[gmx-users] Re: loab imbalance

[Berk Hess]

> From: zhao0139 at ntu.edu.sg
> To: gmx-users at gromacs.org
> Date: Tue, 6 Apr 2010 19:39:30 +0800
> Subject: [gmx-users] Re: loab imbalance
> 
> 
> > 
> > On 6/04/2010 5:39 PM, lina wrote:
> > > Hi everyone,
> > >
> > > Here is the result of the mdrun which was performed on 16cpus. I am not
> > > clear about it, was it due to using MPI reason? or some other reasons.
> > >
> > > Writing final coordinates.
> > >
> > >   Average load imbalance: 1500.0 %
> > >   Part of the total run time spent waiting due to load imbalance: 187.5 %
> > >   Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
> > > X 0 % Y 0 %
> > >
> > > NOTE: 187.5 % performance was lost due to load imbalance
> > >        in the domain decomposition.
> > 
> > You ran an inefficient but otherwise valid computation. Check out the 
> > manual section on domain decomposition to learn why it was inefficient, 
> > and whether you can do better.
> > 
> > Mark
> 
> I search the "decomposition" keyword on Gromacs manual, no match found.
> Are you positive about that? Thanks any way, but can you make it more
> problem-solved-oriented, so I can easily understand.
> 
> Thanks and regards,
> 
> lina

This looks strange.
You have 1 core doing something and 15 cores doing nothing.
Do you only have one small molecule?
How many steps was this simulation?

Berk

 		 	   		  
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