Luca Ferraro wrote:
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 ;-)
Hm, check your input, check your output...
[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
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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