[gmx-users] Re: Re: loab imbalance

[lina]

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.

-Justin

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.

lina