VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 28 2007 - 16:19:41 CDT

Hi,
  I suspect your system is running the card out of memory and
misbehaving as a result of it. Due to the way OpenGL ~1.2 works
with textures, they are allocated with dimensions in even
powers of two. For your 129^3 volume, that means its
actually allocating 256^3, which with the likely internal texture
storage format the Radeon uses probably means that it has attempted
to allocate something over half of the total video memory, which to
me says that it's probably bombing for that reason. If you can
resample or recalculate your grid at one of the other legal APBS
sizes like 97. You'll need one of the new test versions of VMD 1.8.7
in order to be able to run a 97^3 APBS job since the old code was locked
to powers of two.

I'm a bit surprised you don't get console warnings in VMD,
but they may not be returning error codes correctly in the video driver.
It took Apple a couple years to fix the driver bugs that used to
prevent 3-D textures from working at all, so I count myself lucky
that we're getting this far even. :)

One of the things I'm hoping to do for a subsequent rev of VMD is to add
support for non-power-of-two texture maps using OpenGL extensions on
cards that support these capabilities. I don't know if the Apple Radeon
drivers support NPOT, but I can work on that with you and other Mac users
if you're interested in doing some testing.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Sep 28, 2007 at 04:15:02PM -0400, Jim Fonseca wrote:
> Hi,
> I'm trying to display some Volumeslices of data created with the APBS
> plugin. My problem is that once I increase the grid size to
> 129x129x129 (APBS /plugin requires 2^n+1, I believe) my Volumeslice
> gets textured with what appears to data from some other address of my
> video card's memory. Here's a link to the picture.
> http://oak.cats.ohiou.edu/~jf163201/Picture-2.jpg
>
> As neat as that looks, it makes explaining my results fairly
> difficult. :)
>
> I've got a MacBook Pro running OSX 10.4.10 with an ATI X1600 video
> card with 128 megs of video ram. When I load the pot.dx file from
> apbs, VMD tells me:
> Info) Analyzing Volume...
> Info) Grid size: 129x129x129 (32 MB)
> Info) Total voxels: 2146689
>
> The 65x65x65 data set works fine but I'm looking at a pretty large
> system (not the example protein in the image) and the extra grid
> points would really help. It seems it should be able to handle the 32
> MB dataset. Or maybe not?
>
> Thanks for your help
> Jim Fonseca 

-- 
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