AMBER Archive (2009)

Subject: Re: [AMBER] Number of Cycles

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Dec 15 2009 - 11:18:37 CST

On Tue, Dec 15, 2009 at 12:13 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> ah I see I thought Bob was talking about frequency of dumping coordinates of
> any type. I'm not sure why changing ntwr would affect performance but ntwx
> would not- is the the open/close on the restart file, or the communications
> to collect all coordinates?
> thanks
> carlos

I believe he said writing mdcrds does affect performance, but so does
ntwr. However, ntwx is needed for analyzing results, so playing with
this is not a very good idea. However, writing a trajectory frame is
cheaper than writing a restart file because a restart file uses higher
precision and includes velocities (doubling the size of the file).

Also, while the restart file is writing, I'm guessing the non-master
threads are waiting at a barrier? In any case we don't have to
sacrifice performance to write restarts, as they're not terribly
useful, but we need to sacrifice performance to write mdcrds, as
they're the source of our sampling, thus it's a necessary expenditure.

Perhaps I'm missing something.

All the best,
Jason 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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