VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 07 2006 - 11:32:52 CDT

Yuan,
  Yup, this is a problem with the ATI drivers. Try doing this before
you run VMD, then re-test:
  setenv VMDSIMPLEGRAPHICS 1

It looks like the driver you're using doesn't have the ATI vendor name
in the strings that VMD searches when it enables the ATI "safe mode" that
prevents VMD from triggering some known driver bugs. The environment
variable above should help workaround that. If not, I have another couple
of environment variable settings that will lock-out the features that
crash the ATI video driver, if necessary.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 07, 2006 at 12:24:59PM -0400, Yuan Zhang wrote:
> Hi John,
>
> Thanks for your email.
> Here is the output from "where":
> ------------------------------
> (gdb) where
> #0 0x013465fe in s6644 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #1 0x01420f05 in s5064 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #2 0x01347ea2 in s4068 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #3 0x01341e91 in s9918 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #4 0x00f9a784 in s9138 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #5 0x0103dc6c in s9468 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> #6 0x080d13e5 in OpenGLShader::CompileShaders ()
> #7 0x080d1139 in OpenGLShader::LoadShader ()
> #8 0x080cbc68 in OpenGLRenderer::setup_initial_opengl_state ()
> #9 0x080c96f9 in OpenGLDisplayDevice::open_window ()
> #10 0x080c90d0 in OpenGLDisplayDevice::init ()
> #11 0x08165568 in VMDApp::VMDinit ()
> #12 0x0817c4b2 in main ()
> (gdb)
> ------------------------------
>
>
> I don't know about graphics drivers. But I didn't install any by myself.
> I have attached the output from glxinfo for you to look at.
>
> Thanks!
>
> Yuan
>
>
>
>
> On Wed, 2006-06-07 at 11:02 -0500, John Stone wrote:
> > Hi,
> > Based on the output you got from GDB and the VMD startup messages, I'm
> > guessing that this is a problem with your graphics driver, since it is
> > dying early in the startup phase. Can you email me the "where" output
> > in GDB as mentioned in the release notes? That will tell me exactly
> > where VMD was when the problem occurs. I think there's a 99% chance it's
> > being caused by the driver for your ATI Mobility T2 graphics chipset,
> > but getting the "where" output will be helpful in being sure. Is this
> > the ATI fglrx driver, or are you running one of the free drivers?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Jun 07, 2006 at 11:27:51AM -0400, Yuan Zhang wrote:
> > > Hi,
> > >
> > > I am trying to install VMD on my Linux box. I have problem opening a
> > > graphic interface. I followed the instruction on
> > > http://www.ks.uiuc.edu/Research/vmd/current/linuxrelnotes.html and here
> > > is the output from the debugger:
> > >
> > > -----------
> > > [yzhang_at_localhost ~]$ local/biosoftw/bin/vmd -debug
> > > ***
> > > *** Running VMD in debugger, type 'run' at debugger prompt
> > > ***
> > > GNU gdb Red Hat Linux (6.1post-1.20040607.43rh)
> > > Copyright 2004 Free Software Foundation, Inc.
> > > GDB is free software, covered by the GNU General Public License, and you
> > > are
> > > welcome to change it and/or distribute copies of it under certain
> > > conditions.
> > > Type "show copying" to see the conditions.
> > > There is absolutely no warranty for GDB. Type "show warranty" for
> > > details.
> > > This GDB was configured as "i386-redhat-linux-gnu"...(no debugging
> > > symbols found)...Using host libthread_db library
> > > "/lib/tls/libthread_db.so.1".
> > >
> > > (gdb) run
> > > Starting program: /home/yzhang/local/biosoftw/lib/vmd/vmd_LINUX
> > > [Thread debugging using libthread_db enabled]
> > > [New Thread 2770624 (LWP 4771)]
> > > Info) VMD for LINUX, version 1.8.4 (April 17, 2006)
> > > 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: MOBILITY FIREGL T2 Pentium 4 (SSE2) (FireGL)
> > > (GNU_ICD)
> > > Info) Features: STENCIL RN MDE CVA MTX PP PS GLSL(OVF)
> > >
> > > Program received signal SIGSEGV, Segmentation fault.
> > > [Switching to Thread 2770624 (LWP 4771)]
> > > 0x012525fe in s6644 () from /usr/X11R6/lib/modules/dri//fglrx_dri.so
> > > (gdb) q
> > > The program is running. Exit anyway? (y or n) y
> > > ----------------
> > >
> > >
> > > Can anyone tell me how do I proceed?
> > >
> > > Thanks!
> > > Yuan
> > 

-- 
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