[Gate-users] CLHEP library error

Gustaf Lönn gustaflo at kth.se
Tue Mar 1 18:46:40 CET 2016 

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>>:

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>>:

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>> 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>>:

   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>> 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
   _________________________________
    "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
_________________________________
"2 + 2 = 5,  for extremely large values of 2"
_________________________________



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