VMD-L Mailing List

From: Gyimesi Gergely (ggyimesi_at_enzim.hu)
Date: Tue May 17 2005 - 14:19:07 CDT

Helo,

I tried it, got the following result.
I'll paste here the whole output for completeness.

Starting program: /usr/local/lib/vmd/vmd_LINUX
[Thread debugging using libthread_db enabled]
[New Thread -1216734336 (LWP 11171)]
Info) VMD for LINUX, version 1.8.3 (May 15, 2005)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 1 CPU detected.
Info) OpenGL renderer: RADEON 8500 DDR Generic
Info) Features: STENCIL RN MDE CVA MTX PP
Info) Textures: 2-D (2048x2048), 3-D (512x512x512), Multitexture (6)
[New Thread -1308972112 (LWP 11174)]
vmd > Info) Using plugin pdb for structure file /home/mrmaim/downloads/1TBF.pdb
Info) Using plugin pdb for coordinates from file /home/mrmaim/downloads/1TBF.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 3021
Info) Residues: 653
Info) Waters: 323
Info) Segments: 1
Info) Fragments: 328 Protein: 1 Nucleic: 0
Info) Finished with coordinate file /home/mrmaim/downloads/1TBF.pdb.

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1216734336 (LWP 11171)]
0xb72c1093 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
(gdb) where
#0 0xb72c1093 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
#1 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
#2 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
#3 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
:
:
#1523 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
#1524 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
---Type <return> to continue, or q <return> to quit---q
Quit
(gdb)

That last line seems to keep repeating forever..
I hope this helps, shouldn't I have compiled in some kind of support for
debugging, eg. symbols, etc. ?
If there's anything else I can help in, just tell me.

bye,
Greg

On Mon, 16 May 2005 19:51:04 -0500, John Stone wrote
> Hi,
> Can you try doing the following steps for me, and let me know what
> results you get?
> start an xterm, then in that xterm do:
> /bin/csh (use csh so the other commands I list
> will work) source /usr/local/bin/vmd (use the startup script's env
> vars)
> (then immediately quit that VMD) gdb /usr/local/lib/vmd/vmd_LINUX
> (then issue these commands to gdb) run
> (then load a structure that normally crashes your VMD)
> (... then try to crash it) where (this shows where VMD was
> when the crash occured)
>
> If you can email the output to me, I should be able to determine if
> this is another ATI driver problem, or something else.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, May 15, 2005 at 05:16:08PM +0200, Gyimesi Gergely wrote:
> > Helo,
> >
> > Just for your info: I'm having the same problem, with the fglrx-8.10.19 and
> > fglrx-8.12.10 drivers also, with a Radeon 8500 card. I've tried setting
> > VMDSIMPLEGRAPHICS, but it didn't help.. The segfault only happens when
> > loading large molecules (eg. proteins), it works OK for smaller ones. It
also
> > works OK in text mode.
> > Looking forward to anything you can do, after May 20. :-)
> >
> > Gergely Gyimesi
> > Ph.D student
> > Institute of Enzymology,
> > Hungarian Academy of Sciences
> >
> > >Hi,
> > > Try setting this environment variable before starting VMD, it will
> > >disable all of the advanced OpenGL features that VMD uses, in favor of
> > >a more minimalistic and simpler OpenGL 1.1-based functionality:
> > > setenv VMDSIMPLEGRAPHICS 1
> > >
> > >Let me know if this gets you up and running.
> > >
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >
> > >
> > >>Is there any way to work around the fglrx-8.10.19 driver crash? I've
> > >>seen the posts and bug report but would prefer not to downgrade my
> > >>driver. Is there any way to use MESA or some other software rendering
> > >>instead?
> > >>
> > >>
> > >
> > >
> > >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078