Warren, Thanks for getting back to me so quickly. It's good to hear that this problem has been seen before (it's been one of those weeks for strange computer issues).
I guess it shouldn't supprise me that there are issues with proprietary OpenGL on linux (FYI the two machines I've seen this on are using ATI and intel graphics cards). I'll try out the options you mentioned. Your idea about known-working (and non-working) combinations of hardware seems like a very good thing to do. Pete > Pete, > > We have been suffering this same exact symptom with our nVidia-base 64-bit RHEL workstation for over a year. I have spent enough time troubleshooting the issue to have convinced myself that the problem isn't PyMOL -- it is an inability of certain combinations of hardware, Linux kernels, and proprietary OpenGL drivers to handle the vast quantity of immediate mode rendering geometry that PyMOL generates. It seems to be either a sporadic buffer overflow or a race condition within the kernel layer. > > The proprietary nature of the OpenGL drivers prevents anyone other than the hardware vendor from being able to actually understand and solve the problem. Plus, the problem is sporadic -- most of the time everything works fine, but sometimes PyMOL hangs, sometimes all of X11 freezes, and sometimes the whole system comes crashing down. The intractable nature of these Linux stability problems is one of the primary reasons why I recommend Mac OS X over Linux for unix-based PyMOL visualization. > > Note that the settings "nvidia_bugs" and "use_display_lists" may reduce the frequency of the problem on your system. Other than that, my suggestion would be to try different Linux kernels and OpenGL driver versions. > > The combinatorial matrix of possibilities is huge, but maybe we should create a table on the Wiki for people to post working and non-working combinations of Linux kernels, cpu and graphics hardware, and opengl drivers? That's how we used to do things in the old days. I suspect only 5-10% of configurations are truly unworkable, and once enough data is collected from enough people, meaningful patterns would likely emerge. > > Cheers > Warren > > -- > Warren L. DeLano, Ph.D. > Principal Scientist > > . DeLano Scientific LLC > . 400 Oyster Point Blvd., Suite 213 > . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > >> -----Original Message----- >> From: pymol-users-ad...@lists.sourceforge.net >> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of >> Peter Adrian Meyer >> Sent: Thursday, March 23, 2006 9:32 AM >> To: pymol-users@lists.sourceforge.net >> Subject: [PyMOL] sporadic pymol/X-server freezes? >> Hi everyone, >> Has anyone else run into cases where pymol will freeze the >> X-server (pymol doesn't repond to mouse or keyboard input; >> keyboard non-responsive to caps-lock on/off)? The system is >> still stable, I'm able to login remotely and see that pymol >> is running at 100% CPU. Killing pymol results in xorg >> running at 100% CPU (killing the xorg process as root doesn't >> do anything). >> I've only seen this while looking at several maps/masks (but >> that's most of what I use pymol for, so I'm not sure if >> that's the cause). I've seen this error on both suse 10.0 >> and kubuntu (3.10? whatever the lastest apt-get dist upgrade >> got me; two different machines) using source builds of >> pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95. Any suggestions on how to fix this (or get debugging >> information out of pymol to narrow down the problem)? >> Thanks, >> Pete >> Pete Meyer >> Fu Lab >> BMCB grad student >> Cornell University >> ------------------------------------------------------- >> This SF.Net email is sponsored by xPML, a groundbreaking >> scripting language that extends applications into web and >> mobile media. Attend the live webcast and join the prime >> developer group breaking into this new coding territory! >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&; >> dat=121642 >> _______________________________________________ >> PyMOL-users mailing list >> PyMOL-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/pymol-users > Pete Meyer Fu Lab BMCB grad student Cornell University
