VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 11 2019 - 15:39:34 CDT

Hi,
  The 'volmap' plugin its associated C code were originally written
outside of and independently of VMD, so they don't really follow
the multithreading or MPI parallelization schemes used in the other
analysis-oriented parts of VMD.

What 'volmap' command/feature are you using currently? There are now
some alternatives to volmap for things like density map calculations that
are substantially faster (GPU accelerated, and/or CPU multithreading) that
may be a viable alternative for you to try out. Let me know what
you're actually doing and I can give further suggestions, or at least
an outlook for when the last bits of 'volmap' will have been superceded
with the new and in-development code.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Mar 10, 2019 at 10:55:43PM +0000, McGuire, Kelly wrote:
> I was told VMD can be used on a node with multiple CPUs, is this true?
> What about VMD's plugins though, such as Volmap? Can VMD and plugins use
> multiple CPUs and, thus, be able to use more RAM when selecting
> memory-per-cpu in my submit script?
>
> Kelly L. McGuire
>
> PhD Candidate
>
> Biophysics
>
> Department of Physiology and Developmental Biology
>
> Brigham Young University
>
> LSB 3050
>
> Provo, UT 84602 

-- 
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/