From: Peter D. <du...@ce...> - 2004-10-14 12:06:03
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Chen, Kernel: 2.4.26 (I observe the same with 2.4.25) Distribution: Debian (straight SARGE, and pymol was acquired with apt-get, so no funny compiling business here) Python: 2.3 (2.4 is also there, but only for testing purposes) I've noticed on other mailing lists, that people have reported similar error messages with other packages. This is how I found the original solutions. I just wanted to report that it also occurs with Pymol. Perhaps you are right, perhaps it's a python problem, but I'm not prepared to roll back to 2.2 to test it. > What Linux are you using? Seems it's not a problem on RedHat linux, I am > running both 7.3 and EL-AS, with 2.4.20 and 2.4.21 kernel respectively, > and the exact same NVIDIA version without any problem at all. > Although we are using python2.2, looks like you are using python2.3, maybe > that's the problem? > > Best > Chen Robert, According to what I've managed to learn from googling around a bit, this problem doesn't occur on 2.6.x kernels. > I'm running Fedora Core 2 with: > (II) Module glx: vendor="NVIDIA Corporation" > compiled for 4.0.2, module version = 1.0.6111 > > And: > 2.6.8-1.521 #1 Mon Aug 16 09:01:18 EDT 2004 i686 athlon i386 GNU/Linux > > With no problems whatsover... > > Robert Well, I'm glad to hear this problem isn't as endemic for Pymol users as I had feared. What surprised me was that it happened on a fresh Debian install. The solutions I had posted earlier *do* solve the problem (they did for me), so hopefully the information will be useful to some people who encounter it. Regards, Peter _.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _ -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` : '. | | | |'. '. | | | |'. '. | | | |'. '.: '. '.| | | | '. '.| | | | '. '.| | | | '. '. '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `. `-..,..-' `-..,..-' `-..,..-' ` Laboratory of Dr. Didier Picard University of Geneva Department of Cell Biology Scinces III 30, Quai Ernest-Ansermet 1211 Geneva 4 Switzerland Tel: +41 22 379 3254 Fax: +41 22 379 6442 Email: du...@ce... http://www.picard.ch/DP/DPhome.html _.--'"`'--._ _.--'"`'--._ _.--'"`'--._ _ -:`.'|`|"':-. '-:`.'|`|"':-. '-:`.'|`|"':-. '.` : '. | | | |'. '. | | | |'. '. | | | |'. '.: '. '.| | | | '. '.| | | | '. '.| | | | '. '. '. `.:_ | :_.' '. `.:_ | :_.' '. `.:_ | :_.' '. `. `-..,..-' `-..,..-' `-..,..-' ` |
From: VlaDar <da...@pa...> - 2004-10-15 01:02:15
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There is one another solution. You can install Nvidia linux drivert with "-force-tls=classic" option. The command line loks like this : > NVIDIA-Linux-x86-1.0-5336-pkg1.run -force-tls=classic cheers Vladimir Message: 7 Date: Wed, 13 Oct 2004 18:12:11 +0200 From: Pet...@ce... To: pym...@li... Subject: [PyMOL] Warning: Nvidia 6111 drivers for linux Hello. I did a scan (albeit brief) of the mailing list for this issue, but didn't find it, so I decided to post it FYI. I wanted to mention a serious issue I just discovered after installing the new nvidia drivers for linux (specifically regarding the "NVIDIA-Linux-x86-1.0-6111-pkg1.run" driver, though I imagine the same is true for all other 6111 drivers), on a 2.4.x kernel, as well as the solution. It may be important to make a note of this somewhere in the FAQ or installation instructions (or perhaps it would be easy to fix in one of the pymol scripts). PROBLEM: ======== Running Pymol gives the following message: Traceback (most recent call last): File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 90, in ? import pymol File "/usr/lib/python2.3/site-packages/pymol/__init__.py", line 306, in ? import _cmd ImportError: libnvidia-tls.so.1: cannot handle TLS data SOLUTIONS: ========== There are 2 solutions to this problem. (1) either rename /usr/lib/tls to something else, or delete it entirely. Pymol then works perfectly ok. However, since this is akin to "If it hurts, cut it off", it might break something down the line. Do note though, that the files contained within this dir are also in /usr/lib (not a symbolic link). (2) edit /etc/default/nvidia-glx (if it exists, for me it didn't), and set USE_TLS to 0. Reboot. Surely there must be another editable config file somewhere with this option, but I haven't found it. According to a thread on PyKDE, "The tls (thread local storage) stuff only works if you are running a tls-enabled glibc on a 2.6 kernel, and when installing nvidia-glx, you are normally asked by debconf on what to use." This suggests anyone running the new nvidia drivers on a 2.4.x kernel may encounter this problem. Admittedly, I haven't tested them on a 2.6.x kernel, so I can't be sure the problem doesn't occur there either. Hope this helps someone. Cheers, |
From: Charles M. <cm...@in...> - 2004-11-02 19:00:23
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FYI for people with this problem. The EASIEST solution is the same that people are using for ut2004 and doom3 in linux oddly enough. Just run: LD_PRELOAD=/usr/lib/libGL.so pymol - Charlie |
From: D. J. A. <de...@ia...> - 2004-11-17 22:23:27
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On Tue, Nov 02, 2004 at 01:59:56PM -0500, Charles Moad wrote: > FYI for people with this problem. The EASIEST solution is the same that > people are using for ut2004 and doom3 in linux oddly enough. Just run: > > LD_PRELOAD=/usr/lib/libGL.so pymol I read on the O list that a new set of drivers were made available Nov 5. It'll be interesting to hear how they fare with PyMOL, and if any difficulties get cleared up by them. -- D. Joe Anderson, Asst. Sci. 2252 Molecular Biology Bldg. BBMB Research Computing Support www.bb.iastate.edu/computing bbs...@ia... |