VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 29 2009 - 17:38:21 CDT

Ahmet,
  Do you have another GPU you can put into this system for testing?
If you swap out the GPU that's in there now for another one, (even
the same model) I wouldn't be surprised if the problem goes away.
Given your descriptions below, it seems that it should be pretty
easy to reproduce the problem with a different GPU if it's something
other than the particular GPU in your machine. I'd see if you can
borrow one from another machine for an hour so you can figure out
what's going on there.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 29, 2009 at 10:42:41AM -0400, Ahmet Bakan wrote:
> Hi John,
> I tried, but no changes. Is there anything else I could try?
> Thanks,
> Ahmet
>
> On Mon, Sep 28, 2009 at 5:34 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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 

-- 
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