VMD-L Mailing List

From: Rob (spamrefuse_at_yahoo.com)
Date: Tue Dec 08 2009 - 01:03:29 CST

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.