[Gate-users] CLHEP library error

Andrej Studen Andrej.Studen at ijs.si
Wed Mar 2 09:52:27 CET 2016 

Hi!

This probably will not help, but what I did was that I searched my 
libraries for the offending symbol, and found out that it only appears 
in physics lists and processes:

#>for f in `ldd /data0/studen/software/install/Gate-slc/bin/Gate | awk 
'{print $3;}' | sed -n '/net/p'`; do echo $f; nm $f | grep 
GammaParticipants; done;

/net/f9pc22/data0/studen/software/install/geant4-slc/lib64/libG4physicslists.so
00000000000a2fa0 W _ZN10G4QGSModelI19G4GammaParticipantsE10GetStringsEv
00000000000a27a0 W 
_ZN10G4QGSModelI19G4GammaParticipantsE4InitERK9G4NucleusRK17G4DynamicParticle
00000000000a2d80 W _ZN10G4QGSModelI19G4GammaParticipantsEC1Ev
00000000000a2d80 W _ZN10G4QGSModelI19G4GammaParticipantsEC2Ev
00000000000a2780 W _ZN10G4QGSModelI19G4GammaParticipantsED0Ev
00000000000a26e0 W _ZN10G4QGSModelI19G4GammaParticipantsED1Ev
00000000000a26e0 W _ZN10G4QGSModelI19G4GammaParticipantsED2Ev
00000000000a2f20 W 
_ZNK10G4QGSModelI19G4GammaParticipantsE16ModelDescriptionERSo
00000000000a26c0 W 
_ZNK10G4QGSModelI19G4GammaParticipantsE17GetWoundedNucleusEv
00000000000a26d0 W 
_ZNK10G4QGSModelI19G4GammaParticipantsE20GetProjectileNucleusEv
0000000000309740 V _ZTI10G4QGSModelI19G4GammaParticipantsE
00000000000e3960 V _ZTS10G4QGSModelI19G4GammaParticipantsE
00000000003096e0 V _ZTV10G4QGSModelI19G4GammaParticipantsE
                  U _ZTV19G4GammaParticipants

/net/f9pc22/data0/studen/software/install/geant4-slc/lib64/libG4processes.so
0000000000bd6850 t _GLOBAL__I_G4GammaParticipants.cc
0000000000bd69a0 T 
_ZN19G4GammaParticipants18SelectInteractionsERK17G4ReactionProduct
0000000000bd71c0 W _ZN19G4GammaParticipantsD0Ev
0000000000bd71a0 W _ZN19G4GammaParticipantsD1Ev
0000000000bd71a0 W _ZN19G4GammaParticipantsD2Ev
00000000015f1380 V _ZTI19G4GammaParticipants
000000000124ce40 V _ZTS19G4GammaParticipants
00000000015f1320 V _ZTV19G4GammaParticipants

However both libG4processes.so and libG4physicslists.so seem to be the 
default Geant4 libraries for Gustaf. Btw - this is V7.1 w/ Geant10.1

Cheers

A.




On 03/02/16 09:25, Gustaf Lönn wrote:
> Hi again!
>
> I removed all the previous versions of geant4 and gate and did a full 
> recompilation from scratch with new build directories. Contrary to 
> what I stated before I am not using ubuntu but a Rocks 6.1.1 
> distribution of linux for cluster simulations.
>
> When I try to run gate I still get the same error:
>
> Symbol `_ZTV19G4GammaParticipants' has different size in shared 
> object, consider re-linking
> Gate: symbol lookup error: Gate: undefined symbol: 
> ZN12G4AllocStats6numCatE
>
> In my bash script I have:
> source /home/gate/gate_sources2/root/bin/thisroot.sh
> source /home/gate/gate_sources2/geant4.10.01.p03-install/bin/geant4.sh
> export Path=$PATH: /home/gate/gate_sources2/gate_v7.1-install/bin/
>
> and "ldd /home/gate/gate_sources2/gate_v7.1-install/bin/Gate” returns 
> the following output:
>
> inux-vdso.so.1 =>  (0x00007fffb4fff000)
> libG4Tree.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4Tree.so 
> (0x00007f2df3227000)
> libG4FR.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4FR.so 
> (0x00007f2df3013000)
> libG4GMocren.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4GMocren.so (0x00007f2df2dd2000)
> libG4visHepRep.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4visHepRep.so 
> (0x00007f2df2b4b000)
> libG4RayTracer.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4RayTracer.so 
> (0x00007f2df2921000)
> libG4VRML.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4VRML.so 
> (0x00007f2df270a000)
> libG4vis_management.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4vis_management.so 
> (0x00007f2df243e000)
> libG4modeling.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4modeling.so 
> (0x00007f2df2188000)
> libG4interfaces.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4interfaces.so 
> (0x00007f2df1f52000)
> libG4persistency.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4persistency.so 
> (0x00007f2df1cb6000)
> libG4analysis.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4analysis.so 
> (0x00007f2df1854000)
> libG4error_propagation.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4error_propagation.so 
> (0x00007f2df1619000)
> libG4readout.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4readout.so (0x00007f2df1411000)
> libG4physicslists.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4physicslists.so 
> (0x00007f2df10f7000)
> libG4run.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4run.so 
> (0x00007f2df0e8c000)
> libG4event.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4event.so 
> (0x00007f2df0c1d000)
> libG4tracking.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4tracking.so 
> (0x00007f2df09df000)
> libG4parmodels.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4parmodels.so 
> (0x00007f2df07cb000)
> libG4processes.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4processes.so 
> (0x00007f2def07d000)
> libG4digits_hits.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4digits_hits.so 
> (0x00007f2deeddd000)
> libG4track.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4track.so 
> (0x00007f2deebc2000)
> libG4particles.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4particles.so 
> (0x00007f2dee868000)
> libG4geometry.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4geometry.so 
> (0x00007f2dee3f6000)
> libG4materials.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4materials.so 
> (0x00007f2dee14f000)
> libG4graphics_reps.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4graphics_reps.so 
> (0x00007f2dedf11000)
> libG4intercoms.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4intercoms.so 
> (0x00007f2dedcc6000)
> libG4global.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4global.so 
> (0x00007f2deda7d000)
> libG4clhep.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4clhep.so 
> (0x00007f2ded7ee000)
> libG4zlib.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4zlib.so 
> (0x00007f2ded5d8000)
> libG4geomUSolids.so => 
> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4geomUSolids.so 
> (0x00007f2ded332000)
> libCore.so => /home/gate/gate_sources2/root/lib/libCore.so 
> (0x00007f2dec985000)
> libCint.so => /home/gate/gate_sources2/root/lib/libCint.so 
> (0x00007f2dec003000)
> libRIO.so => /home/gate/gate_sources2/root/lib/libRIO.so 
> (0x00007f2debaf8000)
> libNet.so => /home/gate/gate_sources2/root/lib/libNet.so 
> (0x00007f2deb77e000)
> libHist.so => /home/gate/gate_sources2/root/lib/libHist.so 
> (0x00007f2deb00c000)
> libGraf.so => /home/gate/gate_sources2/root/lib/libGraf.so 
> (0x00007f2deac05000)
> libGraf3d.so => /home/gate/gate_sources2/root/lib/libGraf3d.so 
> (0x00007f2dea8d9000)
> libGpad.so => /home/gate/gate_sources2/root/lib/libGpad.so 
> (0x00007f2dea5d5000)
> libTree.so => /home/gate/gate_sources2/root/lib/libTree.so 
> (0x00007f2dea18d000)
> libRint.so => /home/gate/gate_sources2/root/lib/libRint.so 
> (0x00007f2de9f59000)
> libPostscript.so => /home/gate/gate_sources2/root/lib/libPostscript.so 
> (0x00007f2de9cd9000)
> libMatrix.so => /home/gate/gate_sources2/root/lib/libMatrix.so 
> (0x00007f2de9879000)
> libPhysics.so => /home/gate/gate_sources2/root/lib/libPhysics.so 
> (0x00007f2de95db000)
> libMathCore.so => /home/gate/gate_sources2/root/lib/libMathCore.so 
> (0x00007f2de9161000)
> libThread.so => /home/gate/gate_sources2/root/lib/libThread.so 
> (0x00007f2de8f0d000)
> libdl.so.2 => /lib64/libdl.so.2 (0x0000003af2400000)
> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003af2800000)
> libSM.so.6 => /usr/lib64/libSM.so.6 (0x0000003afe000000)
> libICE.so.6 => /usr/lib64/libICE.so.6 (0x0000003afe400000)
> libX11.so.6 => /usr/lib64/libX11.so.6 (0x0000003af5000000)
> libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003af6000000)
> libexpat.so.1 => /lib64/libexpat.so.1 (0x0000003af6c00000)
> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003afd400000)
> libm.so.6 => /lib64/libm.so.6 (0x0000003af2000000)
> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003af6400000)
> libc.so.6 => /lib64/libc.so.6 (0x0000003af1c00000)
> libz.so.1 => /lib64/libz.so.1 (0x0000003af2c00000)
> libpcre.so.0 => /lib64/libpcre.so.0 (0x0000003af3800000)
> /lib64/ld-linux-x86-64.so.2 (0x0000003af1800000)
> libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x0000003afa800000)
> libssl.so.10 => /usr/lib64/libssl.so.10 (0x0000003b00800000)
> libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x0000003af6800000)
> libuuid.so.1 => /lib64/libuuid.so.1 (0x0000003af7400000)
> libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x0000003af5400000)
> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x0000003b00400000)
> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x0000003aff800000)
> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x0000003afd800000)
> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x0000003aff400000)
> libXau.so.6 => /usr/lib64/libXau.so.6 (0x0000003af5800000)
> libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x0000003affc00000)
> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x0000003aff000000)
> libresolv.so.2 => /lib64/libresolv.so.2 (0x0000003af3c00000)
> libselinux.so.1 => /lib64/libselinux.so.1 (0x0000003af3400000)
>
> any ideas of what might be wrong? I will appreciate all the help I can 
> get.
>
> //
> Gustaf
>
>> 1 mars 2016 kl. 18:59 skrev David Boersma 
>> <david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>>:
>>
>> Hej Gustaf,
>>
>> Now we are talking about two different situations: "the system" and 
>> "my private computer". Did you get the same linking errors on both of 
>> them?
>>
>> I guess that "the system" is your main priority. So then it would be 
>> more useful to look at the ldd output for your setup at that system. 
>> I'm looking forward to your investigation results tomorrow. :)
>>
>> /DavidB
>>
>> Den 01/03/2016 kl. 18:46, skrev Gustaf Lönn:
>>> Hello!
>>>
>>> I’m not sure about the exact release and I don’t have access to the
>>> system at this very moment.
>>> I belive there is a previous version of geant4 installed in another
>>> directory, but I think it is geant4.9.6.
>>> I did not use the make clean command during the previous recompilation
>>> but deleted the build directory etc. so I believe it was completely from
>>> scratch?
>>>
>>> As I mentioned I don’t have access to the system at this moment but I
>>> was clever enough to export the ldd Gate output to my private computer
>>> so I’ll post it below. At first glance I don’t spot any odd
>>> dependencies, all are linked to
>>> gate_sources2/geant4.10.01.p03-install/lib64. I’ll investigate further
>>> tomorrow when I have access to the system.
>>>
>>> //
>>> Gustaf
>>>
>>> ldd Gate output:
>>>
>>> linux-vdso.so.1 =>  (0x00007fff1a7ff000)
>>> libG4Tree.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4Tree.so
>>> (0x00007f4f64ff5000)
>>> libG4FR.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4FR.so
>>> (0x00007f4f64de1000)
>>> libG4GMocren.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4GMocren.so
>>> (0x00007f4f64ba0000)
>>> libG4visHepRep.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4visHepRep.so 
>>> (0x00007f4f64919000)
>>> libG4RayTracer.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4RayTracer.so 
>>> (0x00007f4f646ef000)
>>> libG4VRML.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4VRML.so
>>> (0x00007f4f644d8000)
>>> libG4vis_management.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4vis_management.so
>>> (0x00007f4f6420c000)
>>> libG4modeling.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4modeling.so
>>> (0x00007f4f63f56000)
>>> libG4interfaces.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4interfaces.so
>>> (0x00007f4f63d20000)
>>> libG4persistency.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4persistency.so
>>> (0x00007f4f63a84000)
>>> libG4analysis.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4analysis.so
>>> (0x00007f4f63622000)
>>> libG4error_propagation.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4error_propagation.so
>>> (0x00007f4f633e7000)
>>> libG4readout.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4readout.so
>>> (0x00007f4f631df000)
>>> libG4physicslists.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4physicslists.so
>>> (0x00007f4f62ec5000)
>>> libG4run.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4run.so
>>> (0x00007f4f62c5a000)
>>> libG4event.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4event.so
>>> (0x00007f4f629eb000)
>>> libG4tracking.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4tracking.so
>>> (0x00007f4f627ad000)
>>> libG4parmodels.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4parmodels.so 
>>> (0x00007f4f62599000)
>>> libG4processes.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4processes.so 
>>> (0x00007f4f60e4b000)
>>> libG4digits_hits.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4digits_hits.so
>>> (0x00007f4f60bab000)
>>> libG4track.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4track.so
>>> (0x00007f4f60990000)
>>> libG4particles.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4particles.so 
>>> (0x00007f4f60636000)
>>> libG4geometry.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4geometry.so
>>> (0x00007f4f601c4000)
>>> libG4materials.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4materials.so 
>>> (0x00007f4f5ff1d000)
>>> libG4graphics_reps.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4graphics_reps.so
>>> (0x00007f4f5fcdf000)
>>> libG4intercoms.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4intercoms.so 
>>> (0x00007f4f5fa94000)
>>> libG4global.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4global.so
>>> (0x00007f4f5f84b000)
>>> libG4clhep.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4clhep.so
>>> (0x00007f4f5f5bc000)
>>> libG4zlib.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4zlib.so
>>> (0x00007f4f5f3a6000)
>>> libG4geomUSolids.so =>
>>> /home/gate/gate_sources2/geant4.10.01.p03-install/lib64/libG4geomUSolids.so
>>> (0x00007f4f5f100000)
>>> libCore.so => /home/gate/gate_sources2/root/lib/libCore.so
>>> (0x00007f4f5e753000)
>>> libCint.so => /home/gate/gate_sources2/root/lib/libCint.so
>>> (0x00007f4f5ddd1000)
>>> libRIO.so => /home/gate/gate_sources2/root/lib/libRIO.so
>>> (0x00007f4f5d8c6000)
>>> libNet.so => /home/gate/gate_sources2/root/lib/libNet.so
>>> (0x00007f4f5d54c000)
>>> libHist.so => /home/gate/gate_sources2/root/lib/libHist.so
>>> (0x00007f4f5cdda000)
>>> libGraf.so => /home/gate/gate_sources2/root/lib/libGraf.so
>>> (0x00007f4f5c9d3000)
>>> libGraf3d.so => /home/gate/gate_sources2/root/lib/libGraf3d.so
>>> (0x00007f4f5c6a7000)
>>> libGpad.so => /home/gate/gate_sources2/root/lib/libGpad.so
>>> (0x00007f4f5c3a3000)
>>> libTree.so => /home/gate/gate_sources2/root/lib/libTree.so
>>> (0x00007f4f5bf5b000)
>>> libRint.so => /home/gate/gate_sources2/root/lib/libRint.so
>>> (0x00007f4f5bd27000)
>>> libPostscript.so => /home/gate/gate_sources2/root/lib/libPostscript.so
>>> (0x00007f4f5baa7000)
>>> libMatrix.so => /home/gate/gate_sources2/root/lib/libMatrix.so
>>> (0x00007f4f5b647000)
>>> libPhysics.so => /home/gate/gate_sources2/root/lib/libPhysics.so
>>> (0x00007f4f5b3a9000)
>>> libMathCore.so => /home/gate/gate_sources2/root/lib/libMathCore.so
>>> (0x00007f4f5af2f000)
>>> libThread.so => /home/gate/gate_sources2/root/lib/libThread.so
>>> (0x00007f4f5acdb000)
>>> libdl.so.2 => /lib64/libdl.so.2 (0x0000003af2400000)
>>> libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003af2800000)
>>> libSM.so.6 => /usr/lib64/libSM.so.6 (0x0000003afe000000)
>>> libICE.so.6 => /usr/lib64/libICE.so.6 (0x0000003afe400000)
>>> libX11.so.6 => /usr/lib64/libX11.so.6 (0x0000003af5000000)
>>> libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003af6000000)
>>> libexpat.so.1 => /lib64/libexpat.so.1 (0x0000003af6c00000)
>>> libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003afd400000)
>>> libm.so.6 => /lib64/libm.so.6 (0x0000003af2000000)
>>> libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003af6400000)
>>> libc.so.6 => /lib64/libc.so.6 (0x0000003af1c00000)
>>> libz.so.1 => /lib64/libz.so.1 (0x0000003af2c00000)
>>> libpcre.so.0 => /lib64/libpcre.so.0 (0x0000003af3800000)
>>> /lib64/ld-linux-x86-64.so.2 (0x0000003af1800000)
>>> libcrypto.so.10 => /usr/lib64/libcrypto.so.10 (0x0000003afa800000)
>>> libssl.so.10 => /usr/lib64/libssl.so.10 (0x0000003b00800000)
>>> libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x0000003af6800000)
>>> libuuid.so.1 => /lib64/libuuid.so.1 (0x0000003af7400000)
>>> libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x0000003af5400000)
>>> libgssapi_krb5.so.2 => /lib64/libgssapi_krb5.so.2 (0x0000003b00400000)
>>> libkrb5.so.3 => /lib64/libkrb5.so.3 (0x0000003aff800000)
>>> libcom_err.so.2 => /lib64/libcom_err.so.2 (0x0000003afd800000)
>>> libk5crypto.so.3 => /lib64/libk5crypto.so.3 (0x0000003aff400000)
>>> libXau.so.6 => /usr/lib64/libXau.so.6 (0x0000003af5800000)
>>> libkrb5support.so.0 => /lib64/libkrb5support.so.0 (0x0000003affc00000)
>>> libkeyutils.so.1 => /lib64/libkeyutils.so.1 (0x0000003aff000000)
>>> libresolv.so.2 => /lib64/libresolv.so.2 (0x0000003af3c00000)
>>> libselinux.so.1 => /lib64/libselinux.so.1 (0x0000003af3400000)
>>>
>>>
>>>
>>>
>>>
>>>> 1 mars 2016 kl. 18:03 skrev David Boersma 
>>>> <david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>
>>>> <mailto:david.boersma at physics.uu.se>>:
>>>>
>>>> Hi Gustaf,
>>>>
>>>> Which Ubuntu release are you using?
>>>>
>>>> I tried to reproduce your error on a Ubuntu 14.04 machine, also 64bit.
>>>> Since you mentioned that you are using geant4 10.01.p03, which is
>>>> relatively new (released Feb 5), I wondered if that is maybe the
>>>> culprit. But it does not look like it, because I can build and run
>>>> Gate v7.1 just fine with that release. So my bet is that the errors
>>>> that you report are not due to Gate or Geant4 code.
>>>>
>>>> (I even tried building geant4 with multithreading enabled -- which one
>>>> should NOT do for any production purposes because Gate is not yet
>>>> ready for multithreading -- but even with MT-geant4 Gate can be built
>>>> and it runs without linking errors, even though the results with MT
>>>> are not to be trusted.)
>>>>
>>>> So...
>>>>
>>>> (1) Could you just quote the full output of ldd completely here in an
>>>> e-mail (if the discussion below does not help you to solve it 
>>>> yourself)?
>>>>
>>>> The idea is that ldd tells you to which libraries an executable really
>>>> gets linked. The results are sometimes surprising and instructive. For
>>>> instance you mention that you used a bash script to set your
>>>> environment correctly for building Gate, but maybe you still have
>>>> similar settings for a different Geant4 version in your ~/.bash*
>>>> files, which might create all kinds of havoc. The ldd utility can help
>>>> to identify such issues.
>>>>
>>>> (2) The G4GammaParticipants size error makes me suspect that you maybe
>>>> did not truly recompile from scratch (because its base class
>>>> G4QGSParticipants depends on Random.hh, which has CLHEP-dependent
>>>> code, so that class may indeed change size during a rebuild). Running
>>>> 'make clean' is not enough. "From scratch" means: start with a new,
>>>> empty build directory, and run ccmake <sourcedir> in it. Why is this
>>>> necessary? Well, cmake and make are very clever at keeping track of
>>>> dependencies, but that is a very hard task and they are not perfect.
>>>>
>>>> (3) I am very mystified by this _ZN12G4AllocStats6numCatE error. With
>>>> the c++filt utility you can see that this is indeed pointing to the
>>>> numCat data member of G4AllocStats, which gets *declared* in the
>>>> Geant4 source tree in this header file:
>>>>
>>>> ./source/geometry/volumes/include/G4EnhancedVecAllocator.hh
>>>>
>>>> ... but the funny thing is that this header file does not get included
>>>> by *any* other source file, neither in the geant4 10.01.p03 sources
>>>> nor in Gate 7.1 [1]! The only way I can think of this error to pop up
>>>> is by confusion with a different geant4 version. Do you have other
>>>> geant4 versions installed on your system?
>>>>
>>>> Hope that helps,
>>>> David B.
>>>>
>>>> [1] It is mentioned in the sources.cmake file as a header file, of
>>>> course. But that does not cause it to actually be #included anywhere.
>>>> The 4.9.6 release notes mention that the use of G4EnhancedVecAllocator
>>>> is disabled in some navigation class, and probably that was the only
>>>> usage. Which suggests that the impostor Geant4 library on your system
>>>> is older than 4.9.6. :)
>>>>
>>>>
>>>>
>>>> Den 01/03/2016 kl. 13:22, skrev Gustaf Lönn:
>>>>> Hello!
>>>>>
>>>>> First of all I want to express my gratitude for all the valuable 
>>>>> help so
>>>>> far.
>>>>>
>>>>> I did a full recompile from scratch linked Gate to the correct G4. I
>>>>> still receive the symbol errors previously posted.
>>>>>
>>>>> I’m not sure on how I should interpret the results from the ldd 
>>>>> command.
>>>>>
>>>>> //
>>>>> Gustaf
>>>>>> 1 mars 2016 kl. 11:50 skrev David Sarrut
>>>>>> <David.Sarrut at creatis.insa-lyon.fr 
>>>>>> <mailto:David.Sarrut at creatis.insa-lyon.fr>
>>>>>> <mailto:David.Sarrut at creatis.insa-lyon.fr>
>>>>>> <mailto:David.Sarrut at creatis.insa-lyon.fr>>:
>>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> maybe still a linking error. Be sure to recompile everything from
>>>>>> scratch and be sure Gate is linked with the correct G4 only ...
>>>>>>
>>>>>> Check with ldd to List Dynamic Dependencies of an executable, it 
>>>>>> could
>>>>>> help
>>>>>>
>>>>>> David
>>>>>>
>>>>>> On Tue, Mar 1, 2016 at 11:29 AM, Gustaf Lönn <gustaflo at kth.se 
>>>>>> <mailto:gustaflo at kth.se>
>>>>>> <mailto:gustaflo at kth.se>
>>>>>> <mailto:gustaflo at kth.se>> wrote:
>>>>>>
>>>>>>   Hello!
>>>>>>
>>>>>>   I tried to recompile both G4 and Gate without the external clhep.
>>>>>>   That took care of the initial library error. However, I received
>>>>>>   the following error when trying to run Gate:
>>>>>>
>>>>>>   Symbol `_ZTV19G4GammaParticipants' has different size in shared
>>>>>>   object, consider re-linking
>>>>>>   Gate: symbol lookup error: Gate: undefined symbol:
>>>>>>   _ZN12G4AllocStats6numCatE
>>>>>>
>>>>>>   I think ”GammaParticipants" originate from G4GammaParicipants.hh
>>>>>>   and ”AllocStats" from G4EnhancedVectorAllocator.hh
>>>>>>
>>>>>>   In my bash script I removed the path and library path associated
>>>>>>   with system clhep, otherwise it is unchanged.
>>>>>>
>>>>>>   any ideas?
>>>>>>
>>>>>>   //Gustaf
>>>>>>>   1 mars 2016 kl. 08:01 skrev David Sarrut
>>>>>>>   <David.Sarrut at creatis.insa-lyon.fr 
>>>>>>> <mailto:David.Sarrut at creatis.insa-lyon.fr>
>>>>>>> <mailto:David.Sarrut at creatis.insa-lyon.fr>
>>>>>>>   <mailto:David.Sarrut at creatis.insa-lyon.fr>>:
>>>>>>>
>>>>>>>   Hello,
>>>>>>>
>>>>>>>   it should be a path issue. The simplest way is to use the G4
>>>>>>>   embedded clhep and to not use external clhep. Once G4 is
>>>>>>>   compiled, recompile Gate, without external clhep also.
>>>>>>>
>>>>>>>   hope it helps,
>>>>>>>   David
>>>>>>>
>>>>>>>   On Mon, Feb 29, 2016 at 6:52 PM, Gustaf Lönn <gustaflo at kth.se 
>>>>>>> <mailto:gustaflo at kth.se>
>>>>>>> <mailto:gustaflo at kth.se>
>>>>>>>   <mailto:gustaflo at kth.se>> wrote:
>>>>>>>
>>>>>>>       Hello!
>>>>>>>
>>>>>>>       I have encountered a problem with the CLHEP libraries when
>>>>>>>       I’m trying to run Gate. Instead of searching for the external
>>>>>>>       2.2.0.4 CLHEP library the program wants to use the libG4chlep
>>>>>>>       and therefore terminates. I use x86 Ubuntu 64bit.
>>>>>>>
>>>>>>>       I have followed the installation/compilation instructions and
>>>>>>>       set the external CLHEP options to ”on” and set the following
>>>>>>>       paths:
>>>>>>>
>>>>>>>       Geant4
>>>>>>>       CLHEP_CONFIG_EXECUTABLE:
>>>>>>>       /home/gate/gate_sources2/2.2.0.4-install/bin/clhep-config
>>>>>>>       CLHEP_INCLUDE_DIR:
>>>>>>>       /home/gate/gate_sources2/2.2.0.4-install/include
>>>>>>>       CLHEP_LIBRARY:
>>>>>>>       /home/gate/gate_sources2/2.2.0.4-install/lib/libCLHEP.so
>>>>>>>
>>>>>>>       Gate
>>>>>>>       CLHEP_CONFIG_EXECUTABLE:
>>>>>>>       /home/gate/gate_sources2/2.2.0.4-install/bin/clhep-config
>>>>>>>       CLHEP_INCLUDE_DIR:
>>>>>>>       /home/gate/gate_sources2/2.2.0.4-install/include
>>>>>>>
>>>>>>>       In my bash script I have the following:
>>>>>>>
>>>>>>>       export
>>>>>>>       PATH=$PATH:/home/gate/gate_sources2/2.2.0.4-install/bin:
>>>>>>>       /home/gate/gate_sources2/2.2.0.4-install/include
>>>>>>>
>>>>>>>       export
>>>>>>>
>>>>>>> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/gate/gate_sources2/2.2.0.4-install/lib
>>>>>>>
>>>>>>>       source /home/gate/gate_sources2/root/bin/thisroot.sh
>>>>>>>
>>>>>>>       source
>>>>>>>       /home/gate/gate_sources2/geant4.10.01.p03-install/bin/geant4.sh
>>>>>>>
>>>>>>>       PATH=$PATH:/home/gate/gate_sources2/gate_v7.1-install/bin
>>>>>>>
>>>>>>>       export
>>>>>>>
>>>>>>> LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/gate/gate_sources2/geant4.10.01.p03-install/lib64
>>>>>>>
>>>>>>>       Does anyone have any idea about what might be wrong? I’m
>>>>>>>       grateful for any suggestions!
>>>>>>>
>>>>>>>       Best Regards
>>>>>>>       Gustaf L
>>>>>>>       _______________________________________________
>>>>>>>       Gate-users mailing list
>>>>>>> Gate-users at lists.opengatecollaboration.org 
>>>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>>>>       <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>>   David Sarrut, Phd
>>>>>>>   Directeur de recherche CNRS
>>>>>>>   CREATIS, UMR CNRS 5220, Inserm U1206
>>>>>>>   Centre de lutte contre le cancer Léon Bérard
>>>>>>>   28 rue Laënnec, 69373 Lyon cedex 08
>>>>>>>   Tel : 04 78 78 51 51 <tel:04%2078%2078%2051%2051> / 06 74 72 05
>>>>>>>   42 <tel:06%2074%2072%2005%2042>
>>>>>>> http://www.creatis.insa-lyon.fr/~dsarrut 
>>>>>>> <http://www.creatis.insa-lyon.fr/%7Edsarrut>
>>>>>>>   _________________________________
>>>>>>>    "2 + 2 = 5,  for extremely large values of 2"
>>>>>>>   _________________________________
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> David Sarrut, Phd
>>>>>> Directeur de recherche CNRS
>>>>>> CREATIS, UMR CNRS 5220, Inserm U1206
>>>>>> Centre de lutte contre le cancer Léon Bérard
>>>>>> 28 rue Laënnec, 69373 Lyon cedex 08
>>>>>> Tel : 04 78 78 51 51 / 06 74 72 05 42
>>>>>> http://www.creatis.insa-lyon.fr/~dsarrut 
>>>>>> <http://www.creatis.insa-lyon.fr/%7Edsarrut>
>>>>>> _________________________________
>>>>>> "2 + 2 = 5,  for extremely large values of 2"
>>>>>> _________________________________
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Gate-users mailing list
>>>>> Gate-users at lists.opengatecollaboration.org 
>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>
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>
>
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