[Gate-users] Dynamic library linking error

[Ryckx Nick]

Dear Gate users,

I am fairly new in the world of Gate and trying to run Gate.

I used the following libraries
- Gate 6.1
- Geant4.9.4.p01
- Root 5.28
- CLHEP 2.1.0.1

I followed the updated install guide, and everything compiled well. When I try running gate, I get the following error:

Gate: symbol lookup error: /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4processes.so: undefined symbol: aTrackAllocator

When using ldd to see if all the libraries are linked, get the following result:

    linux-gate.so.1 =>  (0xb76e6000)
    libGate.so => /opt/simulation/gate6_1/tmp/Linux-g++/Gate/libGate.so (0xb7254000)
    libCore.so => /opt/simulation/root_5_28/lib/libCore.so (0xb6b3c000)
    libG4Tree.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4Tree.so (0xb6b2c000)
    libG4FR.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4FR.so (0xb6b10000)
    libG4GMocren.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4GMocren.so (0xb6acf000)
    libG4visHepRep.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4visHepRep.so (0xb6a4e000)
    libG4RayTracer.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4RayTracer.so (0xb6a32000)
    libG4VRML.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4VRML.so (0xb6a0e000)
    libG4vis_management.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4vis_management.so (0xb6966000)
    libG4modeling.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4modeling.so (0xb68b3000)
    libG4interfaces.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4interfaces.so (0xb6876000)
    libG4run.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4run.so (0xb6832000)
    libG4tracking.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4tracking.so (0xb67eb000)
    libG4processes.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4processes.so (0xb53ad000)
    libG4particles.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4particles.so (0xb52ab000)
    libG4materials.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4materials.so (0xb5223000)
    libG4intercoms.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4intercoms.so (0xb51da000)
    libG4global.so => /opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4global.so (0xb519f000)
    libCLHEP-2.1.0.1.so => /opt/simulation/CLHEP_2_1_0_1/CLHEP/lib/libCLHEP-2.1.0.1.so (0xb505c000)
    libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xb501e000)
    libstdc++.so.6 => /usr/lib/i386-linux-gnu/libstdc++.so.6 (0xb4f33000)
    libgcc_s.so.1 => /lib/i386-linux-gnu/libgcc_s.so.1 (0xb4f14000)
    libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xb4d92000)
    libz.so.1 => /lib/i386-linux-gnu/libz.so.1 (0xb4d7d000)
    libpcre.so.3 => /lib/i386-linux-gnu/libpcre.so.3 (0xb4d3e000)
    libX11.so.6 => /usr/lib/i386-linux-gnu/libX11.so.6 (0xb4c08000)
    libXaw.so.7 => /usr/lib/libXaw.so.7 (0xb4baa000)
    libXt.so.6 => /usr/lib/i386-linux-gnu/libXt.so.6 (0xb4b4e000)
    /lib/ld-linux.so.2 (0xb76e7000)
    libxcb.so.1 => /usr/lib/i386-linux-gnu/libxcb.so.1 (0xb4b2f000)
    libdl.so.2 => /lib/i386-linux-gnu/libdl.so.2 (0xb4b2a000)
    libXext.so.6 => /usr/lib/i386-linux-gnu/libXext.so.6 (0xb4b16000)
    libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb4afd000)
    libXpm.so.4 => /usr/lib/libXpm.so.4 (0xb4aec000)
    libSM.so.6 => /usr/lib/i386-linux-gnu/libSM.so.6 (0xb4ae3000)
    libICE.so.6 => /usr/lib/i386-linux-gnu/libICE.so.6 (0xb4ac9000)
    libXau.so.6 => /usr/lib/i386-linux-gnu/libXau.so.6 (0xb4ac4000)
    libXdmcp.so.6 => /usr/lib/i386-linux-gnu/libXdmcp.so.6 (0xb4abd000)
    libuuid.so.1 => /lib/i386-linux-gnu/libuuid.so.1 (0xb4ab7000)

When using ldd -v (verbose), the extract about libG4processes is
/opt/simulation/geant4_9_4_p01/lib/Linux-g++/libG4processes.so:
        libc.so.6 (GLIBC_2.4) => /lib/i386-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.1.3) => /lib/i386-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.0) => /lib/i386-linux-gnu/libc.so.6
        libc.so.6 (GLIBC_2.1) => /lib/i386-linux-gnu/libc.so.6
        libgcc_s.so.1 (GCC_3.0) => /lib/i386-linux-gnu/libgcc_s.so.1
        libgcc_s.so.1 (GCC_4.0.0) => /lib/i386-linux-gnu/libgcc_s.so.1
        libstdc++.so.6 (CXXABI_1.3) => /usr/lib/i386-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4) => /usr/lib/i386-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.9) => /usr/lib/i386-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.11) => /usr/lib/i386-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (GLIBCXX_3.4.15) => /usr/lib/i386-linux-gnu/libstdc++.so.6
        libstdc++.so.6 (CXXABI_1.3.1) => /usr/lib/i386-linux-gnu/libstdc++.so.6
        libm.so.6 (GLIBC_2.0) => /lib/i386-linux-gnu/libm.so.6
        libm.so.6 (GLIBC_2.1) => /lib/i386-linux-gnu/libm.so.6

Until now, everything seems to be fine, and all my environment variables are sourced OK (source in .bashrc). But when I use ldd -r (reporting all missing objects), I get a whole bunch of errors of this type:

undefined symbol: _ZN14G4EventManager13SetUserActionEP17G4UserEventAction    (/opt/simulation/gate6_1/tmp/Linux-g++/Gate/libGate.so)
or
undefined symbol: _ZN4Cint17G__SourceFileInfo4InitEPKc    (/opt/simulation/root_5_28/lib/libCore.so)

I tried looking through this problem for two weeks, but I'm not getting anywhere.

If someone knows how to solve this issue, please let me know. If it has already been solved in a previous mail exchange, my apologies, but you have got to admit that listing all the exchanges without giving a "search" tool on the Open Gate Collaboration website is not very user-friendly. But that is a small detail.

Best regards,
Nick Ryckx


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