VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Aug 01 2013 - 16:52:19 CDT

Hi Hailin,

Segmentation faults happen when the program tries to access memory that
it did not ask for from the operating system, often when the program
doesn't know where to find something and defaults to looking at null
(which is usually not owned by the program and thus causes a segfault).
If I were to have a guess, I'd say that a required library for VMD or
one of its plugins is missing/not locateable, and so it segfaults when
it tries to load the library.

The way you can check is the ldd command, which will check if a program
or library can find the libraries it needs. For instance, if I run ldd
on the psfplugin, I see that all the needed libraries can be found:

ldd psfplugin.so
    linux-vdso.so.1 => (0x00007fffe79ff000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b79df3cb000)
    /lib64/ld-linux-x86-64.so.2 (0x00002b79df1a6000)

In replacing your hard drive, you may have inadvertently (re)moved a
library, and thus it causes a segfault. Based on your output, I'd make
sure you have all the libraries for VMD
(/home/richard/vmd-1.9.1/lib/vmd/vmd_LINUXAMD64), and the loaded
libraries: (/home/richard/vmd-1.9.1/lib/vmd/plugins/LINUXAMD64/molfile).

Good luck!
-Josh Vermaas

On 08/01/2013 03:03 PM, Hailin Huang wrote:
> 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
> <mailto: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
> <mailto: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