[gmx-users] Regarding getting good performance for mdrun

[Mark Abraham]

Hi,

The different ways of running in parallel are constructed to provide
equivalently correct sampling. This extra output you get with -v is
intended to help you choose how to run efficiently, but if it's confusing
just don't ask for it ;-) It's not something that a new user should be
worried about until they are going to run months worth of a kind of
simulation!

Mark

On Sat, May 5, 2018, 08:59 Dilip.H.N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello all,
> My workstation has 1 node with total 24 cores, 48 logical cores.
>
> 1] I gave the command as: gmx mdrun -v -s abc.tpr -deffnm abc
>
> I got few messages as:-
>
> NOTE: Parallelization is limited by the small number of atoms,
>       only starting 16 thread-MPI ranks.
>       You can use the -nt and/or -ntmpi option to optimize the number of
> threads.
> Using 16 MPI threads
> Using 3 OpenMP threads per tMPI thread
> WARNING: This run will generate roughly 51484 Mb of data
> starting mdrun 'abc system'
> 1000000 steps,   1000.0 ps.
> step 999900, remaining wall clock time:     0 s          imb F 10%
> Writing final coordinates.
> step 1000000, remaining wall clock time:     0 s
>  Average load imbalance: 11.0 %
>  Part of the total run time spent waiting due to load imbalance: 1.7 %
> NOTE: 28 % of the run time was spent communicating energies,
>       you might want to use the -gcom option of mdrun
>
> 2] and then if i give the command as: gmx mdrun -v -s abc.tpr -deffnm
> abc -ntmpi 6 -ntomp 8
> I got:
> Using 6 MPI threads
> Using 8 OpenMP threads per tMPI thread
> step 36800, will finish Sat May  5 12:42:12 2018 imb F  6%
>
> So, My questions are:-
> a) Does the simulation run just with gmx mdrun, effect on the
> trajectories/output files
> b) "28 % of the run time was spent communicating...." Has it affected the
> resulting output..??
> c) what does this imb F means..?? and what is the significance of the
> percentage (say 1.7%) states/defines..??
> c) Any other information regarding these are highly beneficial..
>
> Thank you.
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
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