VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 23 2005 - 15:08:09 CDT

Ok
  The output you sent shows that the crash occurs inside the ATI
graphics driver code while drawing a vertex array. You might try doing
this as a means of avoiding this problem (tcsh syntax):
  setenv VMDSIMPLEGRAPHICS 1

Try doing that and re-run VMD and see if it still crashes in the same
place. If so, I may have another suggestion for you.

  John

On Fri, Sep 23, 2005 at 03:03:03PM -0500, Praedor Atrebates wrote:
> On Friday 23 September 2005 14:36, John Stone wrote:
> > Hi,
> > Your output doesn't include the 'where' command, I need that in
> > order to determine what happened. Also, if you're getting those
> > Tcl warnings at startup, you must not have sourced the VMD startup
> > script correctly according to the sequence of commands I gave you
> > previously, can you try this again?
> [...]
>
> Corrected the tcl problem and re-ran:
>
> gdb output:
>
> Info) VMD for LINUX, version 1.8.3 (February 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: MOBILITY RADEON 9000 DDR Generic
> Info) Features: STENCIL RN MDE CVA MTX PP
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), 3-D (512x512x512), Multitexture (6)
> vmd > Info) Using plugin pdb for structure
> file /home/praedor/Documents/structu
> res/TFA-1-dnakmodel.pdb
> Info) Using plugin pdb for coordinates from
> file /home/praedor/Documents/struct
> ures/TFA-1-dnakmodel.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 1526
> Info) Residues: 194
> Info) Waters: 0
> Warning) Unusual bond between residues 144 and 145
> Warning) Unusual bond between residues 145 and 146
> Info) Segments: 1
> Info) Fragments: 1 Protein: 4 Nucleic: 0
> Info) Finished with coordinate
> file /home/praedor/Documents/structures/TFA-1-dn
> akmodel.pdb.
>
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread -1214478048 (LWP 23715)]
> 0xb74e8133 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> (gdb) where
> #0 0xb74e8133 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #1 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #2 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #3 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #4 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #5 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #6 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #7 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #8 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #9 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #10 0xb74e7999 in __glim_R200TCLDrawArrays ()
> from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #11 0xb74e7999 in __glim_R200TCLDrawArrays ()
>
> praedor
> --
> "The enumeration in the Constitution, of certain rights, shall not be
> construed to deny or disparage others retained by the people."
> --9th Amendment to the Constitution 

-- 
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