Using PTB on Linux

GNU/Linux is the recommended operating system of choice for demanding experimental setups and experimental paradigms.

Due to it being a free and open-source operating system, Linux provides us and you with a couple of advantages:

  • Thanks to its open source nature and constant community development and peer review of its code-base, it generally exhibits less bugs as well as higher performance and robustness in areas of functionality that matter especially for demanding experimental paradigms, e.g., precision and robustness of timing, resource usage and efficiency. The system is also much more flexible and tweakable, should performance tuning and customization be neccessary for special experimental setups.

  • The open access to its source code allows us to review the implementation of important low-level details. This allows us to understand how and why the system behaves a certain way and allows us to implement a better integration between Psychtoolbox and the operating system. Apple’s OS X and Microsoft’s Windows are mostly black boxes for us, leaving us with guess-work about many implementation details, which leads to suboptimal integration with Psychtoolbox.

  • The open development process allows us to participate in the design, implementation, improvement and bug-fixing of crucial operating system components ourselves. We can help to fix and improve the underlying infrastructure and plumbing instead of having to resort to ugly and suboptimal hacks in Psychtoolbox itself to work around the unfixable flaws of a black box.

If you want to use Psychtoolbox with Matlab instead of Octave, on Debian and Ubuntu you can install the matlab-support package after installing Matlab and before installing Psychtoolbox. This package will do the following useful things for us:

“Currently it provides /usr/bin/matlab through the alternatives system, offers to work around incompatibilities between the libraries bundled with MATLAB and system libraries, and provides a helper utility meant to be used by other packages to compile MEX extensions.”

The installation works the same as on Windows or OS X, so follow the instructions on the main download page. However, Psychtoolbox requires a few software libraries to be installed on your Linux system. The installer will tell you what kind of libraries you need to install, should some of them be missing. For the most simple way of installation, read on.

The most convenient way of installation if you have Debian or a Debian derivative, e.g., Ubuntu Linux, is the NeuroDebian repository of neuroscience software. It provides a large number of popular neuroscience related software packages, optimally configured for use on Debian and Ubuntu, with a convenient installation via the package management system of your Linux distribution.

If you install the package octave-psychtoolbox-3, your system will be mostly automatically configured and tuned for use with Psychtoolbox under GNU/Octave. You should still follow the steps “After basic installation” below though:

sudo apt-get install octave-psychtoolbox-3 

If you prefer to run Psychtoolbox with Matlab, first install Matlab, then install this meta-package

sudo apt-get install matlab-psychtoolbox-3 

The Psychtoolbox for Matlab won’t get permanently added to your Matlab path by default. You can execute the following command from a terminal to run a Matlab session with Psychtoolbox added to the path for the duration of that session:

ptb3-matlab

You could then execute Matlabs savepath command to add it permanently if you wanted, or simply call ptb3-matlab when you need to run a Psychtoolbox work session. Read the section “After basic installation” below for one time setup steps.

If you want to do things the hard way, you can can run the function DownloadAdditionsForNeuroDebian from within a Matlab running under Linux. It will install a few additional files needed to run Psychtoolbox with Matlab on Linux.

Debian-7/testing/unstable, Ubuntu 12.10 and later installation

Psychtoolbox-3 for octave is part of current Debian unstable / testing / experimental, as well as the official Debian-7.0 and Ubuntu 12.10 distributions. Everything said in the “Neuro Debian” section applies, except you don’t need to add the Neuro Debian ppa to your software sources. Simply use your favorite package manager to install the psychtoolbox-3 package and you’re done. E.g., in a terminal window on Ubuntu 12.10:

sudo apt-get install psychtoolbox-3

However, this is limited to Octave, Matlab packages aren’t provided. Also the packages shipping with Debian and Ubuntu themselves are usually quite outdated and don’t contain the latest features, bug fixes and improvements, so we recommend going for the NeuroDebian packages mentioned in the previous section.

Choice of Distribution

The Linux specific code in PTB is currently being developed and tested using Ubuntu Linux. We recommend this distribution mostly just because it is beginner friendly and constantly tested with Psychtoolbox. However, there is nothing wrong with other Linux distributions, so feel free to use them, but keep in mind we can only provide you with support for Ubuntu at the moment, and you may need to perform extra setup steps with which we can’t help you. See UsingPsychtoolboxOnUbuntu for more details and instructions on Ubuntu Linux.

Conflicts of libraries shipped with Matlab and system libraries

With some Matlab versions execution of Screen() may lead to MEX file errors.

Commonly these errors arise from outdated versions of libraries like Zlib (libz*) that come included with Matlab and which override the system libraries.

To work around these problems, it is often sufficient to delete or move all lib*.so* files in your Matlab/bin/glnx86 or Matlab/bin/glnxa64 folder that showed up in the MEX file loading errors.

On Debian and Ubuntu you can install the matlab-support package after installing Matlab and before installing Psychtoolbox. This package will automatically take care of moving conflicting libraries out of the way, and other potential compatibility issues.

After basic installation

Once Psychtoolbox works within Matlab or Octave, you should run the script PsychLinuxConfiguration once, with Matlab or Octave started in commandline mode, e.g., matlab -nojvm or octave --no-gui. The script will ask you to provide your administrator/user password and tweak some system settings for optimal performance with Psychtoolbox. Then you will be required to follow the instructions provided by the script, and to reboot your machine once for the setttings to take effect.

Another recommendation is to install a low-latency Linux kernel for optimized timing, e.g., on Ubuntu flavors and probably also Debian flavors:

sudo apt-get install linux-lowlatency

Optimization of the display server settings for good visual timing is achieved by following the Linux instructions in “» help SyncTrouble” and by running the helper scripts XOrgConfCreator and XOrgConfSelector to automatically create and install optimized xorg.conf configuration files for the X-Server. This is especially useful for hybrid graphics laptops and multi-display setups.