VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 15 2016 - 11:27:01 CST

Hi,
  The 'volmap' commands don't exploit GPU acceleration yet, but some of them
have been superceded or augmented by other methods of doing similar things.
In the longer term, the volmap commands are getting updated/replaced by new
implementations that do equivalent calculations but that support GPUs and
also some of the new many-core CPUs that also require a very different
algorithmic approach. If you can tell me what operations you need to be
very fast (other than the "distance" calculation below, I can likely give
some suggestions on how we could accomplish that soon.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 15, 2016 at 11:13:26AM -0600, Karl Decker wrote:
> Hello all! I'm running a script that uses the Volmap distance mapping
> command. The line looks like:
> volmap distance $sel -res 1 -cutoff 7 -minmax "{-40 -40 -40} {40 40 40} -o
> foo.dx
> where $sel is an atomselect selection, as in [atomselect top protein].
> It does not seem, based on performance, that this Volmap operation is
> being accelerated with CUDA. How can we make it so?
>
> Thanks,
> Karl 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/