On Wed, May 12, 2010 at 12:09 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jason,
>
> > Does this exist, and/or is it of any use in pmemd? It would seem as
> > though
> > pmemd would be worth speeding up in this regard more (since it's the
> > 'performance' end of amber). However, since the load balancer is far
> > more
> > sophisticated in pmemd, I see the possibility that it may not help
> > nearly as
> > much.
> >
> > A quick grep shows that there's an ifdef NO_NTT3_SYNC and an ifndef
> > NO_NTT3_SYNC in the pmemd source directory. What's the verdict on
> > this?
>
> Yes, it exists in both sander and pmemd in AMBER 11. I added it to the CVS
> tree about a year ago. It works great for both sander and pmemd improving
> scaling significantly for ntt=3 simulations in both codes. Essentially it
> brings ntt=3 scaling for pmemd inline with the ntt=1 numbers. I recommend
> using it if you want to run large core count long ntt=3 runs. Just 'caveat
> emptor'!!!
>
> Probably this should be a cntrl namelist option and properly documented.
>
Documented, most likely (especially for pmemd if the explanation I gave
seconds before I got your email was accurate). Namelist option....
> Although this then means an if statement inside the inner loop which would
> be bad, or two loops with the if statement factored out.
>
For this reason, pre-processor option sounds best. I don't think the
repeated if statements are particularly desirable for pmemd. (I'm also a
big fan of not duplicating code where it can be avoided, so do-looping twice
to factor out an if statement would not appeal to me. It would still need
an if statement, though, yes? It would just be hit once each timestep rather
than once each non-owned atom per time step). I don't know the exact
computational cost of a conditional evaluation, but it's certainly more
expensive than no conditional evaluation :).
That said, I'm going to recompile with NO_NTT3_SYNC right away. Do we have
comparisons/timings/scaling data for this? If so, where is it? If not, is
it worth doing?
Thanks!
Jason
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 11 2010 - 21:30:06 PDT
