Warren, The RH9 Patch fixed the ray tracing problem. Thanks for your help.
Tonight I will send you specific information about the Debian ray tracing problem. Thanks, Morri On Wed, 21 Jan 2004 08:07:00 -0800 "Warren L. DeLano" wrote: > 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 > > > > > ------------------------------------------------------- > 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 > Morri Feldman
