From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 14 2009 - 14:08:35 CDT

Hi,
  This is almost certainly a failure of your Intel OpenGL driver,
and many others have encountered similar issues with those chipsets/drivers.
You have a few options:
  1) report the bug to Intel in hopes of getting a fixed driver
  2) try installing a newer/different Intel graphics driver
  3) try running with the environment variable VMDSIMPLEGRAPHICS set to 1
  4) buy/install a different brand of GPU that has better Linux driver support

You'll see from searching VMD-L that the issues with the Intel chipsets
(especially these older ones) and their Linux drivers have existed for quite
a long time now. I always advise people to follow option 1) first, as
the bugs won't get fixed unless people tell Intel about them. It's also
good that Intel realizes that they are losing sales to other vendors when,
after following the remaining steps, users end up ultimately going with
option 4) and subsequently avoid Intel's graphics products from then on.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Sep 13, 2009 at 05:16:28PM -0700, Rob wrote:
>
> Hi,
>
> I have installed the recent VMD binaries for linux:
> "VMD for LINUX, version 1.8.7 (August 1, 2009)"
>
> When I type the vmd command (located at /usr/local/bin/vmd),
> I get following output in my terminal:
>
> ============================
> $ vmd
> Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
> 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: 1549MB (77%)
> Info) No CUDA accelerator devices available.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: Mesa DRI Intel(R) 965G GEM 20090114 x86/MMX/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> Segmentation fault
> $
> ==================================
>
> Meanwhile, the OpenGL window has come up for just a second, before
> the segmentation fault occurs, and then that window collapses.
>
> In /var/log/messages, I get this line:
>
> kernel: vmd_LINUX[1316]: segfault at 4 ip 00157eef sp bfd7d4b0 error 4 in libX11.so.6.2.0[110000+12b000]
>
> When I do a strace of vmd, the following text appears when the
> segmentation fault occurs:
>
> =====================================
> ...
> Info) OpenGL renderer: Mesa DRI Intel(R) 965G GEM 20090114 x86/MMX/SSE2
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
> ) = ? ERESTARTNOHAND (To be restarted)
> --- SIGCHLD (Child exited) @ 0 (0) ---
> sigreturn() = ? (mask now [INT CHLD])
> wait4(-1, [{WIFSIGNALED(s) && WTERMSIG(s) == SIGSEGV}], WNOHANG, {ru_utime={0, 977851}, ru_stime={0, 111982}, ru_maxrss=0, ru_ixrss=0, ru_idrss=0, ru_isrss=0, ru_minflt=21923, ru_majflt=0, ru_nswap=0, ru_inblock=0, ru_oublock=0, ru_msgsnd=0, ru_msgrcv=0, ru_nsignals=0, ru_nvcsw=380, ru_nivcsw=137}) = 1728
> wait4(-1, 0xbfd357cc, WNOHANG, 0xbfd35784) = -1 ECHILD (No child processes)
> rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
> write(17, "Segmentation fault\n"..., 19Segmentation fault
> ) = 19
> ...
> ====================================
>
> Any idea what is the problem here?
>
> Is this a problem with vmd, or have I updated to a buggy X library from X.org?
>
> Thanks,
> Rob.
>
>
>

-- 
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