GateSystemComponentListMessenger.cc:
In member function 'virtual void
GateSystemComponentListMessenger::DoInsertion(const G4String&)':
/home/username/gate_v6.2/source/geometry/src/GateSystemComponentListMessenger.cc:75:24:
warning: variable 'newComponent' set but not used
[-Wunused-but-set-variable]
   GateSystemComponent* newComponent=0;
                        ^
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In file included from
/home/username/gate_v6.2/source/geometry/include/GateMDBFieldDecoder.hh:17:0,
                 from
/home/username/gate_v6.2/source/geometry/include/GateMDBFieldReader.hh:19,
                 from
/home/username/gate_v6.2/source/geometry/src/GateMDBFieldReader.cc:19:
/home/username/gate_v6.2/source/digits_hits/include/GateMaps.hh: In
instantiation of 'GateMap<Tkey, Tvalue>::GateMap(size_t, GateMap<Tkey,
Tvalue>**) [with Tkey = G4String; Tvalue = int; size_t = long unsigned
int]':
/home/username/gate_v6.2/source/geometry/src/GateMDBFieldReader.cc:207:99:
  required from here
/home/username/gate_v6.2/source/digits_hits/include/GateMaps.hh:120:19:
error: 'insert' was not declared in this scope, and no declarations were
found by argument-dependent lookup at the point of instantiation
[-fpermissive]
       insert(*iter);
                   ^
/home/username/gate_v6.2/source/digits_hits/include/GateMaps.hh:120:19:
note: declarations in dependent base 'std::map<G4String, int,
std::less<G4String>, std::allocator<std::pair<const G4String, int> > >' are
not found by unqualified lookup
/home/username/gate_v6.2/source/digits_hits/include/GateMaps.hh:120:19:
note: use 'this->insert' instead
[ 15%] Building CXX object
CMakeFiles/Gate.dir/source/geometry/src/GateSystemListMessenger.cc.o
In file included from
/home/username/geant4.9.5.p01-install/include/Geant4/G4PhysicalConstants.hh:27:0,
                 from
/home/username/geant4.9.5.p01-install/include/Geant4/globals.hh:71,
                 from
/home/username/gate_v6.2/source/geometry/include/GateMDBFieldReader.hh:15,
                 from
/home/username/gate_v6.2/source/geometry/src/GateMDBFieldReader.cc:19:
/home/username/2.1.1.0/CLHEP/include/CLHEP/Units/PhysicalConstants.h:80:21:
warning: 'CLHEP::electron_charge' defined but not used [-Wunused-variable]
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