[gmx-users] Performance values

Szilárd Páll pall.szilard at gmail.com
Mon Aug 7 16:01:23 CEST 2017

Indeed, "Wall t" is real application wall-time, nanoseconds/day is the
typical molecular dynamics performance unit that corresponds to the
effective amount of simulation throughput (note that this however
depends on the time-step and without that specified it is not useful
to compare to other runs), so often it is useful to use it convert it
to time/step.

On Fri, Jul 28, 2017 at 10:20 AM, Maureen Chew <maureen.chew at oracle.com> wrote:
> 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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