[Gate-users] CLHEP library error
David Boersma
david.boersma at physics.uu.se
Wed Mar 2 11:10:00 CET 2016
Hej,
Well, the plot thickens. "Linux Rocks" is a pretty cool name for a linux
distribution. :)
Next hypothesis to check: "it's due to an internal bug in the
compiler/linker on your system".
Since we are on different distributions it's possible that I cannot
reproduce your problem because of different versions of the compiler
(gcc) and the linker (ld). Maybe the compiler/linker on rocks 6.1.1 has
a bug that the versions on Ubuntu 14.04 do not have.
Version details for Ubuntu 14.04:
ld: GNU ld (GNU Binutils for Ubuntu) 2.24
gcc: gcc (Ubuntu 4.8.4-2ubuntu1~14.04.1) 4.8.4
Could you tell me the version details on your system? It's also possible
that Rocks does not use gcc/ld at all but some completely different
compiler and linker program, e.g. the intel compiler. I had a quick look
at the Rocks 6.1.1 online docs but could find any info about that.
I have an account on UPPMAX, I could try to reproduce the error on that
system. And/Or maybe better: you could try to configure a different
compiler/linker on your system, e.g. similar to the Ubuntu ones, and see
if that makes the error go away.
Mvh,
DavidB
Den 02/03/2016 kl. 09:52, skrev Andrej Studen:
> 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
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>>>>>> <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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