Visual Cognitive Neuroscience

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====== VPixx setup (second try) ======
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====== This is the second try ======

2024-01-26

I "broke" the display two days ago when trying to fix a package upgrade issue that was stopping the graphics card driver from working, I think.  The main error seemed to be that there was a newer version of some package installed, but an older version was needed, so I finally just tried removing everything.  Then the display stopped working.  So I decided to re-install the OS from scratch.  

I had just finally gotten the 3DPixx glasses to work reliably, too!  The trick had been to run PsychLinuxConfiguration in Octave, which I had apparently neglected to do last October during my first try at setting everything up.  

Will need to re-install:

  * MATLAB
  * Octave
  * PTB
  * **NOT** all my old files; they are still there, because ''/home'' was/is on a different partition!

====== Xubuntu installation ======

From my usb drive with 22.04.01 LTS.

====== CRT setup with custom xorg.conf file ======

2024-01-26

Copied (pulled) git repo "CRT" to grogu.  

Did:

<code bash>
sudo cp -p xorg.conf.new.1024x768_120 /etc/X11/xorg.conf.d/xorg.conf
</code>
 
... then rebooted.  It worked!  Display was in 1024x768 mode by default, with 119.8 Hz option available. 

====== Graphics card driver after initial Xubuntu installation======

Output (partial) of ''lspci -v'':

<code bash>
01:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Polaris 20 XL [Radeon RX 580 2048SP] (rev ef) (prog-if 00 [VGA controller])
	Subsystem: Advanced Micro Devices, Inc. [AMD/ATI] Polaris 20 XL [Radeon RX 580 2048SP]
	Flags: bus master, fast devsel, latency 0, IRQ 139
	Memory at a0000000 (64-bit, prefetchable) [size=256M]
	Memory at b0000000 (64-bit, prefetchable) [size=2M]
	I/O ports at 3000 [size=256]
	Memory at b2200000 (32-bit, non-prefetchable) [size=256K]
	Expansion ROM at 000c0000 [disabled] [size=128K]
	Capabilities: <access denied>
	Kernel driver in use: amdgpu
	Kernel modules: amdgpu
</code>


====== Octave and PTB installation ======

2024-01-26

Octave via apt.

PTB via NeuroDebian:

[[http://neuro.debian.net/install_pkg.html?p=octave-psychtoolbox-3]]


====== AMD GPU drivers installation ======

2024-01-26

I.e. from their website:

[[https://www.amd.com/en/support/previous-drivers/graphics]]

Unlike last attempt, I paid attention to the exact OS version number, and downloaded the one that matches the version given by ''uname -a'': 22.04.1

Did: 

<code bash>
dpkg -i amdgpu-install_5.4.50401-1_all.deb
</code>

No errors when installing, unlike last time.  

However, VBLSyncTest and all other PTB demos I have tried have **all failed**.

The end of the error message, which is mostly repeats of the first line here:

<code matlab>
PTB-ERROR: PsychOSKDGetBeamposition: Invalid headId -1 provided! Must be between 0 and 5. Aborted.
PTB-WARNING: PsychGetCurrentGPUSurfaceAddresses(): Invalid headId -1 (greater than max 5) provided for DCE-4+ display engine!
PTB-WARNING: Couldn't even collect one single valid flip interval sample! Sanity range checks failed!
PTB-WARNING: Could be a system bug, or a temporary timing problem. Retrying the procedure might help if
PTB-WARNING: the latter is the culprit.
PTB-WARNING: Couldn't collect valid flip interval samples! Fatal VBL sync failure!
PTB-WARNING: Either synchronization of doublebuffer swapping to the vertical retrace signal of your display is broken,
PTB-WARNING: or the mechanism for detection of swap completion is broken. In any case, this is an operating system or gfx-driver bug!
PTB-WARNING: PsychGetCurrentGPUSurfaceAddresses(): Invalid headId -1 (greater than max 5) provided for DCE-4+ display engine!


PTB-INFO: OpenGL-Renderer is Intel :: Mesa Intel(R) UHD Graphics 630 (CFL GT2) :: 4.6 (Compatibility Profile) Mesa 23.0.4-0ubuntu1~22.04.1
PTB-INFO: VBL startline = 768 , VBL Endline = -1
PTB-INFO: Beamposition queries unsupported or defective on this system. Using basic timestamping as fallback.
PTB-INFO: Timestamps returned by Screen('Flip') will be therefore less robust and accurate.
PTB-INFO: Measured monitor refresh interval from VBLsync = 0.000000 ms [inf Hz]. (0 valid samples taken, stddev=1000000000.000000 ms.)
PTB-INFO: Reported monitor refresh interval from operating system = 16.689197 ms [59.918999 Hz].
PTB-INFO: Small deviations between reported values are normal and no reason to worry.

WARNING: Couldn't compute a reliable estimate of monitor refresh interval! Trouble with VBL syncing?!?

WARNING: Mismatch between measured monitor refresh interval and interval reported by operating system.
This indicates massive problems with VBL sync.


----- ! PTB - ERROR: SYNCHRONIZATION FAILURE ! -----

One or more internal checks (see Warnings above) indicate that synchronization
of Psychtoolbox to the vertical retrace (VBL) is not working on your setup.
</code>


Notice that the refresh interval is given as roughly 60 Hz.  It is always given as this value, no matter what I set the monitor to do, and verified via ''glxgears''.

====== Installed MATLAB and image processing toolbox ======

Installed in ''/usr/local/MATLAB/R2023a/''

====== Installed SPM8 ======

2024-01-26

On previous try had installed SPM12, but because the HolesFMRI study was done in SPM8, I wanted to try this for consistency.

Installed in ''/usr/share/MATLAB/spm8''

===== Installed bspmview =====

See:

[[https://www.bobspunt.com/software/bspmview/]]

Installed in ''/usr/share/MATLAB/spm8/toolbox''


====== Installed VPixx software ======

From

[[https://vpixx-support.atlassian.net/wiki/spaces/support/pages/41123939/Software+Download]]

Did 

<code bash>
dpkg -i vpixx-software-tools.deb 
</code>


2024-01-29

PTB VBLSyncTest still not working -- maybe I should try installing ''Screen.mex'' because right now I think PTB is calling a file named ''Screen.m''.

====== Looking for Datapixx.mex file ======

<code bash>
anthony@grogu:~$ locate Datapixx.mex
/usr/local/share/VPixx Software Tools/Software Tools/Matlab/mexfiles/Windows/matlab/Datapixx.mexw64
/usr/local/share/VPixx Software Tools/Software Tools/Matlab/mexfiles/linux/matlab/Datapixx.mexa64
/usr/local/share/VPixx Software Tools/Software Tools/Matlab/mexfiles/macOS/matlab/Datapixx.mexmaci64
</code>

<code matlab>
octave:3> Datapixx('Open?')

In place of the expected Octave .mex binary plugin file this placeholder file was executed:

  Datapixx.m

This MEX file seems to be missing or inaccessible on your Octave path or it is dysfunctional:

  Datapixx.mex

The following directory should be the *first one* on your Octave path:
 /usr/share/psychtoolbox-3/PsychBasic/Octave5LinuxFiles64/ 


NOTE: You may want to acquire paid support for future issues like this.
Please type 'PsychPaidSupportAndServices' to learn more.


error: Missing, inaccessible or dysfunctional Psychtoolbox Mex file for this system, or Octave path wrong. Read the help text above carefully!!\n
error: called from
    AssertMex at line 113 column 5
    Datapixx at line 24 column 1
</code>

Did this, like I had done during First Try.  I.e. made link named "Datapixx.mex" to Datapixx_octave5.mex file.

<code bash>
anthony@grogu:Downloads$ sudo ln -sf /usr/local/share/VPixx\ Software\ Tools/Software\ Tools/Matlab/mexfiles/linux/octave/Datapixx_octave5.mex /usr/share/psychtoolbox-3/PsychHardware/DatapixxToolbox/DatapixxBasic/Datapixx.mex
</code>

This worked, in the sense that doing the following worked instead of giving the error above:

<code matlab>
octave:3> Datapixx('Open')
ans = 1
</code>

====== Making link to Screen.mex file ======

2024-01-30

Now to try a similar thing with Screen.mex?

Well, I was wrong (above) when I thought that PTB was calling Screen.m instead of Screen.mex:

<code matlab>
octave:5> which Screen
'Screen' is a function from the file /usr/share/psychtoolbox-3/PsychBasic/Screen.mex
</code>

So, I don't think there is anything to do for this goal.

====== Installing OEM Kernel ======

2024-01-30

I'm following my documentation from the First Try.

First, check which version of the Linux kernel is currently installed:

<code bash>
anthony@grogu:~$ uname -a
Linux grogu 6.5.0-15-generic #15~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Jan 12 18:54:30 UTC 2 x86_64 x86_64 x86_64 GNU/Linux
</code>

====== Tried installing AMD Pro driver several different ways, gave up ======

2024-02-20

I eventually broke the x server or whatever so that there were no graphics, and decided to do a clean install of Xubuntu instead of trying to fix it.  I never got PTB to work even a little bit, although I did get progressively "better" error messages.  At the end, the error message was only complaining that I had the wrong versions of mesa-related packages.