VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Nov 26 2013 - 18:42:09 CST

Hi Robert,

Based on when the segfault is occurring, and the general list of things
that break on an upgrade, it might just be a version mismatch caused by
conflicting versions of the nvidia driver package. This happens to me
when nvidia-current gets upgraded, as it will pick up the new driver,
but won't get rid of the old ones. One thing I would check is the result
of ldd vmd_LINUXAMD64 in /usr/local/lib. On my system, which uses
version 319.37, this is what a fraction of it looks like:
libGL.so.1 => /usr/lib/nvidia-current/libGL.so.1 (0x00002b4635b53000)
     libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1
(0x00002b4635e82000)
     libcudart.so.4 => not found
     libnvidia-tls.so.319.37 =>
/usr/lib/nvidia-current/tls/libnvidia-tls.so.319.37 (0x00002b4637a31000)
     libnvidia-glcore.so.319.37 =>
/usr/lib/nvidia-current/libnvidia-glcore.so.319.37 (0x00002b4637c34000)
Libcudart isn't actually needed unless you need one of the commands that
uses GPU acceleration, but the other 4 had better resolve, and should
all resolve to libraries corresponding to the right version (in my case
319.37). Manually removing old installed versions of the nvidia drivers
is how I tend to fix these problems when they come up.

In terms of the rlwrap "fun" you've been having, I know this seems like
a stupid thing to do, but unless you need rlwrap for something else, the
stock VMD distribution actually works better without rlwrap installed,
as then the script just complains about a missing rlwrap command rather
than a malformatted command that causes an exit and will load vmd. In
using this approach, it doesn't look like anything obvious is broken.

-Josh Vermaas

On 11/26/13, 4:15 PM, 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
>