VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 01 2005 - 15:45:26 CST

Hi,
  This is a familiar problem with the ATI Linux video drivers.
Please try the newest test version of VMD and let me know if it
runs better for you. This version contains special code that
avoids problems witht he ATI Linux video drivers:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 29, 2005 at 01:25:57PM +0100, Martin Grana wrote:
> Hi all,
>
> I've just installed vmd-1.83 on a laptop with Centos 4.2 as Linux
> distro. (Vmd 1.83 runs smooth and nicely on 'my' Debian sarge.)
>
> This problem was posted on 23th september, so I've ran gdb as
> recommended that time. I've corrected tcl locations in the "configure"
> file, reconfigured (LINUX OPENGL TK TCL options), and installed
> again; problem persists. Next, gdb output for "run" and "where":
>
> #####################################
>
> (gdb) run
> Starting program: /usr/i386/lib/vmd/vmd_LINUX
> [Thread debugging using libthread_db enabled]
> [New Thread 2250080 (LWP 6945)]
> 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: FireMV 2400 PCI 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/ubs/martin/virgile/mgrana/pdbs/1G60.pdb
> Info) Using plugin pdb for coordinates from file
> /home/ubs/martin/virgile/mgrana/pdbs/1G60.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 4305
> Info) Residues: 831
> Info) Waters: 361
> Info) Segments: 1
> Info) Fragments: 370 Protein: 7 Nucleic: 0
> Info) Finished with coordinate file
> /home/ubs/martin/virgile/mgrana/pdbs/1G60.pdb.
>
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread 2250080 (LWP 6945)]
> 0x011a20e3 in s9426 () from
> /usr/X11R6/lib/modules/dri//atiogl_a_dri.so
>
> (gdb) where
> #0 0x011a20e3 in s9426 () from
> /usr/X11R6/lib/modules/dri//atiogl_a_dri.so
> #1 0x011a1949 in s9426 () from
> /usr/X11R6/lib/modules/dri//atiogl_a_dri.so
> #2 0x011a1949 in s9426 () from
> /usr/X11R6/lib/modules/dri//atiogl_a_dri.so
> #3 0x011a1949 in s9426 () from
> /usr/X11R6/lib/modules/dri//atiogl_a_dri.so
> ...
> ...
> ... (the same line ad infinitum)
> #####################################
>
> By the way, I don't understand this "//". Is this *all* the error? if
> yes, where should I tell vmd to look at the correct location,
> "/usr/X11R6/lib/modules/dri/atiogl_a_dri.so"?
>
> Many thanks in advance for your time and help.
>
> with the best,
> Martin Grana 

-- 
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