AMBER Archive (2008)

Subject: RE: AMBER: Amber parallel version on CPU power of 2 only

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jan 29 2008 - 08:39:21 CST

Hi Fatima,

Amber 9 should support non-power of 2 cpus for sander.MPI. However, the
efficiency will go down if you use non-powers of two since the code switches
from using a bindary tree to a standard allreduce for communication of
forces. How much this hurts will depend on your MPI implementation. You
could for example find that say 12 cpus is actually slower than 16 cpus.

In Amber 8 you need to recompile a special parallel binary that has
-DNOBTREE defined in config.h. Note, however that this will turn off the
binary tree for ALL processor counts, so 8 cpus with the NOBTREE code will
run slower than 8 cpus with the regular code. (this is not the case with
amber 9)..

Alternatively if you are using a method supported by PMEMD, regular MD / GB
etc then I would suggest using PMEMD. It will give you better performance
and doesn't have the power of two processor limitation that sander does. See
$AMBERHOME/src/pmemd.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of
> fatima.chami_at_durham.ac.uk
> Sent: Tuesday, January 29, 2008 05:39
> To: amber_at_scripps.edu
> Subject: AMBER: Amber parallel version on CPU power of 2 only
>
>
> Dear Amber's users,
>
> Sander.MPI runs on 2,4,8,16,32,64 but not on any other
> number of processors
> which is not a power of 2 !!
>
> is there a way to solve this restriction ?
>
>
> many thanks
>
> fatima
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