[gmx-users] Re: Re: loab imbalance

Justin A. Lemkul jalemkul at vt.edu
Tue Apr 6 14:58:16 CEST 2010

lina wrote:
>> 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
> There must be another bible manual I do not know. I checked the one 
> GROMACS Groningen Machine for Chemical Simulations USER MANUAL
> Version 3.3 and 3.2. Can you tell me which manual was the one you
> mentioned (better provide the links that I can download if easy for
> you). 

Since you're using Gromacs 4, you should probably be reading the Gromacs 4.0 manual:



> Thanks,
> lina


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


More information about the gromacs.org_gmx-users mailing list