[gmx-users] Re: loab imbalance

[lina]

> > > 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

I do not think there was only 1 core doing something and other 15 cores
doing nothing.

Below is the time-consumed on 8 cpus and 16 cpus. I tried twice to
compare the results. 

8cpus:
	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:  52292.000  52292.000    100.0
                       14h31:32
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    523.244     19.720     16.523      1.453
Finished mdrun on node 0 Tue Apr  6 05:09:47 2010

16cpus:

	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:  96457.000  96457.000    100.0
                       1d02h47:37
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    283.696     10.701      8.957      2.679
Finished mdrun on node 0 Mon Apr  5 01:36:18 2010

Thanks and regards,

lina