Carla Jamous wrote:
Hi everyone,
Lately I've been using gromacs version 3.3.3. Yesterday, I started
simulations in a cluster where gromacs version is 4.0.3.
Why start with 4.0.3? You should be using the latest stable version (4.0.7).
After a run, I got this error message:
Average load imbalance: 0.5 %
Part of the total run time spent waiting due to load imbalance: 0.3 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
X 0 % Y 0 %
Average PME mesh/force load: 0.898
Part of the total run time spent waiting due to PP/PME imbalance: 2.7 %
I don't have a clue what this means & how can I fix it?
There's nothing that needs to be fixed, per se. "Load imbalance" has to do with
how well divided the system in terms of PP/PME balance (discussed in the Gromacs
manual - read about domain decomposition). The very small percent imbalance you
got means you probably achieved decent performance given however this PP/PME
imbalance. There are many threads in the list archive about how to make things
faster and what this all means. The manual should be the first port of call,
after which you should have a look in the archives. If you want to try to
optimize something about your system, we will need a lot more information - the
DD grid, .mdp file, how many nodes are being assigned for PME (and whether or
not you're doing it manually), etc.
-Justin
Please can anyone help?
Thank you
Carla
--
========================================
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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