<div dir="ltr">Hello Gate users,<div><br></div><div>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.</div>
<div><br></div><div>Thank you,</div><div><br></div><div>-Amy</div><div><br></div><div><br></div><div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div>Following procedures from <a href="http://wiki.opengatecollaboration.org/index.php/New_Compilation_ProcedureV6.2" target="_blank">http://wiki.opengatecollaboration.org/index.php/New_Compilation_ProcedureV6.2</a></div>
<div><br></div></div><div style="font-family:arial,sans-serif;font-size:13px">##### ACQUIRE A CLUSTER NODE #####</div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div><br></div><div>qsub -I -l select=1:ngpus=1:gpu_model=k20,walltime=2:00:00</div>
<div><br></div><div><br></div><div>##### LOAD NEEDED MODULES #####</div><div><br></div><div>module add gcc/4.8.1 cmake/2.8.12 cuda-toolkit/5.5.22 fftw/2.1.5-double</div><div><br></div><div><br></div><div>##### INSTALLING CLHEP #####</div>
<div><br></div></div><div style="font-family:arial,sans-serif;font-size:13px">cd /home/username</div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div><br></div><div>wget <a href="http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/clhep-2.1.1.0.tgz" target="_blank">http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/clhep-2.1.1.0.tgz</a></div>
<div>tar -zxf clhep-2.1.1.0.tgz</div><div>cd <a href="http://2.1.1.0/CLHEP" target="_blank">2.1.1.0/CLHEP</a></div><div>./configure --prefix=$PWD</div><div>make -j 4</div><div>make install</div></div><div style="font-family:arial,sans-serif;font-size:13px">
export PATH=$PATH:/home/username/<a href="http://2.1.1.0/CLHEP/bin" target="_blank">2.1.1.0/CLHEP/bin</a></div><div style="font-family:arial,sans-serif;font-size:13px">export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/<a href="http://2.1.1.0/CLHEP/lib" target="_blank">2.1.1.0/CLHEP/lib</a></div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">##### INSTALLING ROOT #####</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">cd /home/username</div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div><br>
</div><div>wget <a href="ftp://root.cern.ch/root/root_v5.30.06.source.tar.gz" target="_blank">ftp://root.cern.ch/root/root_v5.30.06.source.tar.gz</a></div><div>tar -zxf root_v5.30.06.source.tar.gz</div><div>mv root root_v5.30.06</div>
<div>./configure linuxx8664gcc --prefix=$PWD</div><div>make -j 4</div><div>make install</div></div><div style="font-family:arial,sans-serif;font-size:13px">source /home/username/root_v5.30.06/bin/thisroot.sh</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">##### INSTALLING GEANT #####</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">cd /home/username</div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div><br></div><div>wget <a href="http://geant4.web.cern.ch/geant4/support/source/geant4.9.5.p01.tar.gz" target="_blank">http://geant4.web.cern.ch/geant4/support/source/geant4.9.5.p01.tar.gz</a></div>
<div>tar -zxf geant4.9.5.p01.tar.gz</div><div>mkdir geant4.9.5.p01-build</div><div>mkdir geant4.9.5.p01-install</div><div>cd geant4.9.5.p01-build</div><div>ccmake ../geant4.9.5.p01</div><div># Press c to configure</div><div>
# Errors or warnings may pop-up on the 1st attempt</div><div># Press e</div></div><div style="font-family:arial,sans-serif;font-size:13px">CMAKE_INSTALL_PREFIX     /home/username/geant4.9.5.p01-install</div><div class="im" style="font-family:arial,sans-serif;font-size:13px">
<div>GEANT4_INSTALL_DATA      ON</div><div>GEANT4_USE_SYSTEM_CLHEP  ON</div><div># Press c to configure again</div><div># Press e (ignore developer warnings)</div><div># Press g to generate the Makefile</div><div>make -j 4</div>
<div>make install</div></div><div style="font-family:arial,sans-serif;font-size:13px">source /home/username/geant4.9.5.p01-install/bin/geant4.sh</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px">##### INSTALLING GATE #####</div><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">
cd /home/username</div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div><br></div><div>wget <a href="http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/gate_v6_2_tar_gz_15843.gz" target="_blank">http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/gate_release/2012/08/gate_v6_2_tar_gz_15843.gz</a></div>
<div>tar -zxf gate_v6_2_tar_gz_15843.gz</div><div>mkdir gate.6.2-build</div><div>mkdir gate.6.2-install</div><div>cd gate.6.2-build</div><div>ccmake ../gate_v6.2</div><div># Press c to configure</div></div><div style="font-family:arial,sans-serif;font-size:13px">
CMAKE_INSTALL_PREFIX     /home/username/gate_v6.2-install</div><div class="im" style="font-family:arial,sans-serif;font-size:13px"><div>GATE_USE_OPTICAL    ON</div><div># Press c to configure</div><div># Press c to configure again</div>
<div># Press g to generate the Makefile</div></div><div style="font-family:arial,sans-serif;font-size:13px">export CPLUS_INCLUDE_PATH=/home/username/root_v5.30.06/include:$CPLUS_INCLUDE_PATH</div><div class="im" style="font-family:arial,sans-serif;font-size:13px">
<div>make -j 4</div><div><br></div><div>[[ Stuck here ]]-------------------------------------------------------------</div><div><br></div></div><div style="font-family:arial,sans-serif;font-size:13px">...</div><div style="font-family:arial,sans-serif;font-size:13px">
[  8%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateSurfaceList.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[  8%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateRegularParam.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[  8%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateVVolume.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[  9%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateOutputVolumeID.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[  9%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateSystemComponentListMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">
[  9%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateMDBCreators.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">/home/username/gate_v6.2/source/geometry/src/GateSystemComponentListMessenger.cc: In member function ‘virtual void GateSystemComponentListMessenger::DoInsertion(const G4String&)’:</div>
<div style="font-family:arial,sans-serif;font-size:13px">/home/username/gate_v6.2/source/geometry/src/GateSystemComponentListMessenger.cc:75:24: warning: variable ‘newComponent’ set but not used [-Wunused-but-set-variable]</div>
<div style="font-family:arial,sans-serif;font-size:13px">   GateSystemComponent* newComponent=0;</div><div style="font-family:arial,sans-serif;font-size:13px">                        ^</div><div style="font-family:arial,sans-serif;font-size:13px">
[  9%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateVGeometryVoxelTranslator.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[  9%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxel.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 10%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelRangeTranslatorMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">
[ 10%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxelParameterizedMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 10%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateMultiSensitiveDetector.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 10%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateWedgeComponent.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 10%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelInterfileReader.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 10%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateElTub.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 11%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateObjectRepeaterListMessenger.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 11%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateTranslationMoveMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 11%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateEcatSystem.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 11%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateWedgeMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 11%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateHexagoneMessenger.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 11%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateEcatAccelSystem.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 12%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateCylinderMessenger.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 12%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateVoxelOutput.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 12%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateOrbitingMoveMessenger.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 12%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateArrayRepeater.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 12%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateCompressedVoxelOutput.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 13%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateOscTranslationMoveMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">
[ 13%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateSystemComponent.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 13%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateGeometryVoxelImageReader.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 13%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateDMapoperators.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 13%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateMDBFieldDecoder.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 13%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GatePVParameterisation.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 14%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateVoxelBoxParameterizedMessenger.cc.o</div>
<div style="font-family:arial,sans-serif;font-size:13px">[ 14%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateSystemListManager.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">[ 14%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateBoxReplica.cc.o</div>
<div class="im" style="font-family:arial,sans-serif;font-size:13px"><div>[ 14%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateCylindricalPETSystemMessenger.cc.o</div><div>[ 14%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateRegularParameterization.cc.o</div>
<div>[ 14%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateMDBFieldReader.cc.o</div></div><div style="font-family:arial,sans-serif;font-size:13px">In file included from /home/username/gate_v6.2/source/geometry/include/GateMDBFieldDecoder.hh:17:0,</div>
<div style="font-family:arial,sans-serif;font-size:13px">                 from /home/username/gate_v6.2/source/geometry/include/GateMDBFieldReader.hh:19,</div><div style="font-family:arial,sans-serif;font-size:13px">                 from /home/username/gate_v6.2/source/geometry/src/GateMDBFieldReader.cc:19:</div>
<div style="font-family:arial,sans-serif;font-size:13px">/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]’:</div>
<div style="font-family:arial,sans-serif;font-size:13px">/home/username/gate_v6.2/source/geometry/src/GateMDBFieldReader.cc:207:99:   required from here</div><div style="font-family:arial,sans-serif;font-size:13px">/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]</div>
<div style="font-family:arial,sans-serif;font-size:13px">       insert(*iter);</div><div style="font-family:arial,sans-serif;font-size:13px">                   ^</div><div style="font-family:arial,sans-serif;font-size:13px">
/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</div>
<div style="font-family:arial,sans-serif;font-size:13px">/home/username/gate_v6.2/source/digits_hits/include/GateMaps.hh:120:19: note: use ‘this->insert’ instead</div><div class="im" style="font-family:arial,sans-serif;font-size:13px">
[ 15%] Building CXX object CMakeFiles/Gate.dir/source/geometry/src/GateSystemListMessenger.cc.o</div><div style="font-family:arial,sans-serif;font-size:13px">In file included from /home/username/geant4.9.5.p01-install/include/Geant4/G4PhysicalConstants.hh:27:0,</div>
<div style="font-family:arial,sans-serif;font-size:13px">                 from /home/username/geant4.9.5.p01-install/include/Geant4/globals.hh:71,</div><div style="font-family:arial,sans-serif;font-size:13px">                 from /home/username/gate_v6.2/source/geometry/include/GateMDBFieldReader.hh:15,</div>
<div style="font-family:arial,sans-serif;font-size:13px">                 from /home/username/gate_v6.2/source/geometry/src/GateMDBFieldReader.cc:19:</div><div style="font-family:arial,sans-serif;font-size:13px">/home/username/<a href="http://2.1.1.0/CLHEP/include/CLHEP/Units/PhysicalConstants.h:80:21" target="_blank">2.1.1.0/CLHEP/include/CLHEP/Units/PhysicalConstants.h:80:21</a>: warning: ‘CLHEP::electron_charge’ defined but not used [-Wunused-variable]</div>
</div></div>