VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 12 2007 - 17:29:11 CDT

Pawel,
  Did you verify that the system variable is being detected by VMD
at startup? What do your VMD startup messages say now? It could also
simply be a bug in 3-D (volumetric) texturing in the ATI driver. Does
color by "Volume" work for you, or does that similarly produced a solid
black object? With VMD 1.8.5, the VolumeSlice representation should be
relatively insensitive to various driver bugs because texture coordinates
are explicitly calculated for the vertices of the VolumeSlice plane, so
as long as the video driver does its job, I would expect you to see a
correctly textured slide plane. If you change the background color
to white, do you see a black slice plane, or do you see nothing at all?

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 12, 2007 at 09:00:45AM +0100, Pawel Wielgus wrote:
> Dear John,
>
> after exporting the system variable, I can see sth like this:
>
> Info) File loading in progress, please wait.
> Info) Using plugin cube for structure file test.cube
> cubeplugin) trying to read cube data set 0
> Info) Analyzing Volume...
> Info) Grid size: 80x80x80 (7 MB)
> Info) Total voxels: 512000
> Info) Min: 0.000000 Max: 0.706192 Range: 0.706192
> Info) Computing volume gradient map for smooth shading
> Info) Added volume data, name=test.cube : Gaussian Cube: kom density=scf
> Info) Using plugin cube for coordinates from file test.cube
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file test.cube.
>
> Looks not bad. But that's all. I still can't see anything on my screen
> when the VolumeSlice representation is chosen :(
>
>
> Pawel
>
>
>
> John Stone wrote:
> > Pawel,
> > Ah, I see the issue. Well, you have a choice of either force-enabling
> > full rendering functionality (and risking crashes due to a number of
> > known ATI driver bugs that are to my knowledge still not fixed based
> > on recent reports from others), or using a different machine or a different
> > video card. If you wish to take your chances with the ATI video driver
> > and tell VMD to enable all rendering features, you can do this by
> > setting the environment variable VMDDISABLEATILINUXWORKAROUND, like this:
> > setenv VMDDISABLEATILINUXWORKAROUND 1
> >
> > After setting that environment variable, you should be able to start
> > VMD again, but without the functionality limitations imposed by default
> > when an ATI Linux driver is detected. Do not be surprised if you manage
> > to crash VMD, the X server, or even lockup your machine, as I've seen all
> > of these situations occur with both the open source and ATI provided
> > drivers for Linux. Oddly, the same hardware works fine with the ATI
> > provided Windows driver, so I think this is mainly an issue with their
> > Linux driver series.
> >
> > If you're able to use VMD reliably with full features with your ATI
> > Linux driver I would be very interested to hear about it, as many other
> > ATI users have encountered stability problems when using the advanced OpenGL
> > rendering features. Any tips that help others with their ATI drivers
> > are appreciated.
> >
> > If you have stability problems when full functionality is enabled I would
> > report this to ATI on their support forums. If you don't get a response
> > from them, then it may be time to consider getting a different video card
> > if working with volumetric data is important to you.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Mar 09, 2007 at 04:54:26PM +0100, Pawel Wielgus wrote:
> >
> >>Thanks for your reply.
> >>When my VMD starts, one can read:
> >>
> >>Info) ATI Linux driver detected, limiting features to avoid driver bugs.
> >>Info) OpenGL renderer: MOBILITY RADEON X300 Generic
> >>Info) Features: STENCIL MDE CVA MTX PP PS GLSL(OVF)
> >>Info) GLSL rendering mode is NOT available.
> >>Info) Textures: 2-D (2048x2048), 3-D (2048x2048x2048), Multitexture (8)
> >>
> >>I really don't know what 'limiting features' mean. What I know for sure
> >>is that I really had lots of troubles when compiling ATI fglrx drivers.
> >>And I did it finally only against 2.6.10 kernel. But that's a long story...
> >>
> >>What do you think? Any special features in fglrx configuration needed ?
> >>
> >>
> >>Pawel
> >>
> >>
> >>
> >>
> >>John Stone wrote:
> >>
> >>>Pawel,
> >>> Yes, the VolumeSlice representation has been available for some time
> >>>and should work fine so long as you have a video card that supports
> >>>3-D (volumetric) texturing. You can check this by reading the VMD OpenGL
> >>>related startup messages. You should see a texturing info line like
> >>>the one I've pasted below:
> >>> Info) OpenGL renderer: ZFB, VIS
> >>> Info) Features: STENCIL MSAA(16) MDE MTX GAS
> >>> Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> >>>
> >>>The important part of that status line is: "3-D (512x512x512)"
> >>>
> >>>What video chipset are you using? Have you checked to make sure
> >>>that you're using the latest video driver available for your hardware?
> >>>
> >>> John Stone
> >>> vmd_at_ks.uiuc.edu
> >>>
> >>>On Fri, Mar 09, 2007 at 04:27:17PM +0100, Pawel Wielgus wrote:
> >>>
> >>>
> >>>>Dear VMD Users,
> >>>>
> >>>>may I ask you a question concerning the visualization of volumetric data?
> >>>>I have a simple example of density for CH4 (just for graphical testing)
> >>>>in a Gaussian03 cube format. The volumetric data is read properly, and
> >>>>using 'Drawing method = Isosurface' I can easily get the density.
> >>>>
> >>>>But as only I switch to 'Drawing method = VolumeSlice' everything
> >>>>disapears. As far as I know the volume slices (along cartesian axis) are
> >>>>possible with VMD-1.8.5.
> >>>>
> >>>>What wrong am I doing ? Should I switch any options on ? Could you give
> >>>>me any hint?
> >>>>
> >>>>
> >>>>Regards
> >>>>
> >>>>
> >>>>Pawel Wielgus
> >>>>
> >>>>
> >>>
> >>>
> > 

-- 
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