<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=Windows-1252"> </head> <body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""> Hej <div class=""> </div> <div class="">Yes using the same versions, which is one reason why we are so confused about this issue. It stopped working when we tried to run a different geant4 version with gate. Since then it has not worked, despite our efforts to restore it and reinstall it.</div> <div class=""> </div> <div class="">I will try to install gate7.2 with the corresponding dependencies to see if it works.</div> <div class=""> </div> <div class="">//</div> <div class="">Gustaf <div> <blockquote type="cite" class=""> <div class="">2 mars 2016 kl. 11:56 skrev David Boersma <<a href="mailto:david.boersma@physics.uu.se" class="">david.boersma@physics.uu.se</a>>:</div> <div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hej Gustaf,<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Den 02/03/2016 kl. 11:26, skrev Gustaf Lönn:<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> 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 </blockquote> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">- 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.<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">- 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.<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">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?<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">/David<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> <blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""> // Gustaf <blockquote type="cite" class="">2 mars 2016 kl. 11:10 skrev David Boersma <<a href="mailto:david.boersma@physics.uu.se" class="">david.boersma@physics.uu.se</a> <<a href="mailto:david.boersma@physics.uu.se" class="">mailto:david.boersma@physics.uu.se</a>>>: 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: <blockquote type="cite" class="">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: <blockquote type="cite" class="">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 <blockquote type="cite" class="">1 mars 2016 kl. 18:59 skrev David Boersma <<a href="mailto:david.boersma@physics.uu.se" class="">david.boersma@physics.uu.se</a> <<a href="mailto:david.boersma@physics.uu.se" class="">mailto:david.boersma@physics.uu.se</a>><<a href="mailto:david.boersma@physics.uu.se" class="">mailto:david.boersma@physics.uu.se</a>>>: 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: <blockquote type="cite" class="">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) <blockquote type="cite" class="">1 mars 2016 kl. 18:03 skrev David Boersma <<a href="mailto:david.boersma@physics.uu.se" class="">david.boersma@physics.uu.se</a> <<a href="mailto:david.boersma@physics.uu.se" class="">mailto:david.boersma@physics.uu.se</a>><<a href="mailto:david.boersma@physics.uu.se" class="">mailto:david.boersma@physics.uu.se</a>> <<a href="mailto:david.boersma@physics.uu.se" class="">mailto:david.boersma@physics.uu.se</a>>>: 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: <blockquote type="cite" class="">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 <blockquote type="cite" class="">1 mars 2016 kl. 11:50 skrev David Sarrut <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">David.Sarrut@creatis.insa-lyon.fr</a> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>>>: 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 <<a href="mailto:gustaflo@kth.se" class="">gustaflo@kth.se</a> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>>> 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 <blockquote type="cite" class="">1 mars 2016 kl. 08:01 skrev David Sarrut <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">David.Sarrut@creatis.insa-lyon.fr</a> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>> <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr" class="">mailto:David.Sarrut@creatis.insa-lyon.fr</a>>>: 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 <<a href="mailto:gustaflo@kth.se" class="">gustaflo@kth.se</a> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>> <<a href="mailto:gustaflo@kth.se" class="">mailto:gustaflo@kth.se</a>>> 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 <a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> -- 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" _________________________________ </blockquote> -- 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 <a href="http://www.creatis.insa-lyon.fr/~dsarrut" class="">http://www.creatis.insa-lyon.fr/~dsarrut</a> <http://www.creatis.insa-lyon.fr/%7Edsarrut> _________________________________ "2 + 2 = 5, for extremely large values of 2" _________________________________ </blockquote> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote> </blockquote> </blockquote> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">Gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:Gate-users@lists.opengatecollaboration.org" class="">mailto:Gate-users@lists.opengatecollaboration.org</a>> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" class="">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote> </blockquote> <span style="font-family: Helvetica; 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