VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 27 2001 - 15:04:55 CST

Brian,
  I took a look at your core file and it appears that your
VMD binary is dying in a simple call to XOpenDisplay(). VMD
passes in the value of the "DISPLAY" or "VMDGDISPLAY" environment
variables depending on what they are set to. What did you have
your DISPLAY variable set to when you ran this binary? If it is
NULL, it is possible that you have a buggy X library that doesn't
do any consistency checking of its own, causing the seg fault.
By and large though, I wouldn't expect _any_ X application to run
without the DISPLAY variable set. (VMD won't even get as far as
starting up since the xterm console will fail to startup).
My suggestion is to examine your X server installation, as we
haven't had that problem before. Out of curiosity, what happens
when you run one of the VMD binaries that we distribute?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 26, 2001 at 12:32:53PM -0600, John Stone wrote:
> Brian,
> Can you send me a copy of your vmd_LINUX binary and the core file? I can
> probably figure out what's going on if I have those items.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Nov 26, 2001 at 10:23:49AM -0800, B. Bennion wrote:
> > hello,
> >
> > I remembered the problem with pcre.c The config script is a little
> > backwards. It adds prce if the python option is not set, but doesn't add
> > it when python is wanted.
> >
> > Anyway, other problems.
> >
> >
> > Which opengl libraries where used in the creation of vmd 1.7.1? Do I need
> > to get newer ones?
> >
> >
> > I am compiling for linux RH7.1 with the OPENGL option. Things compile
> > fine.
> > When I run I get a segmentation fault. The core points to:
> >
> > #5 0x0808a637 in OpenGLDisplayDevice::open_window () at eval.c:41
> >
> >
> > The lib files are shown below:
> >
> > Core was generated by `vmd_LINUX'.
> > Program terminated with signal 11, Segmentation fault.
> > Reading symbols from /usr/lib/libz.so.1...done.
> > Loaded symbols for /usr/lib/libz.so.1
> > Reading symbols from /usr/lib/libGL.so.1...done.
> > Loaded symbols for /usr/lib/libGL.so.1
> > Reading symbols from /usr/lib/libGLU.so.1...done.
> > Loaded symbols for /usr/lib/libGLU.so.1
> > Reading symbols from /usr/X11R6/lib/libXext.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libXext.so.6
> > Reading symbols from /usr/X11R6/lib/libX11.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libX11.so.6
> > Reading symbols from /usr/lib/libtk.so...done.
> > Loaded symbols for /usr/lib/libtk.so
> > Reading symbols from /usr/lib/libtcl.so...done.
> > Loaded symbols for /usr/lib/libtcl.so
> > Reading symbols from /lib/libdl.so.2...done.
> > Loaded symbols for /lib/libdl.so.2
> > Reading symbols from /lib/libutil.so.1...done.
> > Loaded symbols for /lib/libutil.so.1
> > Reading symbols from /usr/lib/libstdc++-libc6.2-2.so.3...done.
> > Loaded symbols for /usr/lib/libstdc++-libc6.2-2.so.3
> > Reading symbols from /lib/i686/libm.so.6...done.
> > Loaded symbols for /lib/i686/libm.so.6
> > Reading symbols from /lib/i686/libc.so.6...done.
> > Loaded symbols for /lib/i686/libc.so.6
> > Reading symbols from /usr/X11R6/lib/libSM.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libSM.so.6
> > Reading symbols from /usr/X11R6/lib/libICE.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libICE.so.6
> > Reading symbols from /usr/X11R6/lib/libXmu.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libXmu.so.6
> > Reading symbols from /usr/X11R6/lib/libXi.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libXi.so.6
> > Reading symbols from /lib/ld-linux.so.2...done.
> > Loaded symbols for /lib/ld-linux.so.2
> > Reading symbols from /usr/X11R6/lib/libXt.so.6...done.
> > Loaded symbols for /usr/X11R6/lib/libXt.so.6
> >
> >
> >
> > Brian
> >
> >
> >
> > Graduate Research Assistant
> > Dep. Medicinal Chemistry, University of Washington
> > Tel# (206)616-2779
> > BOX 357610 Seattle WA 98195
> >
> > email--bbennion_at_u.washington.edu
> > web page--http://students.washington.edu/bbennion
>
> --
> 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 

-- 
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