Problems installing PTB on Linux

Bugs & Features
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The NeuroDebian site is not working so I cannot install PsychToolbox. The line “After selecting a release the setup code will be shown here.” is not being replaced with the needed commands after selecting the OS release. There is a post about this on the NeuroDebian listserve dated Aug 26th but there has been no response. I guess the maintainer is on vacation or something.

So now I’m trying a manual download of the .zip file and then ran the command SetupPsychtoolbox in the Matlab command window per the PTB instructions. I was able to download the file but it asked for a license even though I’m running it on Ubuntu and not Mac or Windows. Has the licensing requirements changed?

I went ahead and accepted the 14 day trial as I am scheduled to start running experiments Monday. The instructions indicated I needed to use the Terminal command sudo apt build-dep psychtoolbox-3 but I got the error message that “You must put some ‘deb-src’ URIs in your sources.list”.

Any suggestions?

Joe

Joe

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The solution posted at apt - Error :: You must put some 'source' URIs in your sources.list - Ask Ubuntu solved the deb-src problem. On Ubuntu, I went to the software updates GUI and clicked on “source code” and closed the GUI. After that the udo apt build-dep psychtoolbox-3 command worked.

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Ran into new error message of Cannot initiate the connection to in.archive.ubuntu.com:80 when performing sudo apt build-dep psychtoolbox-3. The solution was provided at "Cannot initiate the connection to in.archive.ubuntu.com:80" when trying to run "sudo apt-get update" behind proxy - Ask Ubuntu , which was to change the Software Update setting from “server for the US” to “main server”.

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New problem is that Matlab command window now comes up as a blank white square after running the PsychLinuxConfiguration script. Rebooted computer but still blank. Tried several times, no good. Google AI suggested using the Terminal with “matlab -cefdisablegpu”. It worked! I googled and couldn’t even find where it got this idea! Anyway, even more strangely, it fixed the problem. I can start Matlab even from the symbolic link without needing this option any more. No idea what is going on. Yet more funky behavior by Matlab2025a’s new graphics engine I am guessing.

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I’m also getting error messages from apt about neurodebian’s public key being invalid, so neurodebian seems to be completely off-line, at least for now.

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For context, I’m trying to install PTB 3.0.22.1 on Ubuntu 24.04.3 dual boot with Windows 11 with Matlab R2025a Release 1 on a Dell Optiplex 7090 with 16GB RAM and an Nvidia GeForce GTX 1660 SUPER video card (tried a Radeon W5700 video card last year but it didn’t work. hoping it might work this time, once I’ve got everything else working).

Running a PTB test script, received error message about a “Mesa OpenGL software renderer is active” that terminated it. Am changing from the proprietary nvidia proprietary driver to the nouveau open source driver by using the Terminal command apt-get purge nvidia* and rebooting. Terminal commandsudo lshw -c video shows success.

The Matlab command window is blank again and matlab -cefdisablegpu did not help. Following another google AI suggesion, resetting matlab preferences by changing ~/.matlab/R2025a to R2025a_old so that it would create new directory fixes the Matlab problem.

New PTB error with the test script:

PTB-ERROR: You are trying to run a Screen() implementation meant only for a native XOrg X-Server
PTB-ERROR: under a XWayland fake X-Server, on top of a Wayland desktop GUI session. This is not
PTB-ERROR: supported, as XWayland has various bugs which would make Psychtoolbox hang/malfunction!
PTB-ERROR:
PTB-ERROR: Please resolve this issue now, by logging out of your desktop session and then logging in
PTB-ERROR: again while choosing a classic X11/XOrg GUI, which uses a suitable native XOrg X-Server.
PTB-ERROR: On Ubuntu Linux, there is usually a drop-down session chooser on your login screen (e.g.,
PTB-ERROR: reachable by clicking onto a little gear icon in the bottom-right corner of the screen),
PTB-ERROR: which offers options with (X11) or (Xorg) in its name, e.g., “Plasma (X11)” or
PTB-ERROR: “Ubuntu on Xorg” or “GNOME on Xorg”. These would be the right choices.
PTB-ERROR: If you really know what you are doing and absolutely want to force running under XWayland
PTB-ERROR: you could execute “clear all; setenv(‘WAYLAND_DISPLAY’); Screen(‘Preference’,‘ConserveVRAM’, 2^19);”
PTB-ERROR: and then retry. This may malfunction or hang in various ugly ways, you have been warned!

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Followed these instructions by logging back in with x11 option. Despite still having nouveau driver active according to sudo lshw -c video, got the message again:

PTB-WARNING: Seems that a Mesa OpenGL software renderer is active! This will likely cause miserable
PTB-WARNING: performance, lack of functionality and severe timing and synchronization problems.
PTB-WARNING: Most likely you are running Psychtoolbox on a Matlab version 8.4 (R2014b) or later and
PTB-WARNING: Matlab is causing this problem by overriding your operating systems OpenGL library with
PTB-WARNING: its own outdated software library. Please run the setup script PsychLinuxConfiguration()
PTB-WARNING: now from your Matlab command window and then quit and restart Matlab to fix this problem.

Given that nouveau is in fact an openGL mesa driver, I guess the question is why it seemed to work at one point.

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To avoid risk of forgetting to use x11 option when logging in, Changed the default back to x11 by editing the etc/gdm3/custom.conf file to set the wayland flag to false.

https://linuxconfig.org/how-to-enable-disable-wayland-on-ubuntu-20-04-desktop

Matlab window went blank again. Had to reset matlab preferences folder again.

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Have been encouraged to try Octave to deal with at least some issues and also because PTB not charging license with Octave.

https://wiki.octave.org/Octave_for_Debian_systems

sudo apt-get install octave sudo apt-get install octave-doc (octave-info and octave-htmldoc and octave-dbg resulted in error messages)

sudo apt-get install octave-control octave-image octave-io octave-optim octave-signal octave-statistics

This resulted in an old version: 8.4.0

AppCenter version is likewise several years out of date.

https://flathub.org/setup/Ubuntu

sudo apt install flatpak

flatpak remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo

sudo apt install gnome-software-plugin-flatpak

reboot

Desktop icon at: /usr/share/applications/org.octave.Octave.desktop

The 8.4.0 version is at /usr/bin/octave

simply clicking on the install button at https://flathub.org/en/apps/org.octave.Octave

or download the .flatpakref file did no good.

Clicking on the popup menu button next to the Install button brought up the commands:

flatpak install flathub org.octave.Octave

flatpak run org.octave.Octave --gui

worked! Running octave 10.2.0

edited /usr/share/applications/org.octave.Octave.desktop

that was installed by the 8.4.0 version so that it had the line:

Exec=flatpak run org.octave.Octave –gui

then rebooted. Now runs the 10.2.0 version.

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SetupPsychtoolbox

PTB warns 10.2.0 Octave is too new!
Will go back to 8.4.0

Changing .desktop file back.

Even after rebooting, still starting up 10.2.0 version.

Calling it a day.

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Uninstalling Octaves:
flatpak list –app
flatpak uninstall --delete-data org.octave.Octave
flatpak uninstall –unused

sudo apt-get remove octave
apt-get remove octave-doc

Installing Octave 7.1.0 via Ubuntu’s App Center.

SetupPsychtoolbox

ERROR: WaitSecs-MEX does not work, most likely other MEX files will not work either.
ERROR: One reason might be that your version 7.1.0 of Octave is incompatible.
ERROR: Another conceivable reason would be missing or incompatible required system libraries on your system.

ERROR: After fixing the problem, restart this installation/update routine.

Installation aborted. Fix the reported problem and retry.

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Using App Center to uninstall Octave 7.1.0

https://www.geeksforgeeks.org/linux-unix/how-to-install-gnu-octave-in-linux/

sudo apt-add-repository ppa:octave/stable

sudo apt-get update

sudo apt-get install octave octave Command line Octave 8.4.0 octave –gui Octave gui starts up with 8.4.0

SetupPsychtoolbox

worked!

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Was getting error messages about help files when starting up Octave.

Fixed Octave error messages by installing sqlite.

https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1924836

https://www.howtoinstall.me/ubuntu/18-04/libqt5sql5-sqlite/

sudo apt install libqt5sql5-sqlite