[gmx-users] domain decomposition and load balancing
kgp.amit at gmail.com
Sat Feb 20 00:23:36 CET 2010
Hi Mark and Justin,
I am using a box of size (20nm)x(20nm)x(60nm)..system is open along z ie
I tried using only two nodes, it gives the same error
There is no domain decomposition for 2 nodes that is compatible with the
given box and a minimum cell size of 0.889862 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
On Fri, Feb 19, 2010 at 3:16 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:
> ----- 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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