[gmx-developers] pencil decomposition

[hess at sbc.su.se]

Hi,

I have added some lines to the pdf manual.
If you have any comments, please tell me.

Berk

> Hi,
>
> The 2D PME decomposition has a large effect on performance on a large
> number of nodes, on a small number the effect is small or slightly
> negative.
> There is no effect on the results and mdrun chooses it automatically,
> which can be done relatively independently of architecture, as Roland
> said.
> So the "normal" user does not need to know about it.
> It might be useful though to add one or two lines on this in the pdf
> manual.
> I am at a workshop right now, so I don't know if I have time to do this
> before the 4.5 manual release.
>
> Berk
>
>
>> 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.
>>
>> Roland
>>
>>
>>
>>> --
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>
>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>> --
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
>
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>