(First, thanks Matt for the great diagnostic advice!)
This sounds to me like a potential threading deadlock, possible
due to the broken threading in RedHat 9. Are you using the stock
version or have you patched glibc?
If you haven't patched your RedHat 9, then one way to be sure
this is the problem is to "set max_threads, 1" before issuing the ray
command. If PyMOL doesn't hang, then you've found the culprit.
If have already patched your RH9, then let's do some more work
to determine what's going on...
Warren L. DeLano, Ph.D.
DeLano Scientific LLC
> -----Original Message-----
> From: pymol-users-admin@... [mailto:pymol-users-
> admin@...] On Behalf Of Matt Franklin
> Sent: Tuesday, January 20, 2004 6:25 PM
> To: Morri Feldman
> Cc: pymol-users
> Subject: Re: [PyMOL] Ray Tracing Crash
> Morri Feldman wrote:
> > I am running pymol .93. When I try to ray trace a scene, the gui
> > white status bar that moves halfway across the screen and then
> > After this the GUI is frozen and must be killed. No error messages
> > shown. The computer is running RedHat 9 and has 4 processors. Has
> > anyone else experienced this problem? Do you have any solutions?
> > This message may double post because I accidentally tried to post it
> > my other email account. Sorry
> > Thanks, Morri
> > Morri Feldman
> Hi Morri -
> The progress bar for raytracing doesn't move linearly - the first half
> of the bar is covered fairly quickly, then more slowly, then very
> slowly, then the last fifth is usually covered in one jump. Are you
> sure you just aren't being impatient? Try raytracing a very simple
> scene, like a single amino acid in spheres mode, to see if it hangs
> then. Also try raytracing parts of your scene in case some funny bit
> your molecule is causing this problem. Finally, try reducing the
> complexity of your surfaces and/or spheres: "set surface_quality, -1"
> is the default).
> Feel free to contact me directly - I'm local! (Although Warren will
> more helpful...)
> - Matt
> Matthew Franklin Phone:(650)225-4596
> Postdoctoral Researcher Fax:(650)225-3734
> Genentech, Inc.
> 1 DNA Way, South San Francisco, CA 94080
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