VMD-L Mailing List

From: Rob (spamrefuse_at_yahoo.com)
Date: Sun Sep 13 2009 - 19:16:28 CDT

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.