You could always try to see if there is some sort of correlation between
atom number and number of allocated variables in the pmemd output files (for
any machine).
HTH,
Jason
On Fri, May 27, 2011 at 7:21 AM, Dmitry Osolodkin <divanych.rambler.ru>wrote:
> Dear Jason,
>
> Unfortunately right now we don't have the system available, and only a
> rough estimate is needed. Is it possible to extrapolate the memory data
> from small systems? If yes, how to do it?
>
>
> On 05/27/2011 08:01 AM, Jason Swails wrote:
> > I think pmemd outputs the number of allocated integers and floating point
> > numbers allocated for each simulation, so run a 0-step minimization and
> look
> > for those numbers.
> >
> > Note that each thread, I believe, allocates about the same amount of
> memory
> > (a little bit more) than the only thread of a serial pmemd job. It has
> some
> > atom-ownership maps in addition to the normal data structures, but that's
> > ~1/3 the size of just the coordinate, velocity, force, and old velocity
> > arrays (which leaves a relatively small imprint).
> >
> > HTH,
> > Jason
> >
> > On Thu, May 26, 2011 at 5:08 PM, Dmitry Osolodkin<divanych.rambler.ru
> >wrote:
> >
> >> Dear AMBER developers,
> >>
> >> we are going to perform a MD simulation for an extremely huge system
> >> (ca. 10 millions atoms, maybe twice more). How to calculate memory
> >> requirements per processor for such task? We'll probably use pmemd.
> >>
> >> Thanks in advance
> >> Dmitry
> >>
> >> --
> >> Dmitry Osolodkin.
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o.qsar.chem.msu.ru
> Phone: +7-495-9393557
> Fax: +7-495-9390290
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 27 2011 - 05:00:03 PDT
