From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 26 2013 - 17:03:22 CST

Hi,
  Try running vmd with "vmd -debug" and see if you can get
gdb to tell you where your problem is occuring. In gdb you
would type "run" and then when the crash occurs, you'd type "where".

My guess is that your video driver upgrade is the culprit based
on the point at which the segfault occurs during startup.

Are you able to run any other CUDA or OpenGL programs on this machine?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 26, 2013 at 05:15:53PM -0500, Robert Wohlhueter wrote:
> Using Ubuntu 13.10 on an AMD64 computer with NVIDIA GTX275 and NVIDIA
> driver 319.32:
> vmd-1.9.1 binary distribution is broken. The same binary on same the
> hardware (with NVIDIA 304 driver)
> under Ubuntu 12.10 worked fine.
>
> Using the original installed vmd.csh script, startup seems to hang because
> of inability to set
> rlwrap (though in fact the file "vmd_completion.dat" is present):
>
> ############################################################################
> bobw_at_winter-linux: ...lib/vmd [56]> /usr/local/bin/vmd
> /usr/local/bin/vmd.wrap
> rlwrap: No match.
> ############################################################################
>
> If I comment out the lines relevant to loading vmd_completion.dat, then
> run the script, the "rlwrap"-error is avoided, but I get no output at all:
>
> ###########################################################################
> obw_at_winter-linux: ...lib/vmd [59]> /usr/local/bin/vmd.nowrap
> /usr/local/bin/vmd
> bobw_at_winter-linux: ...lib/vmd [60]>
> ###########################################################################
>
> But these are probably minor problems. If I by pass the script entirely
> (but with VMDDIR and
> MASTERVMDDIR envvars set manually), I get a little further, before dumping
> core:
>
> ############################################################################
> bobw_at_winter-linux: ...vmd/vmd-1.9.1 [60]>./vmd_LINUXAMD64
> ./vmd_LINUXAMD64
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> 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, 4 CPUs detected.
> Info) Free system memory: 6482MB (81%)
> Segmentation fault (core dumped)
> ###########################################################################
>
> I would guess the problem lies not with Ubuntu 13.10 per se, but with the
> change in video driver between 12.10 and 13.10. I'm reluctant to muck
> around
> with video drivers, in particular to try to revert to NVIDIA 304.x, since
> this
> always breaks a lot of programs. Still my hardward/video driver must be
> fairly commomplace.
>
> Anyone have clues to what's wrong? I'm grateful for any pointers.
>
> Bob Wohlhueter

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/