Re: Colvars simulation running slow?

From: Ajasja Ljubetič (
Date: Wed Sep 10 2014 - 19:58:48 CDT

On 11 September 2014 02:51, Tristan Croll <> wrote:

> ... and now I see I'm just running over old ground. Sorry – I did do a
> search, but obviously didn't hit the right keywords. For anyone that
> comes across this thread in future, the problem (as hashed out in detail
> here:
> is that the colvars calculations are running on a single core).
> This is also described in the user guide

   - *Performance issues:* While NAMD spreads the calculation of most
   interaction terms over many computational nodes, the colvars calculation is
   not parallelized. This has two consequences: additional load on the master
   node, where the colvar calculation is performed, and additional
   communication between nodes. NAMD's latency-tolerant design and dynamic
   load balancing alleviate these factors; still, under some circumstances,
   significant performance impact may be observed, especially in the form of
   poor parallel scaling. To mitigate this, as a general guideline, the size
   of atom groups involved in colvar components should be kept small unless
   necessary to capture the relevant degrees of freedom.


This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:22:50 CST