VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 18 2005 - 11:03:36 CDT

Hi,
  Yeah, this looks like the ATI driver is either blowing the stack or
doing something else that ends with an out-of-bounds memory access.
What happens if you try running VMD like this instead:
  setenv VMD_EXCL_GL_EXTENSIONS GL_ARB_shader_objects
  vmd

Do you still get the crash, or does that allow VMD to run ok?

  John

On Tue, May 17, 2005 at 09:19:07PM +0200, Gyimesi Gergely wrote:
> Helo,
>
> I tried it, got the following result.
> I'll paste here the whole output for completeness.
>
> Starting program: /usr/local/lib/vmd/vmd_LINUX
> [Thread debugging using libthread_db enabled]
> [New Thread -1216734336 (LWP 11171)]
> Info) VMD for LINUX, version 1.8.3 (May 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: RADEON 8500 DDR Generic
> Info) Features: STENCIL RN MDE CVA MTX PP
> Info) Textures: 2-D (2048x2048), 3-D (512x512x512), Multitexture (6)
> [New Thread -1308972112 (LWP 11174)]
> vmd > Info) Using plugin pdb for structure file /home/mrmaim/downloads/1TBF.pdb
> Info) Using plugin pdb for coordinates from file /home/mrmaim/downloads/1TBF.pdb
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 3021
> Info) Residues: 653
> Info) Waters: 323
> Info) Segments: 1
> Info) Fragments: 328 Protein: 1 Nucleic: 0
> Info) Finished with coordinate file /home/mrmaim/downloads/1TBF.pdb.
>
> Program received signal SIGSEGV, Segmentation fault.
> [Switching to Thread -1216734336 (LWP 11171)]
> 0xb72c1093 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> (gdb) where
> #0 0xb72c1093 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> #1 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> #2 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> #3 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> :
> :
> #1523 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> #1524 0xb72c08f9 in s9424 () from /usr/X11R6/lib/modules/dri/fglrx_dri.so
> ---Type <return> to continue, or q <return> to quit---q
> Quit
> (gdb)
>
> That last line seems to keep repeating forever..
> I hope this helps, shouldn't I have compiled in some kind of support for
> debugging, eg. symbols, etc. ?
> If there's anything else I can help in, just tell me.
>
> bye,
> Greg
>
> On Mon, 16 May 2005 19:51:04 -0500, John Stone wrote
> > Hi,
> > Can you try doing the following steps for me, and let me know what
> > results you get?
> > start an xterm, then in that xterm do:
> > /bin/csh (use csh so the other commands I list
> > will work) source /usr/local/bin/vmd (use the startup script's env
> > vars)
> > (then immediately quit that VMD) gdb /usr/local/lib/vmd/vmd_LINUX
> > (then issue these commands to gdb) run
> > (then load a structure that normally crashes your VMD)
> > (... then try to crash it) where (this shows where VMD was
> > when the crash occured)
> >
> > If you can email the output to me, I should be able to determine if
> > this is another ATI driver problem, or something else.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, May 15, 2005 at 05:16:08PM +0200, Gyimesi Gergely wrote:
> > > Helo,
> > >
> > > Just for your info: I'm having the same problem, with the fglrx-8.10.19 and
> > > fglrx-8.12.10 drivers also, with a Radeon 8500 card. I've tried setting
> > > VMDSIMPLEGRAPHICS, but it didn't help.. The segfault only happens when
> > > loading large molecules (eg. proteins), it works OK for smaller ones. It
> also
> > > works OK in text mode.
> > > Looking forward to anything you can do, after May 20. :-)
> > >
> > > Gergely Gyimesi
> > > Ph.D student
> > > Institute of Enzymology,
> > > Hungarian Academy of Sciences
> > >
> > > >Hi,
> > > > Try setting this environment variable before starting VMD, it will
> > > >disable all of the advanced OpenGL features that VMD uses, in favor of
> > > >a more minimalistic and simpler OpenGL 1.1-based functionality:
> > > > setenv VMDSIMPLEGRAPHICS 1
> > > >
> > > >Let me know if this gets you up and running.
> > > >
> > > > John Stone
> > > > vmd_at_ks.uiuc.edu
> > > >
> > > >
> > > >
> > > >>Is there any way to work around the fglrx-8.10.19 driver crash? I've
> > > >>seen the posts and bug report but would prefer not to downgrade my
> > > >>driver. Is there any way to use MESA or some other software rendering
> > > >>instead?
> > > >>
> > > >>
> > > >
> > > >
> > > >
> >
> > --
> > 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