[gmx-users] Networking

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 8 19:47:57 CET 2002

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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