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Description of problem: Flickering of pymol display window when model rotated or display options chosen. The flickering is sufficiently bad that it makes pymol essentially unusable. Version-Release number of selected component (if applicable): pymol-1.4.1-5.20110502svn3947.fc16.x86_64 How reproducible: Always Steps to Reproduce: 1. Launch pymol ('pymol') 2. Load model 3. Attempt to rotate it or click any buttons Actual results: Main window flickers black (looks like it's during any update of the window) and then restores to appropriate appearance. Trying to rotate the molecule causes flickering. Try to click on any button (that would cause redrawing of the window) causes flickering. The flickering is confined to the pymol display window itself (not the entire screen). Expected results: Updates of the window without flickering of the display. Additional info: Pymol reports: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: VMware, Inc. GL_RENDERER: Gallium 0.4 on llvmpipe GL_VERSION: 2.1 Mesa 7.11 Detected 8 CPU cores. Enabled multithreaded rendering. This may be a problem with pymol interacting with other components. I have another version of pymol (1.2.1) compiled from source that worked fine under Fedora 12, but has the same flickering issue when recompiled under Fedora 16. This is on a Toshiba Qosimo system running nouveau drivers that have nouveau.noaccel=1 on boot (as the accelerated mode doesn't seem to work-- scrambled screen after the "F" in a circle loads during boot). The nouveau.noaccel=1 option was also required on Fedora 15 (which I was about to install when I found out that Fedora 16 became available). The nouveau information from dmesg is: [ 3.765997] [drm] Initialized drm 1.1.0 20060810 [ 3.772816] nouveau 0000:01:00.0: power state changed by ACPI to D0 [ 3.772824] nouveau 0000:01:00.0: power state changed by ACPI to D0 [ 3.772837] nouveau 0000:01:00.0: PCI INT A -> GSI 16 (level, low) -> IRQ 16 [ 3.772845] nouveau 0000:01:00.0: setting latency timer to 64 [ 3.776204] [drm] nouveau 0000:01:00.0: Detected an NV50 generation card (0x0a3880a2) [ 3.785286] [drm] nouveau 0000:01:00.0: Attempting to load BIOS image from PRAMIN [ 4.019061] [drm] nouveau 0000:01:00.0: ... appears to be valid [ 4.019064] [drm] nouveau 0000:01:00.0: BIT BIOS found [ 4.019067] [drm] nouveau 0000:01:00.0: Bios version 70.15.24.00 [ 4.019069] [drm] nouveau 0000:01:00.0: TMDS table version 2.0 [ 4.019071] [drm] nouveau 0000:01:00.0: Found Display Configuration Block version 4.0 [ 4.019074] [drm] nouveau 0000:01:00.0: Raw DCB entry 0: 01000323 00010034 [ 4.019076] [drm] nouveau 0000:01:00.0: Raw DCB entry 1: 02014300 00000000 [ 4.019078] [drm] nouveau 0000:01:00.0: Raw DCB entry 2: 02021362 00020010 [ 4.019080] [drm] nouveau 0000:01:00.0: Raw DCB entry 3: 080333c6 0f220010 [ 4.019082] [drm] nouveau 0000:01:00.0: Raw DCB entry 4: 08033382 00020010 [ 4.019083] [drm] nouveau 0000:01:00.0: Raw DCB entry 5: 0000000e 00000000 [ 4.019086] [drm] nouveau 0000:01:00.0: DCB connector table: VHER 0x40 5 16 4 [ 4.019088] [drm] nouveau 0000:01:00.0: 0: 0x00000340: type 0x40 idx 0 tag 0xff [ 4.019090] [drm] nouveau 0000:01:00.0: 1: 0x00001061: type 0x61 idx 1 tag 0x07 [ 4.019093] [drm] nouveau 0000:01:00.0: 2: 0x00000147: type 0x47 idx 2 tag 0xff [ 4.019095] [drm] nouveau 0000:01:00.0: 3: 0x00202346: type 0x46 idx 3 tag 0x08 [ 4.019097] [drm] nouveau 0000:01:00.0: 4: 0x00000400: type 0x00 idx 4 tag 0xff [ 4.019099] [drm] nouveau 0000:01:00.0: 5: 0x00000210: type 0x10 idx 5 tag 0xff [ 4.019101] [drm] nouveau 0000:01:00.0: 6: 0x00000211: type 0x11 idx 6 tag 0xff [ 4.019103] [drm] nouveau 0000:01:00.0: 7: 0x00000213: type 0x13 idx 7 tag 0xff [ 4.019105] [drm] nouveau 0000:01:00.0: 8: 0x00020846: type 0x46 idx 8 tag 0x52 [ 4.019107] [drm] nouveau 0000:01:00.0: 9: 0x00000900: type 0x00 idx 9 tag 0xff [ 4.019113] [drm] nouveau 0000:01:00.0: Parsing VBIOS init table 0 at offset 0x7432 [ 4.059180] [drm] nouveau 0000:01:00.0: 0x7794: Condition still not met after 20ms, skipping following opcodes [ 4.079167] [drm] nouveau 0000:01:00.0: 0x7798: Condition still not met after 20ms, skipping following opcodes [ 4.079193] [drm] nouveau 0000:01:00.0: Parsing VBIOS init table 1 at offset 0x79A9 [ 4.085536] [drm] nouveau 0000:01:00.0: Parsing VBIOS init table 2 at offset 0x8DFC [ 4.085555] [drm] nouveau 0000:01:00.0: Parsing VBIOS init table 3 at offset 0x8E3A [ 4.128075] [drm] nouveau 0000:01:00.0: Parsing VBIOS init table 4 at offset 0x9040 [ 4.128080] [drm] nouveau 0000:01:00.0: Parsing VBIOS init table at offset 0x90A5 [ 4.148071] [drm] nouveau 0000:01:00.0: 0x90A5: Condition still not met after 20ms, skipping following opcodes [ 4.169786] [drm] nouveau 0000:01:00.0: 3 available performance level(s) [ 4.169790] [drm] nouveau 0000:01:00.0: 0: core 135MHz shader 270MHz memory 135MHz timing 2 voltage 800mV [ 4.169794] [drm] nouveau 0000:01:00.0: 1: core 405MHz shader 810MHz memory 324MHz timing 1 voltage 850mV [ 4.169797] [drm] nouveau 0000:01:00.0: 3: core 576MHz shader 1436MHz memory 1800MHz timing 0 voltage 1050mV [ 4.169829] [drm] nouveau 0000:01:00.0: c: core 405MHz shader 810MHz memory 324MHz voltage 850mV [ 4.169861] [drm] nouveau 0000:01:00.0: memory controller reports 1024MiB VRAM [ 4.169863] [drm] nouveau 0000:01:00.0: we calculated 256MiB VRAM [ 4.174680] [TTM] Zone kernel: Available graphics memory: 2019690 kiB. [ 4.174685] [TTM] Initializing pool allocator. [ 4.174718] [drm] nouveau 0000:01:00.0: Detected 1024MiB VRAM [ 4.177437] [drm] nouveau 0000:01:00.0: 512 MiB GART (aperture) [ 4.232190] [drm] nouveau 0000:01:00.0: ACPI backlight interface available, not registering our own [ 4.232199] [drm] Supports vblank timestamp caching Rev 1 (10.10.2010). [ 4.232204] [drm] No driver support for vblank timestamp query. [ 4.450961] [drm] nouveau 0000:01:00.0: allocated 1680x945 fb: 0x1b0000, bo ffff88012c02bc00 [ 4.451042] fbcon: nouveaufb (fb0) is primary device [ 5.805206] Console: switching to colour frame buffer device 210x59 [ 5.821518] fb0: nouveaufb frame buffer device [ 5.821522] drm: registered panic notifier [ 5.821550] [drm] Initialized nouveau 0.0.16 20090420 for 0000:01:00.0 on minor 0 Thanks for any help in trying to sort this out. Let me know if more information would be helpful.
Tested this out with Intel 945GME graphics, no problems. This could be a nouveau driver issue - have you tested other OpenGL based programs, or tried the nvidia drivers? I have a nvidia based machine I'll test with this weekend.
I have not tested other OpenGL programs or the nvidia drivers yet. I'll try to look into to this reasonably soon. Given the noaccel requirement and some of the messages from the nouveau driver on this particular card, I wouldn't be surprised if the driver and its interaction with OpenGL turned out to be the core problem.
The OpenGL programs glxgears, glglobe, zhu3d, and coot seem to work nicely. Celestia didn't render some things (like the Sun and the inner solar system orbits in the demo, though the Earth and Moon worked, and possibly stars--I presume that there should have been stars). But despite these potential issues, Celestia was very smooth and didn't show the flickering present in pymol.
I tested pymol with the nvidia drivers with no problems. I haven't tried the nouveau driver, but my guess is that its a driver issue. I'll also update pymol to 1.5 as soon as its available, that may also resolve the issue.
FWIW I see this flickering in Pymol 1.5.0.3 built from svn when using llvmpipe: LIBGL_ALWAYS_SOFTWARE=1 pymol the problem must be somewhere in the graphics stack
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