Morri, The RH9 Patch is described and published on:
https://rhn.redhat.com/errata/RHBA-2003-136.html I would not expect Debian to suffer from the same crash. If it does, then we may be dealing with a genuine bug in PyMOL (assuming that you're not simply running out of RAM). With respect to Debian, in order to debug the problem, you might want to send me a PyMOL session file which crashes on your system when the next command issued is "ray". Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: Morri Feldman [mailto:morrifeld...@yahoo.com] > Sent: Tuesday, January 20, 2004 10:36 PM > To: Warren L. DeLano; 'Matt Franklin'; 'Morri Feldman' > Cc: 'pymol-users' > Subject: RE: [PyMOL] Ray Tracing Crash > > Warren and Matt, > > Thanks so much for your help. I must be using the > stock glibc because "set max_threads, 1" allows me to > ray trace without crashing. I will tell my system > administrator to patch glibc. Do you know where I > should look for the patch? > > My debian/testing system at home also has trouble ray > tracing especially sticks. When it fails I get a > segmentation fault. Is my problem at home also due to > an unpatched glibc? > > The error message is: > /usr/bin/pymol: line 7: 32460 Segmentation fault > python > /usr/lib/python2.3/site-packages/pymol/__init__.py $* > > Thanks for creating such a great program, > Morri > > --- "Warren L. DeLano" <war...@delanoscientific.com> > wrote: > > Morri, > > > > (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... > > > > Cheers, > > Warren > > > > -- > > mailto:war...@delanoscientific.com > > Warren L. DeLano, Ph.D. > > Principal Scientist > > DeLano Scientific LLC > > Voice (650)-346-1154 > > Fax (650)-593-4020 > > > > > -----Original Message----- > > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users- > > > ad...@lists.sourceforge.net] 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 > > shows > > > a > > > > white status bar that moves halfway across the > > screen and then > > freezes. > > > > After this the GUI is frozen and must be killed. > > No error messages > > are > > > > 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 > > > from > > > > 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 > > of > > > your molecule is causing this problem. Finally, > > try reducing the > > > complexity of your surfaces and/or spheres: "set > > surface_quality, -1" > > (0 > > > is the default). > > > > > > Feel free to contact me directly - I'm local! > > (Although Warren will > > be > > > 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 > > > > > > > > > > > > > > > ------------------------------------------------------- > > > The SF.Net email is sponsored by EclipseCon 2004 > > > Premiere Conference on Open Tools Development and > > Integration > > > See the breadth of Eclipse activity. February 3-5 > > in Anaheim, CA. > > > http://www.eclipsecon.org/osdn > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > ------------------------------------------------------- > > The SF.Net email is sponsored by EclipseCon 2004 > > Premiere Conference on Open Tools Development and > > Integration > > See the breadth of Eclipse activity. February 3-5 in > > Anaheim, CA. > > http://www.eclipsecon.org/osdn > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > ===== > Morris Feldman > 332 Fell ST APT 1 > San Francisco, CA 94102 > 415/672-3227 > > __________________________________ > Do you Yahoo!? > Yahoo! Hotjobs: Enter the "Signing Bonus" Sweepstakes > http://hotjobs.sweepstakes.yahoo.com/signingbonus
