Albert wrote:
Hello:
here is my log file for mdrun:
Writing final coordinates.
step 100000, remaining runtime: 0 s
Average load imbalance: 10.8 %
Part of the total run time spent waiting due to load imbalance: 4.3 %
Steps where the load balancing was limited by -rdd, -rcon and/or -dds:
X 0 % Y 19 % Z 0 %
Average PME mesh/force load: 0.665
Part of the total run time spent waiting due to PP/PME imbalance: 5.7 %
NOTE: 5.7 % performance was lost because the PME nodes
had less work to do than the PP nodes.
You might want to decrease the number of PME nodes
or decrease the cut-off and the grid spacing.
NOTE: 9 % of the run time was spent communicating energies,
you might want to use the -gcom option of mdrun
Parallel run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 2435.554 2435.554 100.0
40:35
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 409.701 22.103 7.095 3.383
gcq#149: "It's Against the Rules" (Pulp Fiction)
As we can see from the end of this log file, the performance is
7.1ns/day, 3.4ns/hour. I am very confused about this output. How could
this happen? Is there only two hours something each day?
I don't understand the problem. 7.095 ns/day * 3.383 hr/ns = 24.002385 hr/day.
-Justin
--
========================================
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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