[gmx-users] domain decomposition and load balancing
mark.abraham at anu.edu.au
Sat Feb 20 00:16:43 CET 2010
----- Original Message -----
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Date: Saturday, February 20, 2010 10:13
Subject: Re: [gmx-users] domain decomposition and load balancing
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Amit Choubey wrote:
> >Hi Mark,
> >I am not using PME calculation.
> >I was hoping mdrun will do the cell allocation itself.
> It will, unless it can't, which is exactly your problem.
> Mark's point stands, regardless of whether or not you're using
> PME. DD requires certain minimum size requirements (which
> are discussed in the manual and the Gromacs 4 paper), so you
> have two choices:
> 1. Read about the options mdrun is telling you about.
> 2. Use fewer nodes so that the DD algorithm can construct
> reasonably-sized domains.
3. Use a larger simulation system so the minimum cell size is larger w.r.t. the cutoffs
4. (If reasonable) Don't use pbc=xy
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