[gmx-users] another question about performance

[Justin A. Lemkul]

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

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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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