[gmx-users] Networking

[David van der Spoel]

On Tue, 8 Jan 2002, Justin MacCallum wrote:

>> Did you use grompp -shuffle -sort
>> It certainly shouldn't be this bad. For a more exact comparison you may 
>> want to have a look at the gromacs benchmarks which you can download from 
>> www.gromacs.org
>> 
>> Groeten, David.
>
>I didn't use the -shuffle or -sort options.  I will rerun the tests using
>those options.  Its my understanding that as molecules diffuse, the
>benifits of these options will decrease.  In other words, spacial
>decomposition isn't implemented yet.  Is that correct?
No spatial decomposition yet. SHuffling gives you different moleculetypes
on different processors. It is a huge win for membranes. Sorting gives you
initially (for the time you are benchmarking) advantages too. Ofcourse
diffusion changes that.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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