From: Luca Ferraro <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: gmx-users@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
<[EMAIL PROTECTED]> Subject: Re: [gmx-users] Preliminary report on
benchmark on Opteron Cluster Infiniband on current CVS version To:
Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID:
<[EMAIL PROTECTED]> 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 ;-)
[EMAIL PROTECTED]:~/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
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.
Berk.
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