VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 04 2005 - 16:26:29 CST

Sabuj,
  I assume you're running VMD 1.8.2? If not, let me know which version
of VMD you're using and I can give more suggestions.

I know that NVidia made a lot of changes that relate to the implementation
of stereoscopic rendering on the Quadro cards. Even now with the most recent
drivers, they have a particularly egregious performance issue that affects
stereo rendering. If you have stereo enabled in your NVidia driver, and
you're running VMD with the "VMDPREFERSTEREO" variable set, but you
_don't_ have VMD displaying in stereo, there's a HUGE performance loss caused
by the way their OpenGL driver implements glDrawBuffer(GL_BACK) when running
in a stereoscopic visual. No other cards/drivers I've ever seen have this
problem, and it's a huge speed hit. My understanding is that NVidia implements
glDrawBuffer(GL_BACK) with a software-based pixel copy when you're running
in a stereo mode but not rendering in stereo. When one calls
glDrawBuffer(GL_BACK_LEFT) or glDrawBuffer(GL_BACK_RIGHT) the problem goes
away and speed is normal (i.e. when you have the stereo mode in VMD
set to CrystalEyes).

All said however, this only affects you if you have the board running in
a stereoscopic mode. Since you didn't say what video mode you're using,
I'm not even certain any of this applies to you. A lot of people with
Quadro cards buy them specifically so they can do stereo, so I thought
I'd mention this particular issue so you're aware of it.

The NVidia X config option for stereo is usually:
  Option "Stereo" "3"

So if you see that in your config files, that may be related to your
performance problem.

  John

On Tue, Jan 04, 2005 at 04:06:39PM -0600, Sabuj Pattanayek wrote:
> Hi,
>
> Ayone know why I would have terrible graphics performance for some of
> the newer and older Linux_x86 nvidia drivers except for v1.0.5336 on my
> quadro 750 xgl card and only for VMD v1.8.2 (not with any other modeling
> programs e.g. chimera, spdbv, ribbons, turbo, o, etc)?
>
> The other driver versions I tested are: 1.0.6229 (latest), 1.0.6111, &
> 1.0.4365 which is "quadro certified" but all of them give really poor
> performance compared to 1.0.5336 in VMD.
>
> These are the settings for all the drivers:
>
> glxinfo | grep direct
> direct rendering: Yes
>
> cat /proc/driver/nvidia/agp/status
> Status: Enabled
> Driver: NVIDIA
> AGP Rate: 4x
> Fast Writes: Enabled
> SBA: Enabled
>
> I also tried switching between agpgart and nvidia's agp for all of the
> drivers but there is no difference. The system is running under a 2.4.28
> kernel. I thought it might be related to the issue below so I included
> the forward.
>
> Thanks
> Sabuj Pattanayek
>
> John Stone wrote:
> >Hi,
> > Generally speaking, remote rendering will be significantly slower
> >than local rendering, so you only want to do this when you have no
> >other choice. This is particularly true for apps that draw a lot of
> >geometry using immediate mode OpenGL. We've made a large number of
> >changes in VMD 1.8.3 to make it more remote-display friendly (and faster
> >in general..) but even so, you'll still notice a big difference between
> >local and remote display performance.
> >
> >You might also experiment with enabling "Display->Cachemode->On" in
> >the GUI of VMD 1.8.3b1, this enables a feature which can give a huge
> >performance boost on remote displays, tiled displays, etc.
> >For the display of a static molecular structure, the display cachemode
> >feature
> >should give you anywhere from a 10x to 50x performance boost over normal
> >rendering. Some machines also get a performance benefit for local
> >rendering when the caching code is enabled, but that's less frequently the
> >case than
> >for remote display. Try that out and let us know how it works for you.
> >
> > John
> >
> >
> >On Tue, Dec 28, 2004 at 03:39:32PM +0100, Greipel.Joachim_at_MH-Hannover.DE
> >wrote:
> >
> >>Hi All,
> >>I am setting up VMD on a DUAL-Opteron machine for rendering on remote
> >>X-Servers which run under Linux and are equipped with NVIDA Quadro
> >>Graphics and Hardware Stereo.
> >>
> >>The rendering on the remote machines worked (even stereo display with
> >>crystal eyes) but unfortunately it was very (!) slow. I just installed
> >>the 1.8.3b1 version and to my surprise the rendering on the remote
> >>machines is now acceptably fast.
> >>
> >>There are slight differences in the startup messages of VMD
> >>
> >>1.8.3b1 ("fast rendering")
> >>
> >>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, 2 CPUs detected.
> >>Info) OpenGL renderer: Quadro4 980 XGL/AGP/SSE2
> >>Info) Features: STENCIL STEREO RN MDE MTX PP
> >>Info) OpenGL Programmable shading is NOT available.
> >>Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> >>
> >>1.8.2 ("slow rendering")
> >>
> >>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, 2 CPUs detected.
> >>Info) OpenGL renderer: Quadro4 980 XGL/AGP/SSE2
> >>Info) Features: STENCIL STEREO RN MTX
> >>Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)
> >>vmd >
> >>
> >>Is there any rational explanation for this behaviour?
> >>Thanks a lot,
> >>
> >>Joachim Greipel
> >>
> >>Medizinische Hochschule Hannover
> >>Germany
> >
> > 

-- 
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