[Gate-users] CLHEP library error
David Boersma
david.boersma at physics.uu.se
Wed Mar 2 11:56:16 CET 2016
Hej Gustaf,
Den 02/03/2016 kl. 11:26, skrev Gustaf Lönn:
> Hej!
>
> I have ld: GNU ld version 2.20.51.0.2-5.36.el6
> and gcc: gcc version 4.4.7 (Red Hat 4.4.7-4)
>
> Gate did work on the cluster up to about one week ago
- With the same geant4 and gate versions? Compiler bugs are rare and
their symptoms can disappear by using a slightly different version of
your code.
- UPPMAX (the Uppsala university cluster) has 23 different versions of
gcc available, ranging from 4.3.6 to 5.3.0, but the 4.4.* series is
conspicuously missing. However I do have access to a Scientific Linux 6
system, with similar compiler details as your system. I'll check.
Speaking of different versions: you could also try to install Geant4
10.02 and Gate v7.2 and see if that maybe works fine. Is there any
reason you absolutely need Gate v7.1?
/David
>
> //
> Gustaf
>> 2 mars 2016 kl. 11:10 skrev David Boersma <david.boersma at physics.uu.se
>> <mailto:david.boersma at physics.uu.se>>:
>>
>> 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><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>
>>>>>>> <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>
>>>>>>>>> <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>
>>>>>>>>> <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>
>>>>>>>>>> <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>
>>>>>>>>>> <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>
>>>>>>>>>> <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>
>>>>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Gate-users mailing list
>>>> Gate-users at lists.opengatecollaboration.org
>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> <mailto:Gate-users at lists.opengatecollaboration.org>
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
More information about the Gate-users
mailing list