AMBER Archive (2009)

Subject: Re: [AMBER] Number of Cycles

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Dec 15 2009 - 13:00:19 CST

Probably not a big deal at 32 - 64 processors - maybe a couple of percent,
unless kraken has i/o issues (I was involved in getting bigben up as an
early user, and there were big i/o issues on that machine that I hope cray
has fixed by now with the xt4's and xt5's). I personally would never do my
runs the way you are because it would drive me nuts to be combining a bunch
of trajectory segments of relatively random length, but I am order-obsessed
at some levels :-) Please note that I started responding to all this
simply because a statement was made about ntwr that was not strictly true
for pmemd, and since I had seen framing issues in earlier email, I wanted to
raise awareness.
Regards - Bob
----- Original Message -----
From: "Niel Henriksen" <niel.henriksen_at_utah.edu>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Tuesday, December 15, 2009 1:11 PM
Subject: RE: [AMBER] Number of Cycles

>If nstlim is evenly divisible by ntwx, then the last mdcrd trajectory frame
>written should I believe correspond to the final restart file. The
>important thing to remember, is that the restart file will always be
>written
>at the final step of the run, regardless of the value of ntwr.

Yes I agree. If all my jobs ended before the wallclock limit there would be
no
problem. However, I am greedy with every second I get, so all of my jobs
get
killed before they end "normally". Thus, to ensure that I don't have
redundant
data, I like to write restart files with every trajectory frame. (I also
write 2 restart
files each ntwr so that if one gets only partially written I have a
back-up). I suppose
I should evaluate whether this approach maximizes the use of resources and
minimizes the total (real) time to complete a simulation.

Off the top your head, if I use somewhere between 32 - 64 processors on a
teragrid machine (say ranger or kraken) for a simulation with 40,000 atoms,
would I get a big performance impact with ntpr=ntwx=ntwr=500?

Thanks,
--Niel
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