Re: [PyMOL] Ray Tracing Crash
Package: pymol Version: 0.93-2 On Thu, Jan 22, 2004 at 08:53:37AM -0800, Morri Feldman wrote: > On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote: > > > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: > > > Regarding my problems raytracing on my debian/testing machine. > > > > What is the exact version of the pymol .deb you're using? 0.93-2? > pymol_0.93-2_i386.deb > > > What architecture are you running on? i386 or something else? > i386, Pentium III > > > Do you use pymol's internal raytracer, or povray? > I invoke the raytracer by typing "ray". I assume this is the internal > raytracer. > > > Does the raytracing-demo from the demo-menu work? > The ray tracing demo works. But after running the raytracing-demo, pymol > will crash if I type either: > hide spheres > show sticks > ray > > or: > hide spheres > show lines > ray Indeed, I can reproduce this here. Thanks for the bug report. I'll try to debug this during the weekend (won't have time tomorrow I guess), please nag me if you don't here back next week. thanks, Michael
Re: [PyMOL] Ray Tracing Crash
On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote: > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: > > Regarding my problems raytracing on my debian/testing machine. > > What is the exact version of the pymol .deb you're using? 0.93-2? pymol_0.93-2_i386.deb > What architecture are you running on? i386 or something else? i386, Pentium III > Do you use pymol's internal raytracer, or povray? I invoke the raytracer by typing "ray". I assume this is the internal raytracer. > Does the raytracing-demo from the demo-menu work? The ray tracing demo works. But after running the raytracing-demo, pymol will crash if I type either: hide spheres show sticks ray or: hide spheres show lines ray Thanks, Morri > > > thanks, > > Michael > > > --- > 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
Re: [PyMOL] Ray Tracing Crash
On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote: > Regarding my problems raytracing on my debian/testing machine. What is the exact version of the pymol .deb you're using? 0.93-2? What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or povray? Does the raytracing-demo from the demo-menu work? thanks, Michael
Re: [PyMOL] Ray Tracing Crash
Regarding my problems raytracing on my debian/testing machine. The system has 128mb of ram. I have attached a pymol session file. To generate the session file, I loaded a very simple molecule into pymol. After loading the session file and executing the ray command I get a segmentation fault. The tail end of pymols output to the shell is show below. As you can see below, while pymol starts up I recieve an error complaining about 'PYMOL_PATH'. I don't know if this error is related to the problems I am having with ray tracing. Please let me know if you would like any more information. -START OF PYMOL'S OUTPUT TO THE SHELL Hit ESC anytime to toggle between text and graphics. Traceback (most recent call last): File "", line 1, in ? File "/usr/lib/python2.3/UserDict.py", line 19, in __getitem__ def __getitem__(self, key): return self.data[key] KeyError: 'PYMOL_PATH' OpenGL based graphics front end: GL_VENDOR: VA Linux Systems, Inc. GL_RENDERER: Mesa GLX Indirect GL_VERSION: 1.2 Mesa 3.4.2 Executive: Loading version 0.92 session... PyMOL>ray /usr/bin/pymol: line 7: 975 Segmentation fault python /usr/lib/python2.3/site-packages/pymol/__init__.py $* -END OF PYMOL'S OUTPUT TO THE SHELL- Best, Morri On Wed, 21 Jan 2004 17:24:48 +0100 Michael Banck wrote: > On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote: > > My debian/testing system at home also has trouble ray > > tracing, especially with sticks. When it fails I get a > > segmentation fault. > > What architecture are you running on? i386 or something else? > > Do you use pymol's internal raytracer, or povray? > > > Is my problem at home also due to an unpatched glibc? > > glibc in debian/testing should be fairly recent. Perhaps it suffers from > a different bug, but the one described earlier should be fixed by now, > if it ever pertained to Debian. > > > The error message is: > > /usr/bin/pymol: line 7: 32460 Segmentation fault > > python > > /usr/lib/python2.3/site-packages/pymol/__init__.py $* > > As Warren said, a detailed description of the scene you were trying to > raytrace would be welcomed. > > > Michael > > > --- > 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 ray_session.pse Description: Binary data
Re: [PyMOL] Ray Tracing Crash
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" > > 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 > > > > > > >
Re: [PyMOL] Ray Tracing Crash
On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote: > My debian/testing system at home also has trouble ray > tracing, especially with sticks. When it fails I get a > segmentation fault. What architecture are you running on? i386 or something else? Do you use pymol's internal raytracer, or povray? > Is my problem at home also due to an unpatched glibc? glibc in debian/testing should be fairly recent. Perhaps it suffers from a different bug, but the one described earlier should be fixed by now, if it ever pertained to Debian. > The error message is: > /usr/bin/pymol: line 7: 32460 Segmentation fault > python > /usr/lib/python2.3/site-packages/pymol/__init__.py $* As Warren said, a detailed description of the scene you were trying to raytrace would be welcomed. Michael
RE: [PyMOL] Ray Tracing Crash
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" > 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
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 with 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 On Tue, 20 Jan 2004 18:35:07 -0800 "Warren L. DeLano" 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 FranklinPhone:(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 > Morri Feldman
RE: [PyMOL] Ray Tracing Crash
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 FranklinPhone:(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
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 FranklinPhone:(650)225-4596 Postdoctoral Researcher Fax:(650)225-3734 Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080
[PyMOL] Ray Tracing Crash
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
