Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#24895 closed defect (wontfix)

pymol crashes session when used on secondary display

Reported by: orbeckst (Oliver Beckstein) Owned by: howarth@…
Priority: Normal Milestone:
Component: ports Version: 1.8.2
Keywords: Cc: jeremyhu (Jeremy Huddleston Sequoia)
Port: pymol

Description

I installed pymol with the default compiler flavour on Mac OS X 10.6.3. When I start it from the command line as pymol while having a second monitor attached then the main pymol window appears on the secondary display but graphics (the DISCLAIMER & Copyright notice) flickers wildly. When clicking or moving the window, the complete quartz session crashes without obvious error messages and I am presented with the graphical login screen.

Running pymol on the single laptop display works, i.e. I can control pymol via the main window and no crash occurs.

The MacBook Pro is in 'Energy saving mode', i.e. the slower nVidia 9400M is used instead of the fast 9600M GT.

port installed pymol
The following ports are currently installed:
  pymol @1.2r2_2 (active)

Pymol output (running on a single display):

 PyMOL(TM) Molecular Graphics System, Version 1.2r2.
 ...
 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: NVIDIA GeForce 9400M OpenGL Engine
  GL_VERSION: 2.1 NVIDIA-1.6.10
 Detected 2 CPU cores.  Enabled multithreaded rendering.
 OpenGL quad-buffer stereo 3D detected and enabled.

Attachments (1)

quickstereotest.zip (50.3 KB) - added by howarth@… 10 years ago.
hardware stereo test

Download all attachments as: .zip

Change History (16)

comment:1 Changed 10 years ago by orbeckst (Oliver Beckstein)

correction: Despite the flicker, pymol is usable on the secondary display (i.e. it does not crash when clicking window elements or GUI controls). However, moving the GL window to the primary display crashes the session. The session also crashes when the GL window is minimized and the djinni-effect warps the window across the display boundary.

comment:2 Changed 10 years ago by orbeckst (Oliver Beckstein)

The crash also occurs when I use the fast nVidia 9600M GT card.

comment:3 Changed 10 years ago by orbeckst (Oliver Beckstein)

Cc: orbeckst@… added

Cc Me!

comment:4 Changed 10 years ago by jmroot (Joshua Root)

Cc: orbeckst@… removed
Keywords: quartz X11 OpenGL nVidia secondary display removed
Owner: changed from macports-tickets@… to howarth@…

Please remember to cc the maintainer.

comment:5 in reply to:  description ; Changed 10 years ago by howarth@…

These issues should be taken upstream. Pymol will attempt to start hardware stereo rendering by default. Not all of the Apple drivers properly support this. I recently reopened a pre-existing radar concerning flashing of the Pymol view window on a GT120 card. In the past, this same issue was fixed for the Radeon HD2600 card which also was a driver bug with hardware stereo support. This issue can be avoided by invoking pymol with the -M option. Unfortunately the author of pymol passed away so we can expect little from upstream to fix this. We can only report this driver bugs to Apple and press them to provided proper hardware stereo support.

comment:6 in reply to:  5 Changed 10 years ago by howarth@…

With regard to the second display issues, I would verify that Xquartz 2.5.1-beta5 shows the same problem and also check on xquartz-dev to make sure it isn't a bug in the Xserver.

comment:7 Changed 10 years ago by howarth@…

I would also suggest testing the secondary display issue with 'pymol -M' to see if the crash is specific to having hardware stereo support available.

comment:8 Changed 10 years ago by jeremyhu (Jeremy Huddleston Sequoia)

Cc: jeremyhu@… added

Cc Me!

comment:9 Changed 10 years ago by jeremyhu (Jeremy Huddleston Sequoia)

This is certainly a bug in the graphics drivers and nothing that we can fix in XQuartz or MacPorts.

comment:10 in reply to:  7 Changed 10 years ago by orbeckst (Oliver Beckstein)

Replying to howarth@…:

I would also suggest testing the secondary display issue with 'pymol -M' to see if the crash is specific to having hardware stereo support available.

The bug as described above does not occur when using pymol -M – no flicker, no crashes when moving the pymol graphics window across displays.

Many thanks for the comments. I'll check if I can submit this bug elsewhere.

pymol -M

...
 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: NVIDIA GeForce 9600M GT OpenGL Engine
  GL_VERSION: 2.1 NVIDIA-1.6.10
 Detected 2 CPU cores.  Enabled multithreaded rendering.

Changed 10 years ago by howarth@…

Attachment: quickstereotest.zip added

hardware stereo test

comment:11 Changed 10 years ago by howarth@…

You can also try building the quickstereotest Xcode project and running on your machine to test the drivers. If the hardware stereo is working properly, it will produce a solid black background with wire-mesh tea kettle that appears to slightly wobble or flicker. Originally, the HD2600 drivers had artifacts in the black background. Currently, the GT120 drivers don't show artifacts in the black background but don't flicker the tea kettle either.

comment:12 in reply to:  11 ; Changed 10 years ago by orbeckst (Oliver Beckstein)

Replying to howarth@…:

You can also try building the quickstereotest Xcode project and running on your machine to test the drivers.

Many thanks. Compiled and ran successfully.

If the hardware stereo is working properly, it will produce a solid black background with wire-mesh tea kettle that appears to slightly wobble or flicker. [...] Currently, the GT120 drivers don't show artifacts in the black background but don't flicker the tea kettle either.

I get

  • white wire-mesh teapot in front of solid black background
  • no flicker
  • moving the OpenGL window to the other display crashes the quartz session (roughly when half of the window is across the boundary)

Thus it seems quite clear that PyMOL is not the culprit and someone could probably mark this ticket as invalid.

Any suggestions where to file a bug for the graphics driver?

comment:13 in reply to:  12 Changed 10 years ago by orbeckst (Oliver Beckstein)

For completeness (even though it has nothing to do with PyMOL anymore): Replying to orbeckst@…:

I get

  • white wire-mesh teapot in front of solid black background
  • no flicker
  • Even without a second display attached, minimizing the OpenGL window with the resulting djinni effect warping it into the (hidden) dock crashes the session.

comment:14 Changed 10 years ago by jmroot (Joshua Root)

Resolution: wontfix
Status: newclosed

comment:15 in reply to:  14 Changed 10 years ago by orbeckst (Oliver Beckstein)

Replying to jmr@…:

File a radar: http://bugreport.apple.com/

Cheers, just did this and linked it to this ticket.

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