[gmx-users] Re: Re: loab imbalance

lina zhao0139 at ntu.edu.sg
Tue Apr 6 15:05:32 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
>>> clear about it, was it due to using MPI reason? or some other
>>> 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
>>> 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
>> manual section on domain decomposition to learn why it was
>> and whether you can do better.
>> Mark
> I search the "decomposition" keyword on Gromacs manual, no match
> 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
and mdrun parameters relevant to controlling performance.


Sorry, the acroread is really not sensitive in searching "domain" or
"decomposition" on version 3.3. I did the same search on version 3.2 and
I found it. I am not so familiar with this manual. Thanks again.


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