VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 27 2009 - 11:56:00 CST

Ramon,
  Thanks for updating us on your problem/solution. This will be
helpful for others that may encounter this problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 27, 2009 at 06:35:15PM +0100, Ramon Crehuet wrote:
> Thanks to all who suggested solutions to my problem. I could finally
> solve it by disabling "desktop effects" in kde 4. In opensuse 11.1 one
> goes to the menu, "configure desktop" then, "desktop" then "desktop
> effects". Unfortunately I have also lost the cube and the transparent
> windows...
> I did not check the option of changing xorg.conf but it probably would
> also have worked. However this way I did not have to restart the X
> server (and I can get the transparent windows with some clicks when not
> using vmd)
> Apparently the problem stems from DRI and xorg, not the card driver or
> the opengl implementation. This is what I have read in other forums.
> Cheers,
> Ramon
>
>
> Dan Wright wrote:
> > I have seen similar problems with OpenGL apps (including but not
> > limited to VMD, and not specific to ATI boards) when using the X
> > server's compositing and rendering extensions to do fancy window
> > effects on Linux. You could try turning that stuff off and see if it
> > fixes the problem. Unfortunately, I don't use OpenSUSE and can't tell
> > you how to do it on that distribution.
> >
> > On Tue, Jan 20, 2009 at 10:36 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >> Ramon,
> >> VMD is already executing with "VMDSIMPLEGRAPHICS" mode, as it detected
> >> your ATI driver and reduced functionality to a "safe subset".
> >> The ATI drivers have had a long history of stability issues on
> >> Linux, which is somewhat surprising since their corresponding
> >> Windows drivers have typically worked well. My suggestion is to try
> >> various different versions of the ATI drivers, both newer, and older
> >> than the one you're using presently. There's a chance that the problems
> >> you're having are specific to particular driver versions, so aside
> >> from waiting for a response from AMD/ATI, I would strongly recommend
> >> experimenting with other driver versions. Perhaps others on VMD-L
> >> with AMD/ATI hardware can comment on their experiences?
> >>
> >> Cheers,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >> On Tue, Jan 20, 2009 at 04:52:06PM +0100, Ramon Crehuet wrote:
> >>> Hi John and Axel,
> >>> You are right. Other OpenGL applications show the same problem...
> >>> I have used the newest driver from ATI... I guess I should post my bug
> >>> there. What kind of information do you think I should post? For example,
> >>> how do I know the bit-depth I am running at?
> >>> I tried 'export VMDSIMPLEGRAPHICS=1' but didn't change anything. A part
> >>> from the (slow?) solution from ATI, do you think I can get VMD running
> >>> somehow. Should I still try the alpha version binaries?
> >>> Cheers,
> >>> Ramon
> >>>
> >>>
> >>> John Stone wrote:
> >>>> Hi,
> >>>> Have you tried updating your ATI driver, this definitely sounds
> >>>> like some sort of new driver bug I haven't seen previously. You might
> >>>> try either a newer or older driver version and see if that affects the
> >>>> behavior you're experiencing. Do any other OpenGL programs run on your
> >>>> system? What color bit-depth are you running at?
> >>>>
> >>>> Cheers,
> >>>> John Stone
> >>>> vmd_at_ks.uiuc.edu
> >>>>
> >>>> On Tue, Jan 20, 2009 at 01:09:27PM +0100, Ramon Crehuet wrote:
> >>>>> Der VMD users,
> >>>>> I've recently installed VMD on an Opensuse 11.1 box with an ATI HD 2400
> >>>>> card using the ATI driver.
> >>>>> When I open the VMD, the OpenGL window (where molecues are displayed) is
> >>>>> transparent. I see the background windows. When I move the molecule then
> >>>>> it shows its content, flickering. Has anybody encountered this problem?
> >>>>> It is really annoying!
> >>>>> Here are the first welcome lines in the console:
> >>>>>
> >>>>> Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
> >>>>> 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: 3476MB (87%)
> >>>>> Info) ATI Linux driver detected, limiting features to avoid driver bugs.
> >>>>> Info) Set the environment variable VMDDISABLEATILINUXWORKAROUND
> >>>>> Info) to enable full functionality on a known-safe driver version.
> >>>>> Info) OpenGL renderer: ATI Radeon HD 2400 XT
> >>>>> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
> >>>>> Info) GLSL rendering mode is NOT available.
> >>>>> Info) Textures: 2-D (4096x4096), 3-D (8192x8192x8192), Multitexture (8)
> >>>>>
> >>>>>
> >>>>> Thanks for your attention,
> >>>>> Ramon
> >> --
> >> 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