From: Axel Kohlmeyer (
Date: Mon Jul 09 2007 - 14:12:00 CDT

On Mon, 9 Jul 2007, SeongJun Heo wrote:

SJH> Recently, I tried to display multi-million atoms system on Linux using 2
SJH> core-2-duo CPUs with 8GB ram. But I found VMD uses just one CPU. How can I
SJH> make VMD use multiple CPUs?

actually VMD _does_ use multiple CPUs, but only for some tasks
and using multithreading (so watch out for the VMD process using
more than 100% CPU). the current version 1.8.6 has some more
multithreading than the previous ones, but there are many more
areas, where multi-threading could be applied (e.g. several measure
subcommands etc.).

please note that the graphics/GUI _have_ to be in a single thread
and also the script interpreters are non-threadable.

on a desktop machine you can benefit a bit from your dual-core setup
by having the Xserver and VMD running on different cores...

but other than that, there is little you can do except
adding more multi-threading to the existing functionality.

the reduced performance of the multi-million atom system
is most likely due to the limitations of your graphics
subsystem. for OpenGL and particularly GLSL this is murder
even for the most capable cards.

even though i have a pretty capable card in my desktop and twice
the cpu power and memory in my desktop, for multi-million atom
systems, i am mostly using either the lines representation
(with linewidth set to 2) or the points rep (with pointsize set
to 6 or larger).


Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.