VMD-L Mailing List

From: Ahmet Bakan (lordnapi_at_gmail.com)
Date: Tue Sep 29 2009 - 09:42:41 CDT

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