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:
http://www.gromacs.org/Documentation/Manual
-Justin
Thanks,
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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