[gmx-users] [Re]: Preliminary report on benchmark on Opteron Cluster Infiniband on current CVS version

[David van der Spoel]

Luca Ferraro wrote:
>> 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"  :-)
>>
>> Cheers,
>>
>> Erik
>>
>>
> 
> <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 ;-)
> 
Hm, check your input, check your output...


> lferraro at poseidon:~/benches/d.lzm>mdrun -foo
> [SNIP] (with no warnings)
> Reading file topol.tpr, VERSION 3.3.99_development_20070215 (single 
> precision)
> starting mdrun 'LYSOZYME (E.C.3.2.1.17) 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 

yes. splitting molecules works automatically with LINCS.


> crossing the splitting? Is there any documentation or notes about 
> technictian details on this new parallel implementation? (I mean beyond 
> the source code).
> 
we're writing a paper.

> 2) -rdd   real      0  The minimum distance for DD communication
> what exactly means? (can you give me any example?)
> 
no.

> Again, thank you in advance for any support.
> 
> luca
> 
> 
> 
No documentation :) for development code....

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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