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.
Although this then means an if statement inside the inner loop which would
be bad, or two loops with the if statement factored out.
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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Received on Tue May 11 2010 - 21:30:02 PDT
