[gmx-users] Fwd: Gromacs: data distribution and work distribution

[Szilárd Páll]

On Wed, Mar 4, 2015 at 5:24 PM, Federico Padua <padua at uni-mainz.de> wrote:
> Dear Gromacs team,
>
> I am interested in the following information about Gromacs since I'm
> writing part of a publication so will be few lines and I would like to
> get the right info directly from the people closer to the code (I read
> the paper). We are using Gromacs version 5.0.4 and we
> would like to know without going too much into details:
>
> - how Gromacs distribute the data to be processed among processors?

Neutral-territory domain decomposition using MPI + OpenMP
multi-threading within a rank.

> - how Gromacs distribute the work among the processors involved in the
> calculation?

Work = ?
Nitpick, but this second question more or less includes the first.
Anyway, I assume here you meant task-decomposition and the answer is:
MPMD task decompostion with MPI (separate PME ranks) and non-bonded
offload to GPUs.

For a fairly detailed overview, you can check our last paper in LNCS
(DOI: 10.1007/978-3-319-15976-8_1), and the wiki's parallelization
page is quite fairly comprehensive too (with a more practical touch to
it).

To understand details of the data-/task-decomposition and the
different parallelization levels, i.e. intra-core: SIMD,
intra-node:threading & accelerators, inter-node: MPI, you may want to
dig up the original papers that describe the various algorithms (DOIs:
10.1002/jcc.20703, 10.1021/ct700301q, doi:10.1016/j.cpc.2013.06.003,
to name a few).

Cheers,
--
Szilárd

>
> Thank you very much in advance for your answer and for your time.
>
>
> Best Regards,
>
> Federico Padua
>
>
>
>
>
>
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