From: Ahmet Bakan (lordnapi_at_gmail.com)
Date: Thu Oct 15 2009 - 12:16:26 CDT

Hi John,

I had a chance to try another GPU, Nvidia 8800 GFX. It works just fine, not
problems with cartoon representation.
I was also looking for troubleshooting for this problem on the web. On
mostly gaming forums, I saw that people have the same problem with 7900 GFX,
but no solutions. I probably will get a newer GPU.
Thanks for the advice.

Best,
Ahmet

On Tue, Sep 29, 2009 at 6:38 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
>