Hardware OpenGL Failure on Ubuntu 16.04.3 - Can not initialize shared resources

First, my system info:

• 4.13.0-26-generic #29~16.04.2-Ubuntu SMP Tue Jan 9 22:00:44 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
• Clean installation of Matlab R2016b (64-bit)
• Video card: AMD/ATI Pitcairn PRO (Radeon HD 7850)

Problems with Vanilla Install

So, I start up Matlab from the command line with no arguments. I've set two environment variables, LIBGL_DEBUG=verbose and MESA_DEBUG=1, to get an idea of any bugs. The software starts with no errors. Next, I issue a simple plot command:

    plot(1,1, 'b*'); grid on;

Matlab creates the plot successfully, but issues a series of errors, saying that there was a low-level graphics error. From the command line I see the following messages:

    libGL: pci id for fd 570: 1002:6819, driver radeonsi
    libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/radeonsi_dri.so
    libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/radeonsi_dri.so
    libGL: dlopen /usr/lib/x86_64-linux-gnu/dri/radeonsi_dri.so failed (/opt/local/MATLAB/R2016b/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /usr/lib/x86_64-linux-gnu/dri/radeonsi_dri.so))

There are many more, but the end result is the same: the linker cannot load the graphics drivers with the libstdc++.so file Matlab has loaded. To fix this issue, I rename the relevant libraries that come with Matlab to force it to use the system libraries (which include version GLIBCXX_3.4.21):

    cd /opt/local/MATLAB/R2016b/sys/os/glnxa64
    mv libstdc++.so.6 libstdc++.so.6.bak
    mv libstdc++.so.6.0.20 libstdc++.so.6.0.20.bak

Problems with Modified Install

With the C++ libraries renamed to force Matlab to link with the system libraries, I restart Matlab. The environment variables are still set, so any libgl or mesa errors should be reported to the terminal. Immediately after the program starts, I receive the following error in Matlab:

    com.jogamp.opengl.GLException: X11GLXDrawableFactory - Could not initialize shared resources for X11GraphicsDevice[type .x11, connection :1, unitID 0, handle 0x0, owner false, ResourceToolkitLock[obj 0x7c1bc33e, isOwner false, <2af5b1a, 46860956>[count 0, qsz 0, owner <NULL>]]]
      at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.createSharedResource(X11GLXDrawableFactory.java:326)
  at jogamp.opengl.SharedResourceRunner.run(SharedResourceRunner.java:297)
  at java.lang.Thread.run(Unknown Source)
    Caused by: java.lang.NullPointerException
  at jogamp.opengl.GLContextImpl.makeCurrent(GLContextImpl.java:688)
  at jogamp.opengl.GLContextImpl.makeCurrent(GLContextImpl.java:580)
  at jogamp.opengl.x11.glx.X11GLXDrawableFactory$SharedResourceImplementation.createSharedResource(X11GLXDrawableFactory.java:297)
  ... 2 more
    Exception in thread "Startup Class Loader" java.lang.InternalError: XXX0 profile[1]: GL3bc -> profileImpl GL4bc !!! not mapped 
  at com.jogamp.opengl.GLProfile.computeProfileMap(GLProfile.java:2047)
  at com.jogamp.opengl.GLProfile.initProfilesForDeviceCritical(GLProfile.java:1917)
  at com.jogamp.opengl.GLProfile.initProfilesForDevice(GLProfile.java:1866)
  at com.jogamp.opengl.GLProfile.initProfilesForDefaultDevices(GLProfile.java:1835)
  at com.jogamp.opengl.GLProfile.access$000(GLProfile.java:79)
  at com.jogamp.opengl.GLProfile$1.run(GLProfile.java:229)
  at java.security.AccessController.doPrivileged(Native Method)
  at com.jogamp.opengl.GLProfile.initSingleton(GLProfile.java:215)
  at com.mathworks.hg.peer.JavaSceneServerPeer.initializeJOGL(JavaSceneServerPeer.java:147)
  at com.mathworks.hg.peer.JavaSceneServerPeer.<clinit>(JavaSceneServerPeer.java:117)
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Unknown Source)
  at com.mathworks.mde.desk.StartupClassLoader.loadClass(StartupClassLoader.java:262)
  at com.mathworks.mde.desk.StartupClassLoader.access$900(StartupClassLoader.java:25)
  at com.mathworks.mde.desk.StartupClassLoader$2.run(StartupClassLoader.java:248)
  at java.lang.Thread.run(Unknown Source)

Additionally, the following messages are displayed in the Terminal output:

    libGL: pci id for fd 570: 1002:6819, driver radeonsi
    libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/radeonsi_dri.so
    libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/radeonsi_dri.so
    libGL: Using DRI3 for screen 0

These messages don't indicate any troubles; it looks like the radeonsi_dri object is loaded successfully. When I try the same plot command as above, I receive the following message in Matlab:

    Caught unexpected fl::except::IInternalException

The figure shows an empty image; the plot has not been created.

Other Notes

• I've also tried renaming the libgcc_s.so.1 library in Matlab's directory so that it uses the system version, but that doesn't change anything.
• There are no errors (EE) in my Xorg.0.log file
• I've successfully benchmarked OpenGL and the video card with glmark2, i.e., OpenGL runs very well with hardware accelleration on my machine, but Matlab has some issue.
• Matlab R2016b ships with libGL.so.1.6.0 (in R2016b/sys/opengl/lib/glnxa64) but my OS version is libGL.so.1.2.0). Could this cause an issue? I tried renaming the libGL files shipped with Matlab to force it to use the system versions, but the error messages are still the same.
• With the modified libstdc++ files, I can run Matlab in software openGL mode via the command matlab -softwareopengl. Plotting works fine, though Mesa spits out the warning/error, "User error: GL_INVALID_ENUM in glGetIntegerv(pname=GL_MAJOR_VERSION)"

[Nico Bast]

I got the same error output on Matlab startup described under "Problems with Modified Install". It seems that no PLOT commands can be executed. Each is terminated by "Caught unexpected fl::except::IInternalException."

Some system info: - Ubuntu 16.04.3 - Matlab 2016a (set for usage of psychtoolbox-3, programmed experiments run fine, no timing issues) - Radeon HD580 (open amdgpu driver)

Furthermore opengl info gives this rather useless output: Version: '' Vendor: '' Renderer: 'None' RendererDriverVersion: '' RendererDriverReleaseDate: '' MaxTextureSize: 0 Visual: '' Software: 1 HardwareSupportLevel: 'none' SupportsGraphicsSmoothing: 0 SupportsDepthPeelTransparency: 0 SupportsAlignVertexCenters: 0 Extensions: {} MaxFrameBufferSize: 0

[Yubo Qiu]

I've ran into the same issue. Currently using Linux Mint 18.3 with a fresh install of Matlab. I've attached the screenshot of the error. I used this code to launch Matlab

LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/local/MATLAB/R2017b/bin/matlab

Using AMD280X

[Nico Bast]

I read that this comment should prevent matlab from using its outdated libstdc library and instead get the systems libstdc. This change of libraries is also done by the "matlab-support" package.

- source: https://github.com/Psychtoolbox-3/Psychtoolbox-3/wiki/Cookbook:-Setting-up-Ubuntu-with-Modern-AMD-Cards

However, neither the preload command nor the matlab-support package help. I still get the errors described under "Problems with Modified Install". To elaborate a little more on this:

- opengl info just returns empty values (no hardware acceleration?) - I cannot plot anything (e.g. plot(1,1)) - however, my experiments with psychtoolbox-3 run fine with good timings. The GPU is adequately addressed.

Does somebody have any suggestions, how to proceed? Thanks and Best,

[Andrew Cox]

Yubo, I tried setting the LD_PRELOAD variable as you suggest, but it does not change the behavior for me.

Nico, I made the same changes as the matlab-support package does (manually), so I think we're on the same page.

I looked through the Psychtoolbox cookbook - it looks like they suggest creating an Xorg.conf file via the tools in Psychtoolbox, but I'm not sure how to apply those changes to my system. Psychtoolbox appears to have a lot of compiled visualization code, so perhaps it is independent of the Matlab implementation.

[Nico Bast]

Dear Andrew,

the tools in Psychtoolbox that create xorg.conf.d files are the XOrgConfCreator and the XOrgConfSelector that can be called within maltab and implemented Psychtoolbox. However, these tools are just for setting up Screens and Display. I would not think that they are related to our problem.

- I found that the error messages described under "Problems with modified install" to not appear if I uninstall psychtoolbox-3. However, ptb3 is mandatory for me.

[Domanic]

Issuing the following as your first matlab command sometimes offers a workaround for similar issues:

opengl neverselect

[Andrew Cox]

Domanic - Sure. You can also start matlab with the -softwareopengl flag or run opengl('set', 'software') within matlab to avoid the issue. However, the software rendering is nowhere near as clean as the hardware-supported rendering. I.e., I'm not looking for a workaround, I'm looking for a solution.

[Thad C]

Having the exact same maddening series of problems/errors with my system. I've also been through the same set of solution attempts with matlab-support pkg.

Installing the amdgpu-pro driver sidesteps the total crash on Matlab startup, but comes with its own bevy of errors/workarounds/warnings when attempting to do anything Psychtoolbox related (...the only reason for machine existence).

Switching to an nvidia gpu and proprietary nvidia driver has the same effect; runs, but broken in other ways.

Seems like this all points to something fundamentally messed up in current Ubuntu 16.04 open source driver implementation(?), the way it interacts with Matlab 2016b's own [inherently broken] OpenGL implementation(?), or remappings done by the matlab-support package(?)...or some combination thereof.

Not trying to point fingers, just want to make some kind of sense out of this dumb low-level crashing, and get back to work!

System & hardware:

• Ubuntu 16.04 (fully apt-get up to date as of Feb.2, 2018)
• AMD Radeon Pro WX 7100
• Matlab 2016b
• ...followed additional package install advice on Psychtoolbox-3 github wiki cookbook (<https://github.com/Psychtoolbox-3/Psychtoolbox-3/wiki/Cookbook%253A-Setting-up-Ubuntu-with-Modern-AMD-Cards PTB cookbook>)

[Andrew Cox]

I should also note that I had Matlab R2016b running just fine with the AMDGPU-PRO drivers up until Jan 15, 2018. Some system file/driver must have updated around then and the Matlab OpenGL hardware acceleration stopped working.

[Thad C]

Good to know, Andrew. ...this is looking more and more like something got screwed up in the opensource driver stack early this year.

I did a few iterations of clean installs of Ubuntu 16.04 and 17.10, and all paths end up in the same failure state after running 'sudo apt update && sudo apt upgrade'. ...I have only new/clean installs to work with, and starting from a fresh Ubuntu 16.04 there are currently 200+ packages with available updates, thus potential culprits for screwing up opengl links (more experienced linux users surely know ways of narrowing that down...?).

As time passes and more [unfortunate] people run 'apt upgrades' that trigger this error , there seem to be more people slipping into the same non-functional state, so hopefully this will get sorted out soon.

I posted similar/cross-referenced information about this error in this Psychtoolbox forum message : https://groups.yahoo.com/neo/groups/psychtoolbox/conversations/messages/22674 So keep an eye out there, and we'll try to cross pollinate any viable solutions & workarounds as the come up.

[Moritz Oberjatzas]

Hello,

I can confirm this problem with Matlab R2017b on a Gentoo Linux installation. It looks like the problem is related to an update of the media-libs/mesa package (on Gentoo). They changed the naming of the renderer and the java opengl implementation in Matlab is not longer able to correctly identify it. Look here: https://jogamp.org/bugzilla/show_bug.cgi?id=1357#c5

A workaround is to downgrade the mesa package (for me it was from 17.2.8 to 17.1.10). After that, hardware acceleration works as expected. Anyways, I also would be interested in a solution (the java libraries shipped with Matlab have to be updated).

Best regards :)

PS: For Ubuntu, there is maybe a solution available, see here https://bugs.launchpad.net/ubuntu/+source/scilab/+bug/1742894

[Andrew Cox]

Moritz, you've nailed it! See the script(s) below for a fix you might be able to leverage on Gentoo.

Answer 1

[Andrew Cox]

The solution from Thad (below) works, but includes some unnecessary complexity if you're not a PsychToolbox User, so I'm summarizing the minimal set of steps below. Step #1 (below) need only be completed once, while steps 2, 3, 4 must be completed for each version of Matlab installed on your machine.

1. Install the libjogl2 library (Updated: no longer requires bleeding-edge version):

 # Add libjogl2-java

 sudo apt update -y
 sudo apt install -y libjogl2-java

2. Rename C++ standard library files (repeated from question, above). This ensures that the graphics drivers are loaded with the same standard library as they need rather than the ones Matlab comes bundled with.

 cd $matlabroot/sys/os/glnxa64
 mv libstdc++.so.6 libstdc++.so.6.bak
 mv libstdc++.so.6.0.20 libstdc++.so.6.0.20.bak

3. Change the classpath.txt and librarypath.txt files in $MATLABROOT/toolbox/local. Using my original paths, this path expands to /opt/local/MATLAB/R2017b/toolbox/local

• In classpath.txt, find and comment out the following two lines:

 $matlabroot/java/jarext/gluegen-rt.jar
 $matlabroot/java/jarext/jogl-all.jar

And replace them with the following

 /usr/share/java/jogl2.jar
 /usr/share/java/gluegen2-rt.jar

• In librarypath.txt, add a new line at the end of the file with

 /usr/lib/jni

4. According to the original script provided above, Matlab should now run without any errors. However, to be sure that the default included libraries do not interfere, rename the following libraries in $matlabroot/bin/glnxa64:

 cd $matlabroot/bin/glnxa64
 sudo mv libjogl_desktop.so libjogl_desktop.so.bak
 sudo mv libgluegen-rt.so libgluegen-rt.so.bak
 sudo mv libnativewindow_awt.so libnativewindow_awt.so.bak
 sudo mv libnativewindow_x11.so libnativewindow_x11.so.bak

Finally, in $matlabroot/toolbox/local/classpath rename the 3p_jogl file:

 cd $matlabroot/toolbox/local/classpath
 sudo mv 3p_jogl.jcp 3p_jogl.jcp.bak

And that's it! Problem solved! Hopefully those Xenial-Proposed packages will roll out to the stable branch in the not-too-distant future.

[jg614]

Making these changes on Fedora 27 results in an error:

    Exception in thread "Startup Class Loader" java.lang.NoClassDefFoundError: com/jogamp/opengl/GLException
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Unknown Source)
  at com.mathworks.mde.desk.StartupClassLoader.loadClass(StartupClassLoader.java:262)
  at com.mathworks.mde.desk.StartupClassLoader.access$900(StartupClassLoader.java:25)
  at com.mathworks.mde.desk.StartupClassLoader$2.run(StartupClassLoader.java:248)
  at java.lang.Thread.run(Unknown Source)
Caused by: java.lang.ClassNotFoundException: com.jogamp.opengl.GLException
  at java.net.URLClassLoader$1.run(Unknown Source)
  at java.net.URLClassLoader$1.run(Unknown Source)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.net.URLClassLoader.findClass(Unknown Source)
  at java.lang.ClassLoader.loadClass(Unknown Source)
  at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
  at java.lang.ClassLoader.loadClass(Unknown Source)
  ... 6 more

Additionally, for the benefit of anyone else reading this, the required package for Fedora is jogl2 from the rawhide repository. The stable version is not recent enough currently. You will need to download the source package and use rpmbuild --rebuild to build the package for a stable version of Fedora. It will probably give you an error the first time you try to rebuild it, just install the packages listed using dnf and it should compile fine.

About the exception message, can anyone figure out what's wrong? Plotting fails with another error

    Caught unexpected fl::except::IInternalException

Edit: I double checked and realized I actually didn't have the .jar files in my /usr/share directory. After copying the .jar files from their correct directories, I get

    Warning: librarypath.txt in the startup directory no longer supported. See The Static Path.
Exception in thread "Startup Class Loader" java.lang.UnsupportedClassVersionError: com/jogamp/opengl/GLException : Unsupported major.minor version 52.0
  at java.lang.ClassLoader.defineClass1(Native Method)
  at java.lang.ClassLoader.defineClass(Unknown Source)
  at java.security.SecureClassLoader.defineClass(Unknown Source)
  at java.net.URLClassLoader.defineClass(Unknown Source)
  at java.net.URLClassLoader.access$100(Unknown Source)
  at java.net.URLClassLoader$1.run(Unknown Source)
  at java.net.URLClassLoader$1.run(Unknown Source)
  at java.security.AccessController.doPrivileged(Native Method)
  at java.net.URLClassLoader.findClass(Unknown Source)
  at java.lang.ClassLoader.loadClass(Unknown Source)
  at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
  at java.lang.ClassLoader.loadClass(Unknown Source)
  at java.lang.Class.forName0(Native Method)
  at java.lang.Class.forName(Unknown Source)
  at com.mathworks.mde.desk.StartupClassLoader.loadClass(StartupClassLoader.java:262)
  at com.mathworks.mde.desk.StartupClassLoader.access$900(StartupClassLoader.java:25)
  at com.mathworks.mde.desk.StartupClassLoader$2.run(StartupClassLoader.java:248)
  at java.lang.Thread.run(Unknown Source)

I also get this error if I change the paths in classpath.txt to the original paths of the .jar files.

[Royi Avital]

It seems the packages rolled (See Thad's script in GitHub).

Answer 2

[Kaiyuh]

It is a problem caused by the incompatibility of the graphics card driver, I am not gonna explain what the problem is. The simplest and the best solution for me was:

 1. Open Matlab
 2. Enter "opengl('save','software')"
 3. Restart Matlab

It's done

[Moritz Oberjatzas]

Switching to software rendering did not solve all problems in this case (e.g. plots were not working). Please be aware that the described problem is both

1. Linux specific: An update of the mesa library changed the naming behaviour of the renderer
2. AMD specific: Only specific AMD graphic cards are affected

It is caused by the really bad way of jogl, the Java OpenGL library, how it tries to find the 3D renderer. The steps above to exchange the MATLAB jogl-library with a fixed version are described above and necessary in this specific case.

And by the way, I did not spend many €€€s for a graphics card just to not use it whenever possible :D

[Andrew Cox]

Agreed - Switching to software rendering can side-step the problem for general Matlab use, but many of the plotting capabilities are reduced to uselessness with the lower-quality software OpenGL.

[Tyler Ofstad]

This worked for me -- thank you!

[Walter Roberson]

Sultan Mehmet KALKANOGLU comments to Kaiyuh:

thank you! it is working.

[Levente Környey]

This is the solution, thank you!

I'm not sure about the solution of Andrew.

[Bambi]

Great, thanks. I had problem with that after installing gtsam and now it works.

[Bård Austarå]

This worked for me, many thanks.

Answer 3

[Thad C]

Agreed, changing to OpenGL software rendering is not at all a 'solution'.

Couple updates on the current state of the fix for this error:

• Updates to the functional version of the libjogl2-java package have been accepted into the standard xenial-updates repo (...non-jargony: no longer necessary to add/remove non-standard update source)Updated script here :https://github.com/czuba/sysconfig/raw/master/ubuntuFixJogl_ML2018a.sh
• Unfortunately these jogl errors persist in Matlab 2018a. Hard to imagine releasing a new version knowing it creates a wall of red error text at startup on the most widely used Linux distro out there...
• Notably, the "matlab-support" package necessary to fix other persistent matlab errors on Linux is not currently compatible with Matlab 2018a (as of Mar 28, 2018)

[Royi Avital]

Hi, For some reason your script doesn't recognize Linux Mint 18.3 as Debian Derivative. Though it can be treated as Ubuntu 16.04. Any idea how to fix this?

[Andrew Cox]

Royi Avital, see my accepted answer for the sequence of commands without a script. If you're confident you can proceed as on a Debian derivative, just execute the commands.

[Royi Avital]

@Andrew, The script of Thad says the official repositories are now updated to have the proper versions.

Any chance you look into it and update the answer (Or add one)?

[Royi Avital]

@Thad,

Your script (Which now doesn't add non default repositories) works perfectly on Linux Mint 18.3 with MATLAB R2018b.

On Linux Mint 18.3 the updated libraries are installed from the official repositories.

All I needed to do is remove the lines which checks for Ubuntu.

Thank You.

Answer 4

[Thad C]

There's a workaround solution developing on the Psychtoolobx forum in topic 22674: OpenGL problem in Linux

It's a bug in jogl related to detecting the Mesa drivers by string matching for "Gallium" in the glRenderer string, while the Mesa ppl apparently recently implemented a change in how the open-source driver/version is reported. (...or a rough synopsis of this bug report )

Seems like Matlab R2017b might be doing something similarly rudimentary, because my install still seems to be falling back to OpenGL 3.0 (compatibility profile) instead of enabling the full 4.x core version available from my gfx card. ...tbd.

-Thad.

Save the following as a shell script, then execute from terminal in Ubuntu 16.04

(credit to Andreas Widmann's post on the PTB forum for this workaround...I'm just the messenger)

#!/bin/bash

# ubuntuFixJogl2018.sh
# For Ubuntu 16.04 LTS
# Install Psychtoolbox from NeuroDebian, fix jogl install & matlab links
#
# Script based on proposed solution from Andreas Widmann
# for issue reported in:
# https://groups.yahoo.com/neo/groups/PSYCHTOOLBOX/conversations/topics/22674
#
# blame t.b.czuba 2018-02-09

# verify that the computer is running a Debian derivative
if ! command -v dpkg &> /dev/null; then
    echo "this script is meant to be run on an Ubuntu system"
    exit 1
fi

cd $HOME

# global variables
MATLABROOT="/usr/local/MATLAB/R2017b"  # ...update with your Matlab version/location as needed
TOOLROOT="$HOME/MLtoolbox"
echo "you are logged in as user $USER"
echo "matlab toolboxes will be installed in $TOOLROOT"

# configuration
################################################################################
    # Add repositories for Psychtoolbox-3 installation (via NeuroDebian)
    #   - copy-pasta from 'all software' repository for Ubuntu 16.04
    #   - for different OS options see: http://neuro.debian.net/install_pkg.html?p=matlab-psychtoolbox-3-nonfree
    wget -O- http://neuro.debian.net/lists/xenial.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
    sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
    sudo apt update

      # Install psychtoolbox
      sudo apt install -y matlab-psychtoolbox-3-nonfree

      # Add directories for Matlab toolboxes
      sudo mkdir -v -m 777 "$TOOLROOT"
      sudo chown -v "$USER":"$USER" "$TOOLROOT"

      # symlink default PTB install location to ~/MLtoolbox
      sudo ln -v -s /usr/share/psychtoolbox-3 $TOOLROOT/Psychtoolbox # def PTB location hardcoded by neurodebian

# Fix jogl errors in Matlab (as of Feb 7, 2018)
###################
# (1)
    # ADD XENIAL-PROPOSED repository (necessary as of Feb. 2018)
    sudo sh -c "echo 'deb http://archive.ubuntu.com/ubuntu/ \
    xenial-proposed restricted main multiverse universe' \
    > /etc/apt/sources.list.d/xenial-proposed.list"
    sudo apt update -y
  
  # ONLY INSTALL THE FOLLOWING from xenial-proposed!
  #   (...you don't want to upgrade ALL your packages with bleeding-edge versions)
  sudo apt install -y libjogl2-java/xenial-proposed
  # sudo apt install -y libjogl2-jni/xenial-proposed #...this is included with libjogl2-java in xenial-proposed
  
    # REMOVE XENIAL-PROPOSED repository
    sudo rm /etc/apt/sources.list.d/xenial-proposed.list
    sudo apt update -y
    
###################
# (2)
# Change the classpath.txt and librarypath.txt files in $MATLABROOT/toolbox/local.
#
# In classpath.txt find and comment or delete the following two lines (~line 450):
# $MATLABROOT/java/jarext/gluegen-rt.jar
# $MATLABROOT/java/jarext/jogl-all.jar
# and add instead:
# /usr/share/java/jogl2.jar
# /usr/share/java/gluegen2-rt.jar
#
# In librarypath.txt add at the end of the file (incl. a newline):
# /usr/lib/jni

###################
# (3)
# Now it should already work. To be sure that the MATLAB included libraries
# do not interfere I additionally renamed the following libraries in matlabroot/bin/glnxa64:
# libjogl_desktop.so
# libgluegen-rt.so
# libnativewindow_awt.so
# libnativewindow_X11.so
# which are now provided by the packages installed in (1).
cd $MATLABROOT/bin/glnxa64
sudo mv -v ./libjogl_desktop.so ./libjogl_desktop.so.bak
sudo mv -v ./libgluegen-rt.so ./libgluegen-rt.so.bak
sudo mv -v ./libnativewindow_awt.so ./libnativewindow_awt.so.bak
sudo mv -v ./libnativewindow_x11.so ./libnativewindow_x11.so.bak

#
# In matlabroot/toolbox/local/classpath I additionally renamed
# 3p_jogl.jcp
# to be shure it is not added back to classpath in case it is regenerated.
cd $MATLABROOT/toolbox/local/classpath
sudo mv -v ./3p_jogl.jcp ./3p_jogl.jcp.bak

printf "

###################
#   PTB install & jogl error fix installed
###################
#
# Must manually apply the following edits w/in your Matlab installation
# To determine path to your \$MATLABROOT, fire up Matlab, then enter
#       matlabroot
# in the command window.
#
###################
# Change the classpath.txt and librarypath.txt files in \$MATLABROOT/toolbox/local.
#
# In classpath.txt find and comment or delete the following two lines (~line 450):
#   \$MATLABROOT/java/jarext/gluegen-rt.jar
#   \$MATLABROOT/java/jarext/jogl-all.jar
# and add instead:
#   /usr/share/java/jogl2.jar
#   /usr/share/java/gluegen2-rt.jar
#
# In librarypath.txt add at the end of the file (incl. a newline):
#   /usr/lib/jni
###################

"

[Andrew Cox]

Great work! This completely solved the problem! I've removed the PsychToolbox-specific steps in the accepted answer to generalize the procedure.

[Sushen Joshi]

Hello,

When I tried to do the first step above, after running first 'sudo apt update -y', I got the error in terminal as

E: The repository 'http://archive.ubuntu.com/ubuntu/xenial-proposed restricted Release' does not have a Release file.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.

Thus, I used the option 'deb [trusted=yes]' instead in the sources.list.d file. After that when I again ran (1st) 'sudo apt update -y', I got the following error and I couldn't go any further.

Any idea how to resolve this? As I am yet to do all the steps to solve the main issue.