VMD-L Mailing List

From: Martin Grana (mgrana_at_pasteur.fr)
Date: Tue Nov 29 2005 - 06:25:57 CST

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