VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri Dec 16 2016 - 12:47:54 CST

Hi Karl,

Volmap has this an an option. You just need to pass the -mol flag, and NOT a -o. Then volmap won't write out the result to disk... Unless it checkpoints midway through the calculation. However then you are stuck with the density data in a place where mere mortals can't access it (VMD's memory), since there isn't to my knowledge a tcl or python function to generically return voxel data stored in memory, although I totally can write one!

-Josh

On 12/16/2016 11:09 AM, Karl Decker wrote:
One of my compatriots on this project reminds me volmap communicates with the rest of our code by a file on disk and a disk operation always takes times comparable to a second, which is too long for our preference. Is it too presumptuous to ask for the source code for the volmap distance function so we can keep the result of the volmap function in memory rather than writing it to disk immediately? That would be amazingly helpful.

Thanks,
Karl

On Fri, Dec 16, 2016 at 10:36 AM, Karl Decker <kaelenmitharos_at_gmail.com<mailto:kaelenmitharos_at_gmail.com>> wrote:
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<mailto: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have been superceded or augmented by other methods of doing similar things.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<mailto: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 

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NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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