[gmx-developers] DD support in ASPC

Shirts, Michael (mrs5pt) mrs5pt at eservices.virginia.edu
Tue Mar 6 14:07:35 CET 2012

Adding history dependence also sounds like a job for master, not 4.6.

Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu

> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Tue, 6 Mar 2012 22:11:12 +1100
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] DD support in ASPC
> On 6/03/2012 8:57 PM, Tomáš Trnka wrote:
>> Hello,
>> the ASPC code as currently submitted for 4.6 review doesn't work with domain
>> decomposition. This stems from the fact that I have neither any significant
>> experience in MPI programming nor deep understanding of the DD core.
>> However, supporting DD shouldn't be too hard. For each shell, ASPC keeps a
>> history of its relative displacement from the carrying nucleus and uses it to
>> predict the new position in each integration step. There are no cross-shell
>> dependencies (a shell's history is only used to predict the position for that
>> shell). So the only thing that's necessary for working DD is that when a
>> shell
>> crosses from one node to another, it needs to carry its history over.
>> Could anyone please provide me with some pointers how this can be best
>> achieved? I've tried several approaches but every time the thing got too
>> complicated too soon:
>> 1) extend t_state with the ASPC history arrays - main problems with this were
>> that t_state is touched in hundreds of places throughout the code; also the
>> placement of shells onto individual DD nodes would need to be recorded
>> somewhere (another global index?)
> What's a nucleus? If it's an atom, then things should be reasonably
> straightforward, piggy-backing the existing accounting for which atoms
> belong to which processor. If it's not an atom, then expressing a
> nucleus as being attached to some appropriate master atom and preceding
> as before might be the way forward.
> Mark
>> 2) keep the history within gmx_shellfc_t and collect/distribute in
>> make_local_shells() - old shell indices would need to be kept somewhere there
>> too to be able to do the collection or possibly the indices could be
>> collected
>> from the nodes, too; I have a bad feeling about doing collection in here as
>> it
>> is called from dd_partition_system, so it's rather counter-intuitive and
>> could
>> break something
>> 3) ???
>> Thanks for any suggestions!
>> Best regards
>> Tomáš Trnka
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