[gmx-users] Re: loab imbalance

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 6 14:30:05 CEST 2010

lina wrote:
>> 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

The title of section 3.17 is "Domain Decomposition" and discusses the algorithm 
and mdrun parameters relevant to controlling performance.


>  problem-solved-oriented, so I can easily understand.
> Thanks and regards,
> lina


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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