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
problem-solved-oriented, so I can easily understand.
Thanks and regards,
lina
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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