VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 28 2009 - 16:34:18 CDT

Hi,
  That looks like the result of corrupted DMA transfers containing
the triangle meshes generated by VMD. This kind of thing is exceedingly
rare, and normally only occurs if:
  a) You have a bad or overloaded power supply (causing GPU "brown out")
  b) You have a failing or overheating GPU
  c) You have a serious kernel bug (not likely)
  d) You have a buggy GPU driver

We've had this occur before, but in our case it has only ever
happened on GPUs that were beginning to fail. Others have encountered
this kind of problem caused by the other scenarios I listed.

You should open up your computer and blow any accumulated dust off of
the GPU, as these kinds of things are frequently the result of overheating.
This can be easily remedied by cleaning out the dust, and making
sure the GPU fan is functioning correctly. Give that a shot and
let us know what you find.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Sep 28, 2009 at 05:22:36PM -0400, Ahmet Bakan wrote:
> Hi All,
>
> I am having a problem with VMD representations for a while now. I checked
> the VMD-l archive, but couldn't find a similar posting.
> I have uploaded some pictures to show the problem:
>
> http://a.imagehost.org/0126/cartoon.jpg
> http://a.imagehost.org/0084/cartoon2.jpg
> http://a.imagehost.org/0989/msms.jpg
> http://a.imagehost.org/0895/msms2.jpg
>
> I have this problem particularly with NewCartoon and MSMS representations.
> I had the same problem with VMD versions older than 1.8.7.
> I currently use 64bit Ubuntu 9.04. Previously, I used OpenSUSE 10.3, and
> still had the problem.
> My graphics card is NVIDIA 7900 GTX. I always install the latest drivers
> from NVIDIA site, and compile them for the kernel that I have.
>
> For the MSMS example that I show above:
> When only the molecule with MSMS representation is displayed, I
> rotate/scale/translate the view with no problems.
> When another molecule with cartoon representation is also displayed, gives
> that weird representation problem.
>
> This is not the general trend though. In the cartoon example, I have the
> problem always.
> This problem comes up usually after I load a couple of molecules and play
> around for a while, but it also sometimes come up at the very beginning of
> a session. In MSMS exmaple, I loaded the two molecules using a TCL script,
> and generated all representations automatically. As soon as I rotate, the
> representations are distorted.
>
> Below is what VMD outputs, when I run it. Please also note that I have the
> same problem when I turn of the X11 Composite extension.
>
> Does this information help anyone to figure out what is wrong with my
> system/configuration? Thanks in advance for any suggestions.
> Best wishes,
> Ahmet
>
> 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, 4 CPUs detected.
> Info) Free system memory: 6900MB (87%)
> 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: GeForce 7900 GTX/PCI/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4) 

-- 
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