Re: [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 mailto:pall.szil...@gmail.com>>
To: Discussion list for GROMACS users mailto:gmx-us...@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 mailto:maureen.c...@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  <mailto:maureen.c...@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  272.50425600.0
>>(ns/day)(hour/ns)
>> Performance:3.9646.054
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Performance values

[Maureen Chew]

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

HTH


On Jul 27, 2017, at 10:15 AM, Maureen Chew  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  272.50425600.0
> (ns/day)(hour/ns)
> Performance:3.9646.054
> 

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Performance values

[Maureen Chew]

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 

and here
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  272.50425600.0
 (ns/day)(hour/ns)
Performance:3.9646.054

 

TIA
—maureen
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Looking for longer running, publicly avail use cases

[Maureen Chew]

I’ve  built GROMACS 2016.2 on SPARC/Solaris - make check and all 2016.2
regression (simple, complex, kernel, freeenergy, rotation, pdb2gmx, essential
dynamics)  tests pass. 

I’d like to do some performance modelling around trying different 
number of openmp threads, mpi threads and ranks so looking for 
larger use cases with longer runs which might be more amenable 
to many cores/threads and high memory throughput.  

Are there any publicly available tests that I could use?  Accompanying
results for validation would be great too.

Thanks in advance.
—maureen
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.