VMD-L Mailing List

From: Karl Decker (kaelenmitharos_at_gmail.com)
Date: Fri Dec 16 2016 - 10:36:42 CST

Thanks for the quick reply! The distance map command really is the main one
as far as Volmap goes. We have some other custom calculations that we're
hoping to implement in C++ somehow, as the inefficiency of doing them in
Tcl is another show-stopper, but it's not clear how we'll do that at the
moment.

Thanks,
Karl Decker

On Thu, Dec 15, 2016 at 11:27 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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 have been superceded or augmented by other methods of doing similar things.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/
>