FYI: Linux users who need to run with the nVidia driver versions 71.47 or 71.67...
The PyMOL 0.99beta01 version available at http://delsci.com/beta is able to avoid the crash. However, performance is reduced by the workaround, so I wouldn't recommend using this build unless you have to. 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: Michael Kutz [mailto:mk...@ttpharma.com] > Sent: Thursday, May 26, 2005 8:29 AM > To: Fischmann, Thierry > Cc: 'Warren DeLano' > Subject: RE: [PyMOL] Linux FC3 upgrade causing pymol core dump > > > Thierry, > The machine i have is a 6221 also. IBM's working on the > problem for us. (there is at least one other person that has > called them with this problem) The solution IBM is proposing > - block out certein memory areas for kernel use. i'll > forward the information when i get it. > > for us, not all 3rd party code works on RHEL 4, so we have to > use RHEL 3. > rhel 4 uses ONLY gcc 3.*, even "backward compatible" gcc is a > 3.* version. the 3rd party software was compiled w/t 2.?? libraries. > > about your crash/bad sector/etc.... run "badblocks" before or > durring reinstall. CAUTION: this will wipe a disk if not > done correctly. > Also, there should be a way, through "linux recover" to > re-build the boot sector if your /boot partition is fine. > (this is another reason why you ALWAYS make /boot a seperate > partition.) if you have support, call redhat for help. I'd > ask my guy how to do this but he's in Raleigh for RHCE training. > > other hints: In your BIOS - turn HyperThreading OFF. > turn your screen-saver off also. > > MK > > > "Fischmann, Thierry" <thierry.fischm...@spcorp.com> wrote on > 05/26/2005 10:42:28: > > > Mike. > > > > I'd be most grateful if you could post the solution. > > > > My machine is an IBM Intellistation with Intel cpu and one of the > > latest NVIDIA quadro graphics cards). The OS is RHEL 4 WS. > I have the > > NVIDIA 7174 driver installed. > > > > I have had pymol installed for a while, and it has worked > well so far > > ... then after reading your message I've started it again, just to > > make sure everything is fine and ... > > > > Nasty crash ! The screen went blank, the keyboard would not > respond, > > and after ~ 1minute the computer rebooted itself on its own. The > > computer now claims that there is an error in the system > disk that is > > not recoverable, and refuses to boot from that disk. > > > > I have been able to reboot from an installation CD in "linux rescue" > > mode. I can see that the partition itself does not seem affected: > > the files are there and "look okay". So maybe only the boot > sector is > > corrupted. I am considering reinstalling everything from > scratch, as > > there may be more than just a boot sector that has become > corrupted (I > > keep my data on a separate system disk, and they are most > likely not > > affected). > > > > No more NVIDIA drivers for me unless I have a solution to > the above ... > > > > Thierry > > -----Original Message----- > > From: Michael Kutz [mailto:mk...@ttpharma.com] > > Sent: Thursday, May 26, 2005 10:00 AM > > To: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] Linux FC3 upgrade causing pymol core dump > > > > > nvidia 7167 & 7174 drivers seem to have issues (see > previous e-mails > > in this list) VMD is also affected, but not many other openGL > > programs. (i can run SPECperf just fine) > > > > The issue you see here may be related to some other > non-pymol issues > > i've seen on my machine. > > my vendor said my other issues may be caused by the nvidia driver > > overwriting some kernel space. > > > > when/if i can, i'll e-mail the solution. > > > > MK > > > > > > pymol-users-ad...@lists.sourceforge.net wrote on 05/26/2005 > 05:16:56: > > > > > Do you have nvidia drivers? > > > If so, may be you came across the same problem I have: > > > > > > I have installed the latest version of Mandriva Linux on a AMD > > > Athlon(tm) MP 2400+ PC with > > > a Quadro4 900 XGL graphich card and the NVIDIA-Linux-x86-1.0-7174 > > > driver > > > > > > When I run pymol and load a pdb file, the program crashes > with the > > > following message: > > > > > > CmdLoad: "GLGA/sup_models/pdb1rzu.ent" loaded as "pdb1rzu". > > > *** glibc detected *** double free or corruption (!prev): > 0x08a76ba0 > > > *** > > > /usr/local/pymol-0.98-precompiled/pymol.com: line 14: 16877 > > > Aborted (core dumped) $PYMOL_PATH/pymol.exe $* > > > > > > However, if I set auto_show_lines=off and auto_show_nonbonded=off > > > BEFORE loading the molecule, the program loads the PDB > file without > > > crashing (and without showing any graphical object, of course). > > > Then, I can use the "show" command/button for any type of > > > representation (ribbons, nonbonded, sticks, ...) EXCEPT > the "lines" > > > representation, which causes a program crash. > > > > > > This happens with both distributed binary and self compiled PyMol > > > versions. I have tried version 0.97 and 0.98 with the > same results. > > > > > > Then, browsing the internet, I came across the following message > > > from > > > Warren: > > > > > > http://sourceforge.net/mailarchive/message.php?msg_id=11735911 > > > > > > and I decided to try the 0_99beta01 version > > > > (http://delsci.com/beta/pymol-0_99beta01-bin-linux-x86-nvidia-test.t > > > gz), which seems to solve my problem for the moment. > > > > > > > > > > > > gerwald jogl wrote: > > > > > > > Hi everyone, > > > > > > > > Just wanted to send in a description of the following situation: > > > > I was using pymol 0.98 precompiled on FC3 today and did an > > > > automatic update during the day (therefore, sorry but I > don't know > > > > which packages where upgraded :-( Afterwards, pymol would start > > > > up, but core dump immediately after loading a pdb file. > > > > The same is happening with the 0.97 precompiled version > and with > > > > my own compile of the 0.98 source code. > > > > This is what I get: > > > > /xsoft/pymol-0.97precompiled/pymol.com: line 14: 19692 > Segmentation > > > > fault (core dumped) $PYMOL_PATH/pymol.exe $* > > > > > > > > or my compile: > > > > /xsoft/pymol-0.98/pymol.com: line 2: 19785 Segmentation > fault > > > > (core dumped) /usr/bin/python > > > > /usr/lib/python2.3/site-packages/pymol/__init__.py $* > > > > > > > > > > > > Any comments on this would be greatly appreciated... > > > > Gerwald > > > > > > > > > > > > ------------------------------------------------------- > > > > SF.Net email is sponsored by: GoToMeeting - the easiest way to > > > > collaborate online with coworkers and clients while > avoiding the > > > > high cost of travel and communications. There is no > equipment to > > > > buy and you can meet as often as you want. Try it > > > > free.http://ads.osdn.com/?ad_id=7402&alloc_id=16135&op=click > > > > _______________________________________________ > > > > PyMOL-users mailing list > > > > PyMOL-users@lists.sourceforge.net > > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > -- > > > > > > -------------------------------------------------- > > > Stefano Trapani, PhD > > > > > > Laboratoire de Virologie Moleculaire & Structurale UMR 2472 > > > CNRS-GIF > > > 1 Av. de la Terrasse, Bat. 14 B > > > 91198 Gif-sur-Yvette FRANCE > > > > > > phone: ++33 1 6982.3856 > > > FAX: ++33 1 6982.4308 > > > -------------------------------------------------- > > > > > > > > > [attachment "trapani.vcf" deleted by Michael Kutz/TTP] > > > > > > > ********************************************************************* > > This message and any attachments are solely for the intended > > recipient. 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