AMBER Archive (2008)

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

From: fatima.chami_at_durham.ac.uk
Date: Tue Jan 29 2008 - 12:19:22 CST

Dear Ross,

So its an inherent restriction to Sander and not to the MPI implementation.

For my system of 11500 sites the 16 CPUS run is my cutoff (2times faster than 1cpu)

I am thinking to use PMEMD to run my MD simulation for a long length of time (20ns)

are input and output files for PMEMD compatibles to the one that sander.mpi uses
cause I will carry on the simulation and not start from scratch

best wishes
fatima

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

>
> 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
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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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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