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

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    • DmitriyMarin
      DmitriyMarin last edited by

      @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
      

      Dmitriy,
      The SAMSON Team, https://s-c.io

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      • R
        Robert last edited by

        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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        • R
          Robert last edited by

          Concerning libSAMSON.so, it is strange because I have it in my directory /NANO-D/SAMSON/0.7.0/Binaries . (and I checked but I think I didn't change the SAMSON-Core.sh script after re-commenting all the lines, so ./SAMSON-Core should open the interface as before...)

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          • DmitriyMarin
            DmitriyMarin last edited by

            On Linux, the SAMSON-Core.sh script is necessary for launching the SAMSON-Core executable since it sets up paths to necessary libraries. That's why when launching just the SAMSON-Core executable you may have an error about missing libraries.

            Could you, please, try modifying the SAMSON-Core.sh script as follows (with different OpenGL versions: 3.2, 4.2, and 4.5):

            MESA_GL_VERSION_OVERRIDE=4.5 ./SAMSON-Core
            

            Dmitriy,
            The SAMSON Team, https://s-c.io

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            • R
              Robert last edited by

              Thank you, I tried with the three versions 3.2, 4.2 and 4.5 but it didn't work ...

              I inserted the line
              MESA_GL_VERSION_OVERRIDE=4.5 ./SAMSON-Core

              just before the final line of ./SAMSON-Core.sh :
              echo "restoring context"

              (I don't know if it is the right place...)

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              • DmitriyMarin
                DmitriyMarin last edited by

                Does the following command in the terminal:

                MESA_GL_VERSION_OVERRIDE=4.5 glxinfo | grep OpenGL
                

                among other output show you (for your version of Mesa):

                OpenGL version string: 4.5 Mesa 18.2.8
                

                Basically, it should specify the version of OpenGL provided by Mesa.

                In the SAMSON-Core.sh script you can try modifying it as follow (see the line with ./SAMSON-Core):

                ...
                export LD_LIBRARY_PATH=$script_dir:.:./SAMSONQtLibs:$LD_LIBRARY_PATH
                
                #ldd SAMSON-Core	#uncomment to have more information if SAMSON crashes
                #echo $LD_LIBRARY_PATH	#uncomment to have more information if SAMSON crashes
                MESA_GL_VERSION_OVERRIDE=4.5 ./SAMSON-Core --logconsole			#available flags --disablenetwork /--import /--logconsole /--logfile "file" /--logdefaultfile
                
                export LD_LIBRARY_PATH=$SAVED_LD_LIBRARY_PATH
                export LC_ALL=$SAVED_LC_ALL
                echo "restoring context"
                

                You can try modifying the OpenGL version to 3.2, 4.2, 4.5. Does it launch SAMSON and do you still have the same problem?

                Dmitriy,
                The SAMSON Team, https://s-c.io

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                • R
                  Robert last edited by

                  Yes, with :
                  MESA_GL_VERSION_OVERRIDE=4.5 glxinfo | grep OpenGL

                  I obtain :
                  OpenGL version string: 4.5 (Compatibility Profile) Mesa 18.2.8

                  I tried this modification you proposed in the ./SAMSON-Core.sh, at the right place, SAMSON launches but I have the same graphical problem be it for 3.2, 4.2 and 4.5 versions ... I get a lot of information in the terminal while SAMSON is launching, do you want me to paste it ? (it is a bit long ...)

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                  • R
                    Robert last edited by

                    In the end of the message when launching SAMSON, I obtain :
                    ....

                      -  "elementName" "Graphene Sheet Creator"
                      -  "elementDeveloperID" "C682B30F-0D21-4CDB-B968-B72E225DDC8F"
                      -  "elementID" "FF9BE415-C812-1C1A-CDBE-78896176B067"
                      -  "elementVersion" "0.7.0"
                      -  "checksumDebug" 0
                      -  "checksumRelease" 0
                      -  "elementDescription" ""
                      -  "elementOS" ""
                      -  "samsonVersion" "0.7.0"
                      -  "forceUpdate" false
                      -----------------------------------------------------------------------
                    

                    =============================================================================

                    QPixmap::scaled: Pixmap is a null pixmap
                    libpng warning: iCCP: known incorrect sRGB profile
                    libpng warning: iCCP: known incorrect sRGB profile
                    "File"
                    "File"
                    "Edit"
                    "Edit"
                    "App"
                    QLayout: Attempting to add QLayout "" to SBGWidgetOnExit "", which already has a layout
                    restoring context

                    DmitriyMarin 1 Reply Last reply Reply Quote 0
                    • DmitriyMarin
                      DmitriyMarin last edited by DmitriyMarin

                      No, there is no need to post the output, it has a lot of information because of the --logconsole flag.

                      We will try to see what we can do about this issue.

                      Dmitriy,
                      The SAMSON Team, https://s-c.io

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                      • DmitriyMarin
                        DmitriyMarin @Robert last edited by

                        @robert

                        This output is totally ok.

                        Dmitriy,
                        The SAMSON Team, https://s-c.io

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                        • DmitriyMarin
                          DmitriyMarin last edited by

                          @Robert

                          What you can also do, if you want to try, is to add a PPA with newer drivers (see this launchpad page) - it provides recently updated X and Mesa free graphics drivers for Intel, etc:

                          sudo add-apt-repository ppa:oibaf/graphics-drivers
                          sudo apt-get update
                          

                          Update with it and may try installing the following package:

                          sudo apt-get install xserver-xorg-video-intel
                          

                          P.s.: if you install packages from this PPA and later want to update Ubuntu to a newer version it is recommended to remove these packages and PPA before upgrading (see this launchpad page).

                          Dmitriy,
                          The SAMSON Team, https://s-c.io

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                          • R
                            Robert last edited by

                            Thanks for these ideas. I tried but it didn't work.
                            I still have the same problem.

                            I will maybe focus on my problem for VMD, as you say it is maybe more general than SAMSON, it is a global graphics problem maybe.
                            Or maybe I could try a complete new installation of SAMSON , don't know if it could rearrange things thanks to the last installed packages...

                            Thanks again, Robert

                            DmitriyMarin 1 Reply Last reply Reply Quote 0
                            • DmitriyMarin
                              DmitriyMarin @Robert last edited by

                              @robert
                              You can try re-installing, but I do not think it will resolve the issue.

                              Dmitriy,
                              The SAMSON Team, https://s-c.io

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                              • R
                                Robert last edited by

                                Hi Dmitryi, hope you are doing well. I tried reinstalling SAMSON but it didn't solve the problem indeed...
                                I don't want you of course to solve my problem for VMD ^^, (I have also written to VMD for assistance) but I can share you this info , maybe it is linked to the problem I have with SAMSON : when I open vmd (which seems, as SAMSON, perfectly installed), I get the following message in the terminal :

                                Info) VMD for LINUXAMD64, version 1.9.3 (December 1, 2016)
                                Info) http://www.ks.uiuc.edu/Research/vmd/
                                Info) Email questions and bug reports to vmd@ks.uiuc.edu
                                Info) Please include this reference in published work using VMD:
                                Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
                                Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
                                Info) -------------------------------------------------------------
                                Info) Multithreading available, 8 CPUs detected.
                                Info) Free system memory: 28GB (90%)
                                Info) Dynamically loaded 2 plugins in directory:
                                Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
                                vmd >

                                bot nothing opens (no VMD interface).

                                Moreover, if I type "menu main status", I get "off", anf if I type "menu main on" (to activate the menu), and again "menu main status", I still get "off". If I type "menu list", I get nothing (meaning that there is no available menu, which is why I don't even get the main menu window opening).

                                What is really strange is that VMD seems to have been perfectly installed, as I can analyse a pdb file as follows :

                                vmd CF_OX_monomer_11_SAMSON.pdb

                                in the terminal gives :

                                Info) VMD for LINUXAMD64, version 1.9.3 (December 1, 2016)
                                Info) http://www.ks.uiuc.edu/Research/vmd/
                                Info) Email questions and bug reports to vmd@ks.uiuc.edu
                                Info) Please include this reference in published work using VMD:
                                Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
                                Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
                                Info) -------------------------------------------------------------
                                Info) Multithreading available, 8 CPUs detected.
                                Info) Free system memory: 28GB (90%)
                                Info) Dynamically loaded 2 plugins in directory:
                                Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
                                Info) File loading in progress, please wait.
                                Info) Using plugin pdb for structure file CF_OX_monomer_11_SAMSON.pdb
                                Info) Using plugin pdb for coordinates from file CF_OX_monomer_11_SAMSON.pdb
                                Info) Determining bond structure from distance search ...
                                Info) Eliminating bonds duplicated from existing structure...
                                Info) Finished with coordinate file CF_OX_monomer_11_SAMSON.pdb.
                                Info) Analyzing structure ...
                                Info) Atoms: 93
                                Info) Bonds: 99
                                Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
                                Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
                                Info) Residues: 1
                                Info) Waters: 0
                                Info) Segments: 1
                                Info) Fragments: 1 Protein: 2 Nucleic: 0
                                vmd > exit
                                Info) VMD for LINUXAMD64, version 1.9.3 (December 1, 2016)
                                Info) Exiting normally.

                                In another computer where VMD works perfectly, I get the following message in the terminal when opening VMD :

                                /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1: no version information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
                                Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
                                Info) http://www.ks.uiuc.edu/Research/vmd/
                                Info) Email questions and bug reports to vmd@ks.uiuc.edu
                                Info) Please include this reference in published work using VMD:
                                Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
                                Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
                                Info) -------------------------------------------------------------
                                Info) Multithreading available, 4 CPUs detected.
                                Info) CPU features: SSE2 AVX AVX2 FMA
                                Info) Free system memory: 681MB (35%)
                                Info) No CUDA accelerator devices available.
                                Warning) Detected X11 'Composite' extension: if incorrect display occurs
                                Warning) try disabling this X server option. Most OpenGL drivers
                                Warning) disable stereoscopic display when 'Composite' is enabled.
                                Info) OpenGL renderer: SVGA3D; build: RELEASE; LLVM;
                                Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
                                Info) Full GLSL rendering mode is available.
                                Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
                                Info) Dynamically loaded 2 plugins in directory:
                                Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
                                vmd >

                                => so OpenGL seems also to be what lacks (at least in the messages in the terminal) for me for VMD to open its menu and graphics, so maybe, concerning SAMSON, it is due to a bad installation of OpenGL, I don't know...

                                Thank you.
                                Regards,
                                Robert

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                                • DmitriyMarin
                                  DmitriyMarin last edited by DmitriyMarin

                                  @Robert

                                  I think, it might be connected to the Wayland display being used instead of Xorg (see: https://forum.samson-connect.net/topic/37/installing-or-running-samson-on-ubuntu-17-04-and-later-versions). I would suggest you to try installing Xorg and disabling Wayland display.

                                  See, e.g.: https://linuxconfig.org/how-to-disable-wayland-and-enable-xorg-display-server-on-ubuntu-18-04-bionic-beaver-linux

                                  Dmitriy,
                                  The SAMSON Team, https://s-c.io

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                                  • R
                                    Robert last edited by

                                    Thank you Dmitryi, I had not seen that trick of disabling Wayland display. I tried and reboot but nothing changed sor SAMSON or VMD display. I don't know how to be sure that Xorg display is used .. When I type "Xorg" (or "Xorg -version") in the terminal I get :

                                    /usr/lib/xorg/Xorg.wrap: Only console users are allowed to run the X server

                                    However when I type "sudo Xorg -version", I get :

                                    X.Org X Server 1.19.6
                                    Release Date: 2017-12-20
                                    X Protocol Version 11, Revision 0
                                    Build Operating System: Linux 4.4.0-138-generic x86_64 Ubuntu
                                    Current Operating System: Linux pl365-pro 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64
                                    Kernel command line: BOOT_IMAGE=/vmlinuz-4.15.0-47-generic root=/dev/mapper/VGsys-root ro
                                    Build Date: 25 October 2018 04:11:27PM
                                    xorg-server 2:1.19.6-1ubuntu4.2 (For technical support please see http://www.ubuntu.com/support)
                                    Current version of pixman: 0.34.0
                                    Before reporting problems, check http://wiki.x.org
                                    to make sure that you have the latest version.

                                    I don't know if it is normal, but I don't have any xorg.conf file in /etc/X11/ (as should be the case according to https://doc.ubuntu-fr.org/xorg). Maybe I should create and edit one such file in that precise directory ?

                                    When I type "locate xorg.conf", I get :

                                    /usr/share/X11/xorg.conf.d
                                    /usr/share/X11/xorg.conf.d/10-amdgpu.conf
                                    /usr/share/X11/xorg.conf.d/10-quirks.conf
                                    /usr/share/X11/xorg.conf.d/10-radeon.conf
                                    /usr/share/X11/xorg.conf.d/40-libinput.conf
                                    /usr/share/X11/xorg.conf.d/70-wacom.conf
                                    /usr/share/doc/xserver-xorg-video-intel/xorg.conf
                                    /usr/share/man/man5/xorg.conf.5.gz
                                    /usr/share/man/man5/xorg.conf.d.5.gz

                                    Maybe I should type "sudo dpkg-reconfigure -phigh xserver-xorg" to reconfigure automatically Xorg, as suggested in ttps://doc.ubuntu-fr.org/xorg ?

                                    Thank you.
                                    Robert

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                                    • DmitriyMarin
                                      DmitriyMarin last edited by

                                      Could you, please, check whether Wayland or X11 display is used, e.g. (please, check for the proper way on Ubuntu):

                                      echo $XDG_SESSION_TYPE
                                      

                                      or

                                      cat /etc/X11/default-display-manager
                                      

                                      or

                                      loginctl show-session $(loginctl | grep $(whoami) | awk '{print $1}') -p Type
                                      

                                      If your system is using Xorg and you still experience problems with OpenGL you may try switching to the lightdm display manager (please, check for Ubuntu 18.04):

                                      sudo dpkg-reconfigure lightdm
                                      sudo apt-get install lightdm
                                      

                                      Dmitriy,
                                      The SAMSON Team, https://s-c.io

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                                      • R
                                        Robert last edited by

                                        Thank you Dmitryi.

                                        cat /etc/X11/default-display-manager
                                        gives me :

                                        /usr/sbin/gdm3

                                        echo $XDG_SESSION_TYPE
                                        gives me :
                                        x11

                                        loginctl show-session 2 -p Type

                                        gives me :

                                        Type=x11

                                        So I think x11 is turned on and not Wayland, so it seems OK.

                                        I then installed lightdm and replaced gdm3 by lightdm as a display manager, thus :

                                        cat /etc/X11/default-display-manager

                                        gives me now :

                                        /usr/sbin/lightdm

                                        I tried launching SAMSON but nothing changed, maybe I have to reboot and re-try..
                                        Thanks,
                                        Robert

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                                        • DmitriyMarin
                                          DmitriyMarin @Robert last edited by

                                          @robert
                                          Yes, could you, please, try rebooting your system.

                                          Dmitriy,
                                          The SAMSON Team, https://s-c.io

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                                          • R
                                            Robert last edited by

                                            Hi Dmitryi, thanks, I tried rebooting, and having the new lightdm display instead of gdm3, but it didn't solve my problem for SAMSON nor for VMD...

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