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

DmitriyMarin

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

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

@Robert

Does it help with the problem you have?

DmitriyMarin

@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

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

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

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

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

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?

Robert

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 ...)

Robert

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

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.

DmitriyMarin

@robert

This output is totally ok.

DmitriyMarin

@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).

Robert

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

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

Robert

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

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

Robert

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

DmitriyMarin

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

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

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

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

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

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