Using Psychophysics Toolbox on Ubuntu

THIS WEBPAGE IS OUTDATED! PLEASE IGNORE IT UNTIL IT HAS BEEN UPDATED!

The most recent beta release (since V3.0.9 revision 2191) contains support for 64bit Matlab / Octave, but one cannot mix running 64bit Matlab on a 32bit Ubuntu and visa versa. Please see below for some potential problems with correctly installing dependencies.

Choice of Kernel

See this page for more info:

https://help.ubuntu.com/community/UbuntuStudio/RealTimeKernel

Comment by Mario

The lowlatency kernel is simple to install, as you explained, and probably good enough for all but the most challenging applications. For example some tables benchmark results with respect to the minimal audio latency that can be reliably achieved: https://wiki.ubuntu.com/RealTime To put this into perspective, a typical os/x system won’t be able to achieve less than about 6-8 msecs, at least I haven’t seen anything better in my testing from Macbook Pro to 8 core mac-pro. The values they achieve (3-4 msecs) are close to the theoretical optimum. Even the default kernel is already at least as good as what the other operating systems have to offer. Compiling a hard realtime kernel yourself is not that simple for beginners, but if you’d really need it you can also download and install a realtime kernel from an older distribution, e.g., 10.04. It would be a tradeoff between gaining hard realtime caps and losing some functionality which was added in later kernels.

Choice of Desktop environment

The recommendation is to use Classic mode; comment from Mario:

Yep. “Ubuntu Classic (no effects)” may be even better. If you use the new Unity UI, that’s the most shiny and untested one – I don’t quite hate it as much as many other people, but so far I don’t see it adding much to the user experience. It’s the usual “let’s add a smartphone or tablet GUI to a desktop/laptop computer, because it looks fancy.”

Both “Ubuntu Classic” and “Unity” use a desktop compositor to create the shiny 3d’ish desktop. This is nice for ergonomy and eye-candy but it can reduce performance and really impair exact presentation timing and timestamping. Same problem as on Windows Vista/7 and OS/X with their desktop compositors.

The Linux guys are working on a solution to make the timing and timestamping as precise with a compositor as without it – I’m involved in that effort. It is a pretty difficult technical problem and progress is slow, but we’ll get there at some point. No similar efforts exist at all on OS/X or Windows afaik – At least none that aren’t known to be extremely broken to the point of being not only useless but harmful.

Psychtoolbox disables the desktop compositor when a fullscreen onscreen window is presented on OS/X, Windows and Linux to achieve correct stimulus onset timing and timestamping and to reduce the performance impact of a compositor.

However, if you are running a machine for real data collection you may want to manually shut down the compositor completely, because a) it is the most reliable way to know it really doesn’t interfere, and b) it frees up additional graphics and system resources, which are usually used even if the compositor is in standby mode.

On Linux 10.10 and earlier this was achieved via Menubar -> System settings -> Appearance -> Desktop effects -> “Off” or something like that.

On 11.04 I think you select the “Ubuntu classic (no effects)” environment.

This will run in a old unsexy, non 3d’ish, “flicker during Windows movements and redraws like WindowsXP” environment, however with drastically reduced GPU resource consumption and no interference at all.

I usually do complex timing tests with the compositor shut down, but normal testing with the compositor on and just switching to standby when fullscreen windows are used.

One catch: On Linux, PTB doesn’t actively switch the compositor to standby. Instead it uses the PsychGPUControl() command as part of the Psychtoolbox installer/updater to configure the compositor to switch itself to standby if it detects a fullscreen window on a display. If you do something like install PTB while Unity is running, then switch to the “Classic” environment, this configuration setting may not transfer. It doesn’t hurt to add the PsychGPUControl command to the top of your script for extra paranoia. Or manually disable it via the GUI.

I’ll probably add some call to PsychGPUControl() to Screen’s OpenWindow function in the future, so this is more fool-proof.

Choice of Graphics Driver

Use the proprietary driver for NVidia. For Intel and probably ATI, the open-source drivers should be sufficient, except for 30 bit support.

Mario again:

But nouveau in its current incarnation isn’t yet suitable for research grade stimulus presentation timing. It’s pretty good performance- and functionality-wise, but the display onset timing has bugs. I’m working with the nouveau-devs to get it properly implemented for a future nouveau release, but it probably won’t be part of the 2011 Linux distros, at least not as a standard install. PTB outputs warnings if you try to run on a too old nouveau- ie. on any nouveau at the moment.

The free software Intel (for half-way recent GPU’s) and ATI (for almost all GPU’s) drivers are in a very good shape in the recent distros. Both should have the most precise and robust timestamping you could find anywhere. Also the only timestamping that works in all display configurations with all display types and settings. Functionality and performance are catching up to the binary drivers in all areas that are relevant to us. I’d expect them to be perfectly usable for the majority of vision science experiments, and for some of them even more than the binary drivers.

Installing Issues

The newer PTB has several dependencies that need to be installed first before PTB will work correctly. Please read the information given by the PTB installer which gives the following instructions:

The Psychtoolbox on GNU/Linux needs the following 3rd party libraries in order to function correctly. If you get “Invalid MEX file errors”, or similar fatal error messages, check if these are installed on your system and if they are missing, install them via your system specific software management tools:

For `Screen()` and OpenGL support

The OpenGL utility toolkit GLUT: glut, glut-3 or freeglut are typical provider packages in most Linux distributions.
GStreamer multimedia framework: At least version 0.10.24 of the core runtime and the gstreamer-base plugins.

For optimal performance use the latest available versions.

A simple way to get GStreamer at least on Ubuntu Linux is to install the ”rhythmbox” or “totem” multimedia-players. You may need to install additional packages to play back all common audio- and video file formats. See help GStreamer.

libusb-1.0 USB low-level access library.
libdc1394 Firewire video capture library.
libraw1394 Firewire low-level access library.

For `PsychKinect()` (See `help InstallKinect`)

libusb-1.0 USB low-level access library.
libfreenect: Kinect driver library.

For `Eyelink()`

The Eyelink core libraries from the SR-Research download website.

If you receive an installation failure soon, then please read the output of help GStreamer first and follow the installation instructions for GStreamer on Linux. Psychtoolbox’s Screen() command will not work without GStreamer!

Also, at least one user had to physically move libdc1394.so.22 from the Matlab. For more information see

http://tech.groups.yahoo.com/group/psychtoolbox/message/12408

Install Instructions on 64-bit Linux

cum grano salis

General setup for PTB and Matlab on Ubuntu 11.04 64-bit:

install low-latency kernel (some info found here - https://help.ubuntu.com/community/UbuntuStudio/RealTimeKernel)
```
sudo add-apt-repository ppa:abogani/ppa
sudo apt-get update
sudo apt-get install linux-lowlatency
```
Install subversion:
```
sudo apt-get install subversion
```
Install Matlab 64-bit (2010b was used for these instructions)
Install PTB using these instructions

Need to fix a few things in matlab for PTB to work

cd $MATLABROOT/sys/os/glnxa64/
sudo mv libstdc++.so.6.0.10 old_libstdc++.so.6.0.10
sudo mv libstdc++.so.6 old_libstdc++.so.6
cd $MATLABROOT/bin/glnxa64/
sudo mv libdc1394.so.22 old_libdc1394.so.22
sudo mv libdc1394.so.22.1.0 old_libdc1394.so.22.1.0
sudo apt-get install libdc1394-22

Finally, solve a Matlab issue specific to Ubuntu 11.04:

sudo ln -s /lib64/x86_64-linux-gnu/libc-2.13.so /lib64/libc.so.6

Alternatively, you could use NeuroDebian install of octave-psychtoolbox-3 (http://neuro.debian.net), but you may still need some of the above steps

Refresh rate setup

This is an example based on setting this up on my rig2display machine.

Use gtf to generate a modeline:

gtf 1024 768 100

This is the output of that command on an example machine:

  # 1024x768 @ 100.00 Hz (GTF) hsync: 81.40 kHz; pclk: 113.31 MHz
  Modeline "1024x768_100.00"  113.31  1024 1096 1208 1392  768 769 772 814  -HSync +Vsync

cvt is another program that works basically the same way

Be sure the modeline is valid for the monitor. Look up the horizontal and vertical sync in the specs
Use xrandr -q to see the modes available and what your graphics system is called (mine is CRT1)

Copy that modeline to make 3 commands:

xrandr --newmode "1024x768_100.00"  113.31  1024 1096 1208 1392  768 769 772 814  -HSync +Vsync
xrandr --addmode CRT1 "1024x768_100.00"
xrandr --output CRT1 --mode "1024x768_100.00"

Paste these into the file /etc/gmd/Init/Defaults just above the /sbin/initctl command. So mine looks like:

xrandr --newmode "1024x768_100.00"  113.31  1024 1096 1208 1392  768 769 772 814  -HSync +Vsync
xrandr --addmode CRT1 "1024x768_100.00"
xrandr --output CRT1 --mode "1024x768_100.00"
/sbin/initctl -q emit login-session-start DISPLAY_MANAGER=gdm

Could also do this by modifying xorg.conf but that looks like a headache, and this works
lspci will tell you the name of the graphics card and other system info if you need it

Linux PTB3 - Multi-GPU HOWTO

This HOWTO assumes that you want to use separate GPU/Display for desktop work and visual stimulation which shall be driven at different resolutions and refresh rates. PTB is assumed to be already installed.

Connect each display to its corresponding graphics card (Desktop display → GPU 0 / primary GPU; Stimulation display → GPU 1 / secondary GPU)
Set up the X-Server either by manually editing xorg.conf or if you are using proprietary(ATI, NVidia) graphics drivers by using the respective GUIs (ATI Catalyst Control Center or NVidia X Server Settings):
1. Assign separate X-Screens to each GPU (Desktop Screen = X-Screen0; Stimulation Screen = X-Screen1)
2. Make sure Xinerama mode is disabled
3. Set the appropriate resolutions and refresh rates
4. Save changes to xorg.conf and quit the editor
5. Restart your X Server with one of the following commands depending on your desktop environment:
```
sudo restart lightdm # OR gdm OR kdm    
```
If everything worked, your designated desktop display should now display the Ubuntu desktop background, while the stimulus display is plain white and can’t be accessed with the mouse pointer. The stimulus screen will, however, contain the gnome panels at the top and bottom.

NOTE: When using Ubuntu 12.04 and the GNOME classic desktop environment, you might encounter the strange behavior described here. To solve the problem simply follow the instructions provided on launchpad and obtain a recent version of gnome-panel.
Now, open Matlab/Octave and run ScreenTest to check for problems in your setup. Most likely, it will tell you that on multi-GPU systems high precision timestamping / low level acess is restricted to one GPU/Screen and which it selected by default. Very likely, it’s GPU0 which shows your desktop.

To set up the secondary GPU for high-precision time-stamping, you need to manually tell PTB which GPU is responsible for which Screen and which of these it shall use for low-level access.

clear Screen
PsychTweak('UseGPUIndex', 1);                 % Use GPU 1 for low-level access
Screen('Preference','ScreenToHead', 1, 0, 0); % Maps X-Screen 1 to RandR-CRTC 0 and GPU-CRTC 0
% NowYourCode ... i.e. ScreenTest

Now, run ScreenTest again and check if the appropriate GPU is used. Keep in mind that your desktop display might now give you the big exclamation mark during the test, because low-level access has been explicitly disabled for it.