[gmx-developers] pencil decomposition

Roland Schulz roland at utk.edu
Thu Sep 2 04:16:10 CEST 2010

On Wed, Sep 1, 2010 at 9:34 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> Hi,
> I note the new pencil decomposition for PME with interest. Presumably
> that's only for the 3DFFT part?

yes pencil decomposition refers to the 2D decomposition for the FFT.

Under what circumstances does it get used? Under what circumstances does the
> old decomposition get used?

it is always used if the number of pme nodes (all nodes if no separate pme
nodes) is larger than the nodes in the X direction of the PP decomposition.

> Does the user need to know anything to use it effectively on different
> hardware? (e.g. BlueGene vs Intel+Infiniband)
We didn't notice any difference in optimal settings between Cray and
Infiniband. We haven't tested BlueGene. Feedback is welcome.

Should any of this get a mention in the manual?

Not sure what would be helpful.


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