[gmx-users] [Re]: Preliminary report on benchmark on Opteron Cluster Infinib

Berk Hess gmx3 at hotmail.com
Wed Apr 18 12:00:24 CEST 2007

>From: Luca Ferraro <l.ferraro at caspur.it>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] [Re]: Preliminary report on benchmark on Opteron 
>Cluster Infiniband on current CVS version
>Date: Wed, 18 Apr 2007 11:53:00 +0200
>>Date: Tue, 17 Apr 2007 19:08:02 +0200 From: Erik Lindahl
>><lindahl at cbr.su.se> Subject: Re: [gmx-users] Preliminary report on
>>benchmark on Opteron Cluster Infiniband on current CVS version To:
>>Discussion list for GROMACS users <gmx-users at gromacs.org> Message-ID:
>><242D227B-350E-4172-AA9D-A4CF0427BD47 at cbr.su.se> Content-Type:
>>text/plain; charset=US-ASCII; format=flowed Hi, On Apr 17, 2007, at
>>6:26 PM, Luca Ferraro wrote:
>>>>/usr/bin/time mpiexec -n ${proc} mdrun_mpi -d 1 ${proc} 1
>>For a start, the domain decomposition flag is "-dd"  :-)
><homer_mode> doh!! </homer_mode> :-P
>.. well, a nice "warning" from mdrun complaining
>"what did you mean with that -foo option?!"
>would be really appreciated in the next release ;-)
>lferraro at poseidon:~/benches/d.lzm>mdrun -foo
>[SNIP] (with no warnings)
>Reading file topol.tpr, VERSION 3.3.99_development_20070215 (single 
>starting mdrun 'LYSOZYME (E.C. in water'
>5000 steps,     20.0 ps.
>OK, I will run these benches again and post (I hope correct this time) 
>results. I also ask for some clarification:
>1) Does the -dd vector (x,y,z) really reflect a spatial splitting of the 
>simulation BOX along the x,y,z axes? What happens to bonded molecules 
>crossing the splitting? Is there any documentation or notes about 
>technictian details on this new parallel implementation? (I mean beyond the 
>source code).

Yes if reflects the splitting.
Bonded molecules are split (and treated correctly).
No, there is no documentation.
This code is not released yet and is not intented to be used yet,
except by the developers.

>2) -rdd   real      0  The minimum distance for DD communication
>what exactly means? (can you give me any example?)

This you only need when you have bonded interactions at distances
larger than the cut-off.


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