VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 08 2009 - 01:17:25 CST

Rob,
  No, it's not VMD. The source of your problem is as I described previously.
You will note that your previous note showed that the crash was occuring
in the X11 driver, not in VMD itself...

Your system has a (buggy) non-accelerated software-based video driver,
and the solution to your problem is to replace it with a real hardware
OpenGL driver. Going further, it is a pitiful waste for you to be
using a software OpenGL rasterizer when you actually already have a
real GPU in your machine! Trust me, you want to install the
proper NVIDIA drivers... You should also heed the warning about
disabling the composite extension on your machine, as it is
famously buggy and has been known to cause problems by itself
irrespective of what video driver is in use.

Cheers,
  John

On Mon, Dec 07, 2009 at 11:03:29PM -0800, Rob wrote:
> Hi,
> As a comment to my earlier problem report below with 1.8.7:
> meanwhile I have installed 1.8.6 and this does not crash!
> Apparently some "improvements" to 1.8.7 made it less
> robust on my Fedora 64 bits Linux system, leading up to
> a 'segmentation fault'.
>
> Would this indicate that something is wrong with VMD and
> not with X11?
>
> If more information is needed to find out what VMD 1.8.7 is
> doing wrong, then please tell me what to do, and I will try
> to help provide this information.
>
> Rob.
>
>
>
> ----- Original Message ----
> From: Rob <spamrefuse_at_yahoo.com>
> To: vmd <vmd-l_at_ks.uiuc.edu>
> Sent: Tue, December 8, 2009 12:25:11 PM
> Subject: vmd 1.8.7 on Intel 64 bit: segmentation fault
>
>
> Hi,
>
> I have Fedora 12 X86_64 64 bits Linux and I installed
> vmd-1.8.7.bin.LINUXAMD64.opengl.tar.gz.
>
> When I start vmd, I get this:
>
> Info) VMD for LINUXAMD64, 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, 8 CPUs detected.
> Info) Free system memory: 5145MB (86%)
> 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: Software Rasterizer
> 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
>
>
> In my /var/log/messages I then get this line:
>
> kernel: vmd_LINUXAMD64[8493]: segfault at 8 ip 0000003278c528b6
> sp 00007fffe05d1b00 error 4 in libX11.so.6.3.0[3278c00000+139000]
>
>
> My graphics card is: nVidia Corporation GeForce 8600 GTS (rev a1)
>
> Any idea what's the problem here?
>
> Is it a bug in VMD, in Xorg, or in other parts of my Linux 64 bits?
>
> Is there a way to work around this using the configure.options when installing vmd?
>
> Thank you!
>
> 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