Hi,
I just checked my topology in VMD and the two atoms in questions are indeed fine, i.e. the hydrogen 8266 is bonded to nitrogen 8265 and to nothing else. However, the decomposition is carried out assigning 8265, the nitrogen, to one processor and assigning 8266, the hydrogen, to the next one. As nitrogen 8265 is the first atom of its residue in the topology, this means that the nitrogen is the "orphan" that is allocated to a different processor than the rest of its residue. If the hydrogen itself was the problem, I'd expect the hydrogen to be misassigned to another processor (e.g. due to a false bond to a residue on that other processor). Is this reasoning correct? And is there any conceivable reason why the nitrogen would be cut out from its residue?
Thank you for your help,
Marian Breuer
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: 01 November 2011 21:49
To: AMBER Mailing List
Subject: Re: [AMBER] Issue with running sander with SHAKE
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 - 16:00:03 PDT
