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

Robert · Apr 16, 2019, 11:07 AM

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

DmitriyMarin · Apr 16, 2019, 11:14 AM

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.

DmitriyMarin · Apr 16, 2019, 11:21 AM

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

Robert · Apr 16, 2019, 11:30 AM

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

DmitriyMarin · Apr 16, 2019, 12:48 PM

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

DmitriyMarin · Apr 16, 2019, 12:56 PM

@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

Robert · Apr 16, 2019, 2:55 PM

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

DmitriyMarin · Apr 16, 2019, 3:04 PM

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.

Robert · Apr 16, 2019, 3:29 PM

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 :

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

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

DmitriyMarin · Apr 16, 2019, 3:37 PM

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.

Robert · Apr 16, 2019, 4:09 PM

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

DmitriyMarin · Apr 16, 2019, 4:23 PM

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.

Robert · Apr 16, 2019, 4:42 PM

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.

DmitriyMarin · Apr 16, 2019, 5:16 PM

@Robert

Does it help with the problem you have?

DmitriyMarin · Apr 16, 2019, 9:51 PM

@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

Robert · Apr 17, 2019, 8:27 AM

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

Robert · Apr 17, 2019, 8:30 AM

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...)

DmitriyMarin · Apr 17, 2019, 8:32 AM

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

Robert · Apr 17, 2019, 9:47 AM

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...)

DmitriyMarin · Apr 17, 2019, 9:55 AM

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?

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