[Gate-users] CLHEP library error

Gustaf Lönn gustaflo at kth.se
Wed Mar 2 11:26:57 CET 2016 

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

//
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
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 --
 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"
_________________________________



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