Hello,
This is a fork of a discussion in the regular amber mailing list, just
asking some quick opinions.
On Tue, Dec 15, 2009 at 12:09 PM, Robert Duke <rduke.email.unc.edu> wrote:
> Hmmm, did I misspeak somewhere here? Changing processor count changes ntwr,
> which controls the restart file write frequency; it does not touch ntwx,
> which is the frequency of dumping trajectory coordinates. Completely
> different deal. I have to leave ntwx pretty much alone, or it would have
> the potential to really muck things up for folks. The restart is of course
> for restarts, and is dumped periodically to prevent total loss of a run in
> the event of some failure, but auto-setting the frequency of writes to this
> file is purely a tradeoff between performance and paranoia about losing data
> in a crash. So as an aside, it is true that too frequently writing the
> trajectory file also has potential to whack performance, but there are
> limits to what you can do about it, and it is cheaper to write than the
> restart (no velocities, less precision). The default for restart rewrites
> in sander is probably excessively cautious.
> Regards - Bob
Scaling ntwr is a 3-line addition to mdread.f ... should we do it? Or
is only pmemd fast enough to notice the difference? :).
Thanks!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Dec 15 2009 - 09:30:05 PST
