[Gate-users] CLHEP library error
David Boersma
david.boersma at physics.uu.se
Tue Mar 1 18:59:49 CET 2016
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>>:
>>
>> 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
>>>>> _______________________________________________
>>>>> Gate-users mailing list
>>>>> Gate-users at lists.opengatecollaboration.org
>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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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>>> <mailto:Gate-users at lists.opengatecollaboration.org>
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>
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