RE: [PyMOL] sporadic pymol/X-server freezes?

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. =20

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.
 =20
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. =20

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. =20

Cheers
Warren

--
Warren L. DeLano, Ph.D.                    =20
Principal Scientist

. DeLano Scientific LLC =20
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> -----Original Message-----
> From: pym...@li...=20
> [mailto:pym...@li...] On Behalf Of=20
> Peter Adrian Meyer
> Sent: Thursday, March 23, 2006 9:32 AM
> To: pym...@li...
> Subject: [PyMOL] sporadic pymol/X-server freezes?
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> Hi everyone,
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> Has anyone else run into cases where pymol will freeze the=20
> X-server (pymol doesn't repond to mouse or keyboard input;=20
> keyboard non-responsive to caps-lock on/off)?  The system is=20
> still stable, I'm able to login remotely and see that pymol=20
> is running at 100% CPU.  Killing pymol results in xorg=20
> running at 100% CPU (killing the xorg process as root doesn't=20
> do anything).
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> I've only seen this while looking at several maps/masks (but=20
> that's most of what I use pymol for, so I'm not sure if=20
> that's the cause).  I've seen this error on both suse 10.0=20
> and kubuntu (3.10?  whatever the lastest apt-get dist upgrade=20
> got me; two different machines) using source builds of=20
> pymol-0.98, and 0.99rc6 with ext-0.98,ext-0.99rc6, and ext-0.95.
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> Any suggestions on how to fix this (or get debugging=20
> information out of pymol to narrow down the problem)?
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> Thanks,
> Pete
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> Pete Meyer
> Fu Lab
> BMCB grad student
> Cornell University
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