From: Sabuj Pattanayek (sabuj.pattanayek_at_Vanderbilt.Edu)
Date: Tue Mar 29 2005 - 11:55:03 CST

Hi,

Unfortunately I can't get pymol-0.97 & 0.98beta29/27 to open a pdb
without crashing instantly. I also tested Chimera (1.2105), O v9.0.7,
and rasmol and these seem to work ok but I guess they aren't using
quads/quad strips. Thanks for your insight, I'll email nvidia with the
contents of your email.

..Sabuj Pattanayek

John Stone wrote:
> Sabuj,
> That's really interesting. It sounds to me like NVidia's new driver
> has some sort of problem with drawing quads or quad strips in immediate mode.
> If that's what's going on, then a lot of other programs are going to crash
> too, not just VMD and Pymol, so I suspect they'll have to fix this very
> soon :-) All of the VMD reps you listed as having problems draw
> quadrilateral strips at some point, so that's my personal guess as
> to what is happening with their new driver. The Isosurface rep is
> one exception, it is drawing triangle strips, so I'm not sure why you'd
> have trouble with it, given that several of the others you listed do
> as well. Please email these results to linux-bugs_at_nvidia.com so they
> are aware of the problem. If you can do similar tests with Pymol,
> that will help convince them it's a new problem with the driver and not
> just one bad software package, which is likely their default assumption.
>
> John
>
> On Tue, Mar 29, 2005 at 11:11:54AM -0600, Sabuj Pattanayek wrote:
>
>>Hi John,
>>
>>This is what I was able to test on vmd 1.8.3, I think 1.8.2 will do the
>>same (note this only affects the quadro cards and not geforce):
>>
>>Representation Result
>>-------------- ------
>>Lines (Default) ok
>>Bonds crash
>>DynamicBonds crash
>>HBonds ok
>>Points ok
>>VDW ok
>>CPK crash
>>Licorice crash
>>Trace crash
>>Tube crash
>>Ribbons ok
>>NewRibbons ok
>>Cartoon crash
>>NewCartoon ok!!!
>>MSMS ok
>>Surf ok
>>Dotted ok
>>Solvent ok
>>Isosurface(points) ok
>>Isosurface(solid) crash
>>Isosurface(wireframe) ok
>>VolumeSlice ok? ..not sure what datatype this wants (never used
>>this before), i was using a brix map but couldn't see anything
>>
>>Thanks,
>>Sabuj Pattanayek
>>
>>David A. Horita wrote:
>>
>>>Hi,
>>>I Haven't tried VMD yet, but Windows XP-pro pymol crashes upon file open
>>>under the 71.84 drivers, but not the 70.78 drivers. (Quadro 1300,
>>>XP-Pro servicepack 2)
>>>David Horita
>>>
>>>-----Original Message-----
>>>From: pymol-users-admin_at_lists.sourceforge.net
>>>[mailto:pymol-users-admin_at_lists.sourceforge.net] On Behalf Of John Stone
>>>Sent: Monday, March 28, 2005 10:10 AM
>>>To: Sabuj Pattanayek
>>>Cc: pymol-users_at_lists.sourceforge.net; vmd-l_at_ks.uiuc.edu
>>>Subject: Re: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167]
>>>nvidia driver
>>>
>>>
>>>Hi,
>>> Have you reported the crashes to NVidia? I'd suggest sending an email
>>>to their linux-bugs_at_nvidia.com mail address. The fact that multiple
>>>packages crash with the new driver indicates that they may have a new
>>>bug in their drivers. You mentioned that making a licorice rep crashes
>>>your VMD on that driver, what about VDW or bonds? Do they have a
>>>similar effect?
>>>
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>On Sat, Mar 26, 2005 at 04:42:42PM -0600, Sabuj Pattanayek wrote:
>>>
>>>
>>>>Yeah I have the same problem in the beta pymol, haven't tried the
>>>>stable
>>>>version:
>>>>
>>>>OpenGL-based graphics engine:
>>>>GL_VENDOR: NVIDIA Corporation
>>>>GL_RENDERER: Quadro4 750 XGL/AGP/SSE/3DNOW!
>>>>GL_VERSION: 1.5.3 NVIDIA 71.67
>>>>Hardware stereo capability detected.
>>>>Adapting to Quadro hardware...
>>>>Detected 2 CPUs. Enabled multithreaded rendering.
>>>>/usr/bin/pymol: line 14: 8852 Segmentation fault
>>>>$PYMOL_PATH/pymol.exe $*
>>>>
>>>>and 7167 won't compile on 2.6.10-11? kernels either, need 2.6.12-rc1,
>>>>haven't tested others. I get similar crashes in VMD 1.8.2+ using 7167
>>>>also. For instance, if you load a pdb and try to make a "licorice"
>>>>representation, vmd just closes/crashes.
>>>>
>>>>I also think this maybe a Quadro problem and not a a problem with
>>>>GeForce cards. I have a GeForce 5500 FX on another machine and it
>>>>doesn't have these programs, and realtime GLSL rendering works very
>>>>nicely in vmd 1.8.3.
>>>>
>>>>Sorry for posting this on both mailing lists, just trying to avoid
>>>>reposting.
>>>>
>>>>..Sabuj Pattanayek
>>>>
>>>>HuiZhe Li wrote:
>>>>
>>>>
>>>>>just upgraded nvidia driver from 6629 to 7167 (Linux, RHEL 4) and
>>>>>pymol crashes when a molecule is load. is there a fix? (pymol worked
>>>>>fine with 6629 driver).
>>>>>
>>>>>OpenGL-based graphics engine:
>>>>>GL_VENDOR: NVIDIA Corporation
>>>>>GL_RENDERER: Quadro FX 1400/PCI/SSE2
>>>>>GL_VERSION: 1.5.3 NVIDIA 71.67
>>>>>Adapting to Quadro hardware...
>>>>>/usr/local/bin/pymol: line 14: 4575 Segmentation
>>>>>fault (core dumped) $PYMOL_PATH/pymol.exe $*
>>>>>
>
>