VMD-L Mailing List

From: Hailin Huang (hailin.huang_at_my.liu.edu)
Date: Thu Aug 01 2013 - 15:03:59 CDT

Dear VMD users,

I came across a VMD crash yesterday and I couldn't fix the problem. It
happened after I installed a new HardDrive to my system:
CentOS 6.4
Kernel Linux 2.6.32-358.14.1.el6.x86_64
GNOME 2.28.2

After the new HardDrive was installed, first attempt to run VMD gave the
following:

$ vmd
csh: No such file or directory
csh: Trying to start from "/home/richard"
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
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: 10449MB (87%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 2 available CUDA accelerators:
Info) [0] GeForce GTX 560 Ti 14 SM_2.0 @ 1.50 GHz, 1.2GB RAM, KTO, OIO, ZCP
Info) [1] GeForce 8400 GS 1 SM_1.1 @ 1.40 GHz, 255MB RAM, ZCP
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce GTX 560 Ti/PCIe/SSE2
Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
Info) Dynamically loaded 2 plugins in directory:
Info) /home/richard/vmd-1.9.1/lib/vmd/plugins/LINUXAMD64/molfile
Segmentation fault (core dumped)

Then I re-installed vmd-1.9.1.bin.LINUXAMD64.opengl.tar.gz, same thing
happened:

$ vmd
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
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: 10295MB (86%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 2 available CUDA accelerators:
Info) [0] GeForce GTX 560 Ti 14 SM_2.0 @ 1.50 GHz, 1.2GB RAM, KTO, OIO, ZCP
Info) [1] GeForce 8400 GS 1 SM_1.1 @ 1.40 GHz, 255MB RAM, ZCP
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce GTX 560 Ti/PCIe/SSE2
Info) Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
Info) Dynamically loaded 2 plugins in directory:
Info) /home/richard/vmd-1.9.1/lib/vmd/plugins/LINUXAMD64/molfile
Segmentation fault (core dumped)

Does anyone know what this segmentation fault means? Any help would be
greatly appreciated.

Best,
Richard