[gmx-users] Performance values

[Maureen Chew]

Szilárd,
Thank you so very much for the reply!    You mention
that time/step is important if trying to do an apples-to-apples
comparison for any given simulation.

I have a few questions - For specific example, use the RNAse reference here:
(http://www.gromacs.org/gpu <http://www.gromacs.org/gpu>)
Influence of box geometry and virtual interaction sites
This is a simulation of the protein RNAse, which contains roughly 24,000 atoms in a cubic box.
The image rnase.png <http://www.gromacs.org/@api/deki/files/224/=rnase.png>, shows a 6 core baseline to be, roughly 50ns/day

First,  assuming this is from rnase_cubic @ ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz <ftp://ftp.gromacs.org/pub/benchmarks/rnase_bench_systems.tar.gz>
which contains these files:
rnase_cubic/rf_verlet.mdp
rnase_cubic/conf.gro
rnase_cubic/topol.top
rnase_cubic/pme_verlet.mdp

3 questions:
- What gmx grompp command was use to generate the tpr file for the result in rnase.png?
	Apologies if its intuitively obvious which mdp  was used
- Aside from -ntmpi and -ntomp parms, what gmx mdrun command was used to obtain
	the 6 core result?
- From that 6 core run, what is the time/step that you refer to?  Is that
	real cycle  and time accounting for neighbor search, force, PME mesh etc,
	and  time/step that you refer to is the wall time/call count?

Thanks in advance!
—maureen


Date: Mon, 7 Aug 2017 16:01:16 +0200
From: Szilárd Páll <pall.szilard at gmail.com <mailto:pall.szilard at gmail.com>>
To: Discussion list for GROMACS users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
Subject: Re: [gmx-users] Performance values


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.
--
Szilárd


On Fri, Jul 28, 2017 at 10:20 AM, Maureen Chew <maureen.chew at oracle.com <mailto: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 <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
> 
> HTH
> 
> 
> On Jul 27, 2017, at 10:15 AM, Maureen Chew <maureen.chew at oracle.com <mailto: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> <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> <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