VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 10 2012 - 11:40:11 CST

Hi,
  Are you using an international input manager such as SCIM?
The point at which your crash is occuring indicate to me
that you may possibly be having trouble with Tk and an input manager.
If you have an international input manager enabled, try turning it off.
There's a known flaw with Tcl/Tk and international input that affects
versions of VMD built with the latest versions of Tcl/Tk. You can avoid
this problem by disabling SCIM (or any other internationalized input manager).

The CUDA errors you're seeing are because you are running a CUDA 4.0
binary of VMD on a Kepler (GeForce 680) GPU, but they are not the
reason for your crash. To get around those CUDA errors, please
download one of the latest test versions of VMD 1.9.2, which is compiled
so as to support the latest Kepler GPUs. Alternately, if you want to
compile VMD 1.9.1 from source code, you can do so, and I can give you
a small change to make to the CUDA flags to allow it to run without errors
on your GeForce 680 cards, even if you compile with CUDA 4.0.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Dec 10, 2012 at 04:19:55PM +0100, Tru Huynh wrote:
> On Mon, Dec 10, 2012 at 04:14:43PM +0100, Tru Huynh wrote:
> > Hi,
> >
> > vmd just crash after starting with:
> > [tru_at_yippy ~]$ vmd
>
> I have downgraded the nvidia driver to 295.71, not better:
>
> [tru_at_yippy 295.71]$ cat /proc/driver/nvidia/version
> NVRM version: NVIDIA UNIX x86_64 Kernel Module 295.71 Thu Aug 2 19:22:08 PDT 2012
> GCC version: gcc version 4.1.2 20080704 (Red Hat 4.1.2-52)
>
> vmd 1.9.1 segfault:
> [tru_at_yippy ~]$ 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, 16 CPUs detected.
> Info) Free system memory: 128441MB (99%)
> Info) Creating CUDA device pool and initializing hardware...
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> CUDA error: invalid device symbol, CUDAClearDevice.cu line 62
> Info) Detected 4 available CUDA accelerators:
> Info) [0] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4.0GB RAM, OIO, ZCP
> Info) [1] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4.0GB RAM, OIO, ZCP
> Info) [2] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4.0GB RAM, OIO, ZCP
> Info) [3] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4.0GB RAM, OIO, ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: GeForce 210/PCI/SSE2
> Info) Features: STENCIL MSAA(4) MDE MTX NPOT PP PS GLSL(OVFG)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Segmentation fault
>
>
> vmd-1.8.7 works:
> [tru_at_yippy ~]$ vmd
> 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, 16 CPUs detected.
> Info) Free system memory: 128443MB (99%)
> Info) Detected 4 available CUDA accelerators:
> Info) [0] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4095MB RAM, OIO, ZCP
> Info) [1] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4095MB RAM, OIO, ZCP
> Info) [2] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4095MB RAM, OIO, ZCP
> Info) [3] GeForce GTX 680 8 SM_3.0 @ 0.71 GHz, 4095MB RAM, OIO, ZCP
> Info) Creating CUDA device pool and initializing hardware...
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
> Info) OpenGL renderer: GeForce 210/PCI/SSE2
> Info) Features: STENCIL MSAA(4) MDE MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> vmd > Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
>
> Tru
>
> --
> Dr Tru Huynh | http://www.pasteur.fr/recherche/unites/Binfs/
> mailto:tru_at_pasteur.fr | tel/fax +33 1 45 68 87 37/19
> Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078