Note that what makes this error so unusual in sander is the fact that
sander employs a residue-based decomposition (so each residue is assigned
in its entirety to a single processor). Thus, the only way this error
would actually occur (assuming there's no bug in the code for for
per-residue decomposition), is if you had a Hydrogen in one residue bonded
to the heavy atom in another residue, which should never happen in
well-designed residues (since a heteroatom -- hydrogen bond should be
terminal, and there's no point in having the H-atom be its own residue).
HTH,
Jason
On Tue, Nov 1, 2011 at 1:37 PM, Breuer, Marian
<marian.breuer.10.ucl.ac.uk>wrote:
> Dear Dr. Case,
>
> Thank you for your quick reply.
> I tried to run my system with 15, 16, 24 and 48 cores, obtaining the same
> error message in each case. Using 14 cores or less is unfortunately not an
> option, given the low speed I observed so far with 14 cores for my system.
> I need to use the AMBER02 polarizable force field which is not implemented
> in pmemd, unfortunately; and the AMOEBA force field, which is implemented,
> would be too expensive for my system.
> Thanks for the clarification regarding sander's residue-based distribution
> method, this was indeed unclear to me.
>
> I will send you my sander files (topology, coordinates, mdin) in a
> separate email as I don't want to send big attachments to everyone in the
> mailing list. (I can of course send them to anyone who is also interested
> in taking a look.)
>
> All the best,
> Marian Breuer
>
> ________________________________________
> From: David A Case [case.biomaps.rutgers.edu]
> Sent: 01 November 2011 12:22
> To: AMBER Mailing List
> Subject: Re: [AMBER] Issue with running sander with SHAKE
>
> On Mon, Oct 31, 2011, Breuer, Marian wrote:
> >
> > I'm currently trying to carry out MD simulations with sander (MPI
> > parallel version, AMBER11) on a protein system using SHAKE bond
> > constraints for bonds containing hydrogen (sander option ntc=2). These
> > work with up to 14 processors, but with any number of cores higher than
> > that the simulations abort in the first step with the error message:
> >
> > partition error in shake on processor 0
> > this processor has atoms 1 through 8265
> > atom 8265 is within this range
> > atom 8266 is not within this range !
>
> Does the code work with 16 processors (or 32, i.e. an even power of 2)?
> Code
> with an even power of 2 has been tested a lot more than for non-powers of
> 2.
> How many processor counts above 14 have you tried?
>
> I know these are big files, but if you could somehow post the prmtop and
> coordinate files involved here (add mdin as well) it would greatly
> accelerate
> finding what is wrong.
>
> As workarounds: can you use pmemd instead of sander? It will be faster
> anyway. Or, if you are on sander, live with 14 processors or fewer?
> (Sander
> may not scale all that well beyond a dozen threads anyway.
>
> > The total number of atoms in my system is 122321, which,
> > when divided by 8265, yields roughly 14.8. This seems to suggest that
> > sander always places 8265 atoms on each of the first 14 cores as long as
> > there are more than 14 cores....
>
> This inference is not valid. Sander uses a residue-based distribution
> method,
> which may have some corner cases that fail.
>
> ....dac
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 01 2011 - 15:00:05 PDT
