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 - 15:04:56 CST

Thanks
fatima

Quoting Robert Duke <rduke_at_email.unc.edu>:

>
> Fatima -
> No problem with starting a run in sander and continuiing it in pmemd. There
>
> are some limitations in terms of what pmemd supports, but it currently does
> all the generic pme and generalized Born stuff (look at manual for list of
> unimplemented capabilities, or simply try running it, and it will refuse to
> do things that it can't do correctly). On mdin input, the biggest difference
>
> is pmemd still only supports the old group-based ways of specifying
> restrained or belly atoms; this is documented through amber 7 at least
> (possibly also 8). PMEMD should be substantially faster though if you have
> a decent interconnect for your cluster, and probably worth using even with
> gigabit ethernet.
> Regards - Bob Duke
>
> ----- Original Message -----
> From: <fatima.chami_at_durham.ac.uk>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, January 29, 2008 1:19 PM
> Subject: RE: AMBER: Amber parallel version on CPU power of 2 only
>
>
> > 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
> >> be read every day, and should not be used for urgent or sensitive issues.
> >>
> >> > -----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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> >>
> >>
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> >
> >
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>
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