Problem of graphics card after SAMSON installation on Ubuntu 18.04 (Intel processors)



  • Hello everyone, I have a problem of SAMSON installation on a new DELL Latitude 7490 computer, Intel processors (i7), Ubuntu 18.04 version.
    (I obtain "VGA compatible controller : Intel Corporation UHD Graphics 620 (rev 07) " when typing "glxinfo | grep OpenGL")

    As you can see, I can open a file in SAMSON as a pdb file, I see the list of atoms on the left window but I see nothing in the right window, and I can't even make it bigger... There seems to be a problem with the graphics card.

    0_1555338920117_SAMSON_capture_ecran.png

    Thank you very much for you help,
    Regards
    Robert



  • Dear @Robert ,

    As I understand, your laptop does not have a dedicated GPU. SAMSON might not properly work on systems with integrated graphics (Intel graphics cards).

    Do you have Mesa driver installed? You can install it via:
    sudo apt-get install build-essential libgl1-mesa-dev



  • Dear Dmitriy,
    Thank youfor your answer. I have (re-)installed this Mesa driver (but actually I had already installed it because I had problems with libOpenGL.so.0 ('cannot open shared object file') and I read the following old discussion in the forum :

    https://forum.samson-connect.net/topic/37/installing-or-running-samson-on-ubuntu-17-04-and-later-versions/13

    that you had solved).

    But SAMSON graphics don't work. Do I need to recompile / rerun SAMSON-Setup.run ?

    I am trying to install the whole MESA library (MESA 3D Graphics library in www.mesa3d.org) because I also have a similar problem in VMD, I don't get any GUI or visual interface (the computer is new and only Ubuntu was installed, it seems that there is not even FLTK (that I have installed or GUI preinstalled).
    Thanks a lot,

    Regards,
    Robert



  • No, there is no need to re-install SAMSON.

    Do you have Windows on this laptop to check if SAMSON works on it?



  • @Robert

    Could you, please, post the full output of the following commands:
    glxinfo | grep OpenGL

    locate libOpenGL.so



  • Thank you Dmitriy. Disgracefully I don't have Windows on a VM Ware, but only Ubuntu in this new laptop...

    The following commands give me :

    glxinfo | grep OpenGL :

    OpenGL vendor string: Intel Open Source Technology Center
    OpenGL renderer string: Mesa DRI Intel(R) UHD Graphics 620 (Kabylake GT2)
    OpenGL core profile version string: 4.5 (Core Profile) Mesa 18.2.8
    OpenGL core profile shading language version string: 4.50
    OpenGL core profile context flags: (none)
    OpenGL core profile profile mask: core profile
    OpenGL core profile extensions:
    OpenGL version string: 3.0 Mesa 18.2.8
    OpenGL shading language version string: 1.30
    OpenGL context flags: (none)
    OpenGL extensions:
    OpenGL ES profile version string: OpenGL ES 3.2 Mesa 18.2.8
    OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20
    OpenGL ES profile extensions:

    locate libOpenGL.so :

    /usr/lib/x86_64-linux-gnu/libOpenGL.so
    /usr/lib/x86_64-linux-gnu/libOpenGL.so.0
    /usr/lib/x86_64-linux-gnu/libOpenGL.so.0.0.0

    It seems that Mesa is installed and supporting OpenGL from this information ... ?

    Do you know if the command "sudo apt-get install build-essential libgl1-mesa-dev", that you suggested me, is enough to install the MESA library needed for OpenGL support, and for SAMSON to work ? (or do I need to install fully MESA ? [as I am trying to do for VMD installation, because of seemingly similar problems])

    Thank you for your help,
    Robert



  • It looks like that you have Mesa with OpenGL 4.5 support which should be enough.

    These packages should be enough: sudo apt-get install build-essential mesa-utils libgl1-mesa-dev
    You do not need to have the full Mesa installation, as far as I understand.



  • Could you, please post the output of the following command:

    # go to the folder with SAMSON executable
    cd ~/NANO-D/SAMSON/0.7.0/Binaries
    ldd ./libSBGRender.so | grep OpenGL
    


  • I get this :

    libOpenGL.so.0 => /usr/lib/x86_64-linux-gnu/libOpenGL.so.0 (0x00007efc8e30f000)
    libQt5OpenGL.so.5 => /usr/lib/x86_64-linux-gnu/libQt5OpenGL.so.5 (0x00007efc8d88c000)

    Thanks again.
    Robert



  • Looks ok. We will see what we can do and will contact you. Sorry, for the issue!



  • @Robert

    Could you, also, please post the output for:

    # go to the folder with SAMSON executable
    cd ~/NANO-D/SAMSON/0.7.0/Binaries
    ldd ./SAMSON-Core | grep libGL
    


  • Dmitriy, sorry for the delay, I was at a meeting.

    No problem for the issue, it is not your fault :) ! Maybe I have badly installed something ... (and the computer is new and few things are pre-installed)

    With the command :
    cd ~/NANO-D/SAMSON/0.7.0/Binaries
    ldd ./SAMSON-Core | grep libGL

    I get :

    libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007f4645619000)
    libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f46453aa000)
    libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007f46427dc000)
    libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007f4641ff9000)

    Thank you
    Robert



  • Thank you, @Robert

    Could you, please, try these commands and see if it shows you anything:

    ldd /usr/lib/x86_64-linux-gnu/libOpenGL.so
    
    cd ~/NANO-D/SAMSON/0.7.0/Binaries
    ldd ./SAMSON-Core | grep "not found" | grep -v "Qt5"
    ldd ./libSBGRender.so | grep "not found" | grep -v "Qt5"
    

    Here we check for dependencies which are not found excluding Qt5 because Qt5 might be included in the script launching SAMSON-Core.
    If you see any output, please, post it here.



  • Thanks Dmitriy.

    "ldd /usr/lib/x86_64-linux-gnu/libOpenGL.so" gives me :

    linux-vdso.so.1 (0x00007ffc4cd2b000)
    libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fda5d9e0000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fda5d5ef000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fda5d3eb000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fda5dec4000)

    ldd ./SAMSON-Core | grep "not found" | grep -v "Qt5" gives me :

    libSAMSON.so => not found
    libSBGCommand.so => not found
    libGUI.so => not found
    libSBGUser.so => not found
    libSBSNeighborSearch.so => not found
    libSBGMain.so => not found
    libSBGProperty.so => not found
    libSBGToolBar.so => not found
    libSBGElement.so => not found
    libSBGInspector.so => not found
    libSBIFile.so => not found
    libSBGRender.so => not found
    libSBGDocument.so => not found
    libSBGUndo.so => not found
    libSBGWidget.so => not found
    libSBIElement.so => not found
    libSBGNotification.so => not found
    libSBGLog.so => not found
    libIO.so => not found
    libSBIPackage.so => not found
    libSBIWebService.so => not found
    libSBGVisualModel.so => not found
    libSBGStructuralModel.so => not found
    libSBGPropertyModel.so => not found
    libSBGInteractionModel.so => not found
    libSBGDynamicalModel.so => not found
    libSBGSimulator.so => not found
    libSBGStateUpdater.so => not found
    libSBGDataGraph.so => not found
    libSBGMenu.so => not found
    libSBGAction.so => not found
    libSBGApp.so => not found
    libSBGEditor.so => not found
    libSBGWindow.so => not found
    libSBGSettings.so => not found
    libData.so => not found
    libSBDColor.so => not found
    libSBDDocument.so => not found
    libSBMVisualModel.so => not found
    libSBDController.so => not found
    libSBMPropertyModel.so => not found
    libSBSSimulator.so => not found
    libSBDApp.so => not found
    libSBGPath.so => not found
    libSBSStateUpdater.so => not found
    libSBMInteractionModel.so => not found
    libSBMDynamicalModel.so => not found
    libSBMStructuralModel.so => not found
    libSBDType.so => not found
    libSBMElement.so => not found
    libSBDQuantity.so => not found
    libSBMModel.so => not found
    libSBDDataGraph.so => not found
    libSBCFunctor.so => not found
    libCore.so => not found
    libSBCKernel.so => not found
    libSBCUndo.so => not found
    libSBCClass.so => not found
    libSBCSignal.so => not found
    libSBCReference.so => not found
    libSBCLog.so => not found
    libSBCMeta.so => not found
    libSBCContainer.so => not found
    libSBCHeap.so => not found
    libSBCSerializer.so => not found

    Finally, the command
    ldd ./libSBGRender.so | grep "not found" | grep -v "Qt5"
    gives me :

    libSBGDocument.so => not found
    libSBGStructuralModel.so => not found
    libSBGDynamicalModel.so => not found
    libSBGVisualModel.so => not found
    libSBGInteractionModel.so => not found
    libSBGPropertyModel.so => not found
    libSBGSimulator.so => not found
    libSBGStateUpdater.so => not found
    libSBGWidget.so => not found
    libSBGDataGraph.so => not found
    libSBGMenu.so => not found
    libSBGAction.so => not found
    libSBGEditor.so => not found
    libSBGApp.so => not found
    libSBGLog.so => not found
    libIO.so => not found
    libSBIPackage.so => not found
    libSBIElement.so => not found
    libSBIWebService.so => not found
    libSBGNotification.so => not found
    libSBGUndo.so => not found
    libData.so => not found
    libSBDApp.so => not found
    libSBGWindow.so => not found
    libSBDColor.so => not found
    libSBDDocument.so => not found
    libSBMVisualModel.so => not found
    libSBMPropertyModel.so => not found
    libSBSSimulator.so => not found
    libSBSStateUpdater.so => not found
    libSBMInteractionModel.so => not found
    libSBMDynamicalModel.so => not found
    libSBMStructuralModel.so => not found
    libSBMModel.so => not found
    libSBMElement.so => not found
    libSBDQuantity.so => not found
    libSBDController.so => not found
    libSBDDataGraph.so => not found
    libCore.so => not found
    libSBCKernel.so => not found
    libSBCFunctor.so => not found
    libSBCUndo.so => not found
    libSBCClass.so => not found
    libSBCSignal.so => not found
    libSBCReference.so => not found
    libSBCLog.so => not found
    libSBCSerializer.so => not found
    libSBGSettings.so => not found
    libSBGPath.so => not found
    libSBDType.so => not found
    libSBCMeta.so => not found
    libSBCContainer.so => not found
    libSBCHeap.so => not found

    It does not seem encouraging as nothing is found ... !
    Regards,
    Robert



  • Sorry, I should have added:

    cd ~/NANO-D/SAMSON/0.7.0/Binaries
    export LD_LIBRARY_PATH=.:./SAMSONQtLibs:$LD_LIBRARY_PATH
    

    So, all these "not found" you posted are ok, since these libraries are actually provided with SAMSON and are placed in the same folder.
    If you redo the ldd check it should not find any "not found" libraries.

    Or you can do this ldd check from the SAMSON-Core.sh launching script after exporting all the libraries (already done in the script) instead of launching ./SAMSON-Core

    We will see what might cause the issue, but might be it smth more general since you said the VMD does not work as well.



  • No problem. Indeed, I don't find any "not found" library anymore with the two ldd checks above :
    ldd ./SAMSON-Core | grep "not found" | grep -v "Qt5"
    ldd ./libSBGRender.so | grep "not found" | grep -v "Qt5"

    When I launch SAMSON (./SAMSON-Core.sh or ./SAMSON-Core), I get the following message in the terminal :

    "
    saving context
    launching SAMSON-Core
    Python found in the system:
    Python executable: /home/rbenda/anaconda3/bin/python3
    Python library has not been loaded: Cannot load library libpython3.6m: (libpython3.6m: cannot open shared object file: No such file or directory)
    "

    I don't know if the problem can be due to this Python library but I don't think so (there might be a problem for SAMSON Apps using Python but it is not yet my case ...).

    I have modified the SAMSON-Core.sh script with vi. I uncommented the two lines
    ldd SAMSON-Core
    echo $LD_LIBRARY_PATH

    and added

    ldd ./SAMSON-Core | grep "not found" | grep -v "Qt5"
    ldd ./libSBGRender.so | grep "not found" | grep -v "Qt5"

    just before the last line echo "restoring context".

    SAMSON windows opens (as usual, but with the usual problem of no molecule appearing when loading a molecule, or the window not following the 'mouse' movement as you could see in the first screen shot I posted). I obtain this message in the terminal :

    saving context
    launching SAMSON-Core
    Python found in the system:
    Python executable: /home/rbenda/anaconda3/bin/python3
    linux-vdso.so.1 (0x00007ffed5fd5000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fab6811d000)
    libOpenGL.so.0 => /usr/lib/x86_64-linux-gnu/libOpenGL.so.0 (0x00007fab67eef000)
    libGLX.so.0 => /usr/lib/x86_64-linux-gnu/libGLX.so.0 (0x00007fab67cbe000)
    libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007fab67a4f000)
    libSAMSON.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSAMSON.so (0x00007fab67647000)
    libSBGCommand.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGCommand.so (0x00007fab6732e000)
    libGUI.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libGUI.so (0x00007fab67000000)
    libSBGUser.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGUser.so (0x00007fab66de2000)
    libSBSNeighborSearch.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBSNeighborSearch.so (0x00007fab66bba000)
    libSBGMain.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGMain.so (0x00007fab66912000)
    libSBGProperty.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGProperty.so (0x00007fab666ff000)
    libSBGToolBar.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGToolBar.so (0x00007fab664e3000)
    libSBGElement.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGElement.so (0x00007fab662ce000)
    libSBGInspector.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGInspector.so (0x00007fab65cfb000)
    libSBIFile.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBIFile.so (0x00007fab65af0000)
    libSBGRender.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGRender.so (0x00007fab65830000)
    libSBGDocument.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGDocument.so (0x00007fab655ce000)
    libSBGUndo.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGUndo.so (0x00007fab653b9000)
    libSBGWidget.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGWidget.so (0x00007fab65162000)
    libSBIElement.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBIElement.so (0x00007fab64f13000)
    libSBGNotification.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGNotification.so (0x00007fab64d06000)
    libSBGLog.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGLog.so (0x00007fab64af4000)
    libIO.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libIO.so (0x00007fab648f1000)
    libSBIPackage.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBIPackage.so (0x00007fab646d1000)
    libSBIWebService.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBIWebService.so (0x00007fab644b3000)
    libSBGVisualModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGVisualModel.so (0x00007fab642a3000)
    libSBGStructuralModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGStructuralModel.so (0x00007fab64037000)
    libSBGPropertyModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGPropertyModel.so (0x00007fab63e27000)
    libSBGInteractionModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGInteractionModel.so (0x00007fab63c16000)
    libSBGDynamicalModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGDynamicalModel.so (0x00007fab63a05000)
    libSBGSimulator.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGSimulator.so (0x00007fab637f5000)
    libSBGStateUpdater.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGStateUpdater.so (0x00007fab635e8000)
    libSBGDataGraph.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGDataGraph.so (0x00007fab6331c000)
    libSBGMenu.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGMenu.so (0x00007fab6310e000)
    libSBGAction.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGAction.so (0x00007fab62ee8000)
    libSBGApp.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGApp.so (0x00007fab62cdd000)
    libSBGEditor.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGEditor.so (0x00007fab62ac0000)
    libSBGWindow.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGWindow.so (0x00007fab6286b000)
    libSBGSettings.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGSettings.so (0x00007fab62652000)
    libData.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libData.so (0x00007fab61b9e000)
    libSBDColor.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDColor.so (0x00007fab61854000)
    libSBDDocument.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDDocument.so (0x00007fab6130b000)
    libSBMVisualModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMVisualModel.so (0x00007fab610fa000)
    libSBDController.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDController.so (0x00007fab60d80000)
    libSBMPropertyModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMPropertyModel.so (0x00007fab60b6f000)
    libSBSSimulator.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBSSimulator.so (0x00007fab60957000)
    libSBDApp.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDApp.so (0x00007fab60743000)
    libSBGPath.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBGPath.so (0x00007fab6052b000)
    libQt5MultimediaWidgets.so.5 => ./SAMSONQtLibs/libQt5MultimediaWidgets.so.5 (0x00007fab6030d000)
    libQt5Multimedia.so.5 => ./SAMSONQtLibs/libQt5Multimedia.so.5 (0x00007fab60002000)
    libQt5Network.so.5 => ./SAMSONQtLibs/libQt5Network.so.5 (0x00007fab5fc6e000)
    libQt5OpenGL.so.5 => ./SAMSONQtLibs/libQt5OpenGL.so.5 (0x00007fab5fa17000)
    libQt5PrintSupport.so.5 => ./SAMSONQtLibs/libQt5PrintSupport.so.5 (0x00007fab5f7a9000)
    libQt5Sql.so.5 => ./SAMSONQtLibs/libQt5Sql.so.5 (0x00007fab5f562000)
    libQt5Widgets.so.5 => ./SAMSONQtLibs/libQt5Widgets.so.5 (0x00007fab5ed2d000)
    libQt5Gui.so.5 => ./SAMSONQtLibs/libQt5Gui.so.5 (0x00007fab5e57d000)
    libQt5Xml.so.5 => ./SAMSONQtLibs/libQt5Xml.so.5 (0x00007fab5e342000)
    libQt5Core.so.5 => ./SAMSONQtLibs/libQt5Core.so.5 (0x00007fab5dc02000)
    libSBSStateUpdater.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBSStateUpdater.so (0x00007fab5d9ee000)
    libSBMInteractionModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMInteractionModel.so (0x00007fab5d7d6000)
    libSBMDynamicalModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMDynamicalModel.so (0x00007fab5d58e000)
    libSBMStructuralModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMStructuralModel.so (0x00007fab5cc31000)
    libSBDType.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDType.so (0x00007fab5ca0f000)
    libSBMElement.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMElement.so (0x00007fab5c7ed000)
    libSBDQuantity.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDQuantity.so (0x00007fab5c5eb000)
    libSBMModel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBMModel.so (0x00007fab5c3dc000)
    libSBDDataGraph.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBDDataGraph.so (0x00007fab5c00b000)
    libSBCFunctor.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCFunctor.so (0x00007fab5bdff000)
    libCore.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libCore.so (0x00007fab5bbfb000)
    libSBCKernel.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCKernel.so (0x00007fab5b9da000)
    libSBCUndo.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCUndo.so (0x00007fab5b7c6000)
    libSBCClass.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCClass.so (0x00007fab5b5a2000)
    libSBCSignal.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCSignal.so (0x00007fab5b396000)
    libSBCReference.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCReference.so (0x00007fab5b169000)
    libSBCLog.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCLog.so (0x00007fab5af5b000)
    libSBCMeta.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCMeta.so (0x00007fab5ad4a000)
    libSBCContainer.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCContainer.so (0x00007fab5ab28000)
    libSBCHeap.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCHeap.so (0x00007fab5a7e1000)
    libSBCSerializer.so => /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries/libSBCSerializer.so (0x00007fab5a477000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fab5a0d9000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fab59ce8000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fab68321000)
    libGLdispatch.so.0 => /usr/lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007fab59a32000)
    libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007fab596fa000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fab594db000)
    libGL.so.1 => /usr/lib/x86_64-linux-gnu/libGL.so.1 (0x00007fab5924f000)
    libstdc++.so.6 => /home/rbenda/anaconda3/lib/libstdc++.so.6 (0x00007fab683ce000)
    libgcc_s.so.1 => /home/rbenda/anaconda3/lib/libgcc_s.so.1 (0x00007fab683b9000)
    libpulse-mainloop-glib.so.0 => /usr/lib/x86_64-linux-gnu/libpulse-mainloop-glib.so.0 (0x00007fab5904a000)
    libpulse.so.0 => /usr/lib/x86_64-linux-gnu/libpulse.so.0 (0x00007fab58dfa000)
    libglib-2.0.so.0 => /home/rbenda/anaconda3/lib/libglib-2.0.so.0 (0x00007fab58cdd000)
    libz.so.1 => /home/rbenda/anaconda3/lib/libz.so.1 (0x00007fab6838f000)
    libicui18n.so.56 => ./SAMSONQtLibs/libicui18n.so.56 (0x00007fab58844000)
    libicuuc.so.56 => ./SAMSONQtLibs/libicuuc.so.56 (0x00007fab5848c000)
    libicudata.so.56 => ./SAMSONQtLibs/libicudata.so.56 (0x00007fab56aa9000)
    libgthread-2.0.so.0 => /home/rbenda/anaconda3/lib/libgthread-2.0.so.0 (0x00007fab6838a000)
    libxcb.so.1 => /home/rbenda/anaconda3/lib/libxcb.so.1 (0x00007fab56880000)
    libpulsecommon-11.1.so => /usr/lib/x86_64-linux-gnu/pulseaudio/libpulsecommon-11.1.so (0x00007fab56602000)
    libdbus-1.so.3 => /home/rbenda/anaconda3/lib/libdbus-1.so.3 (0x00007fab565ae000)
    libpcre.so.1 => /home/rbenda/anaconda3/lib/./libpcre.so.1 (0x00007fab56566000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fab5635e000)
    libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007fab5615a000)
    libsystemd.so.0 => /lib/x86_64-linux-gnu/libsystemd.so.0 (0x00007fab55ed6000)
    libwrap.so.0 => /lib/x86_64-linux-gnu/libwrap.so.0 (0x00007fab55ccc000)
    libsndfile.so.1 => /usr/lib/x86_64-linux-gnu/libsndfile.so.1 (0x00007fab55a53000)
    libasyncns.so.0 => /usr/lib/x86_64-linux-gnu/libasyncns.so.0 (0x00007fab5584d000)
    liblzma.so.5 => /home/rbenda/anaconda3/lib/liblzma.so.5 (0x00007fab55627000)
    liblz4.so.1 => /home/rbenda/anaconda3/lib/liblz4.so.1 (0x00007fab55403000)
    libgcrypt.so.20 => /lib/x86_64-linux-gnu/libgcrypt.so.20 (0x00007fab550e8000)
    libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007fab54ece000)
    libFLAC.so.8 => /usr/lib/x86_64-linux-gnu/libFLAC.so.8 (0x00007fab54c57000)
    libogg.so.0 => /usr/lib/x86_64-linux-gnu/libogg.so.0 (0x00007fab54a4e000)
    libvorbis.so.0 => /usr/lib/x86_64-linux-gnu/libvorbis.so.0 (0x00007fab54823000)
    libvorbisenc.so.2 => /usr/lib/x86_64-linux-gnu/libvorbisenc.so.2 (0x00007fab5457a000)
    libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00007fab5435f000)
    libgpg-error.so.0 => /lib/x86_64-linux-gnu/libgpg-error.so.0 (0x00007fab5414a000)
    /home/rbenda/NANO-D/SAMSON/0.7.0/Binaries:.:./SAMSONQtLibs:/home/rbenda/anaconda3/lib:
    Python library has not been loaded: Cannot load library libpython3.6m: (libpython3.6m: cannot open shared object file: No such file or directory)

    Do you think it is only due to this "libpython3.6m" library problem ?

    Thank you very much for your help, sorry for all theses problems and disturbance...
    Have a nice evening
    Robert



  • Thank you for posting the log, @Robert !

    The fact that it cannot find Python:

    Python found in the system:
    Python executable: /home/rbenda/anaconda3/bin/python3
    Python library has not been loaded: Cannot load library libpython3.6m: (libpython3.6m: cannot open shared object file: No such file or directory)
    

    should not cause any problem when launching SAMSON, it is only used in the Python Scripting Element in SAMSON.

    But there are other lines which might indicate an issue, e.g.:

    libxcb.so.1 => /home/rbenda/anaconda3/lib/libxcb.so.1
    

    Could you, please, try launching SAMSON with the following line commented in the ./SAMSON-Core.sh script:

    export LD_LIBRARY_PATH=${PYTHON_LIBRARY_PATH}:${LD_LIBRARY_PATH}
    

    such that libxcb.so and other libraries won't be used from the anaconda3 installation. If they are still used from there you might want to check your environment variables (see ~/.bashrc) and excluding the path to anaconda3 from there just for the try.

    But, I do not think that might be causing an issue since I am using anaconda3 under Ubuntu 16.04 (I use Python in SAMSON) and I have the same linking.



  • Thanks Dmitriy !

    Indeed, commenting this line in the SAMSON-Core.sh script yields :

    libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f5750b03000)

    instead in the terminal.



  • @Robert

    Does it help with the problem you have?



  • @Robert

    When you executed the glxinfo | grep OpenGL command in the terminal you got:

    ...
    OpenGL core profile version string: 4.5 (Core Profile) Mesa 18.2.8
    ...
    OpenGL version string: 3.0 Mesa 18.2.8
    

    Whilst your system supports OpenGL 4.5 and SAMSON asks for OpenGL 3.2+ during the installation, in some cases, the Mesa driver might provide OpenGL 3.0 for better compatibility. You can specify the version you want using the MESA_GL_VERSION_OVERRIDE environment variable. This should force the correct version of OpenGL to be used. To check how it works, you might do in the terminal smth like this:

    MESA_GL_VERSION_OVERRIDE=4.5 glxinfo | grep OpenGL
    

    Could you, please, try setting this variable in the script that launches SAMSON-Core (please, try versions 3.2, 4.2, and 4.5):

    MESA_GL_VERSION_OVERRIDE=4.5 ./SAMSON-Core
    


  • Hello Dmitryi, thanks for your help.

    Having:
    libxcb.so.1 => /usr/ lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f5750b03000)

    (i.e. the fact that libxcb.so and other libraries are not used from the anaconda3 installation, when commenting the line
    export LD_LIBRARY_PATH=${PYTHON_LIBRARY_PATH}:${LD_LIBRARY_PATH}
    in SAMSON-Core.sh script)

    didn't solve the graphical problem when launching ./SAMSON-Core.sh.

    I have a strange problem since this morning, when I try to launch ./SAMSON-Core directly, instead of ./SAMSON-Core.sh (which "works", i.e. open the SAMSON window but with the graphical problem you know), I obtain an error message :

    ./SAMSON-Core: error while loading shared libraries: libSAMSON.so: cannot open shared object file: No such file or directory.

    I did the two commands:
    MESA_GL_VERSION_OVERRIDE=4.5 glxinfo | grep OpenGL

    MESA_GL_VERSION_OVERRIDE=4.5 ./SAMSON-Core

    but for the second one, I obtain an error message (be it for 4.5, 3.2 or 4.2) ; the same error message as when launching ./SAMSON-Core :

    ./SAMSON-Core: error while loading shared libraries: libSAMSON.so: cannot open shared object file: No such file or directory

    Sorry for so much trouble, hoping to solve it today !( but I have access to another fixed computer where SAMSON works today, so I can also work while trying to solve this problem on my laptop).
    Regards,
    Robert


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