[gmx-users] Performance values

Maureen Chew maureen.chew at oracle.com
Fri Jul 28 10:20:45 CEST 2017

You might find this reference handy - it has a really nice explanation for how to look 
at a log file
Topology preparation, "What's in a log file", basic performance improvements: Mark Abraham, Session 1A <http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation,_%22What's_in_a_log_file%22,_basic_performance_improvements:_Mark_Abraham,_Session_1A>

The “Performance:” values are a throughput measure where both values represent
the same thing in different terms.  In your sample below, 3.964 is the
number of nanoseconds that can be simulated in 24 hours while it takes
6.054 hours to simulate 1 ns


On Jul 27, 2017, at 10:15 AM, Maureen Chew <maureen.chew at oracle.com> wrote:
> Where is it documented how the mdrun performance metrics are calculated ? I?ve
> looked here
> http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html <http://manual.gromacs.org/documentation/2016/user-guide/mdrun-performance.html>
> and here
> http://manual.gromacs.org/documentation/2016.3/manual-2016.3.pdf <http://manual.gromacs.org/documentation/2016.3/manual-2016.3.pdf>
> but seem to have missed  explanation.  
> Are the sample mdrun times below user time or real time?  Generally, wall is real time
> I understand that ?Performance:? is not a linear scale but what is the scale
> in the 2016.3 sample below?
>              Core t (s)   Wall t (s)        (%)
>       Time:    69761.050      272.504    25600.0
>                 (ns/day)    (hour/ns)
> Performance:        3.964        6.054

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