[gmx-users] Performance test

[Javier Luque Di Salvo]

Dear community,
I share the results of scaling- performance test. I used this command and
checked the core usage with the help of htop tool (http://hisham.hm/htop/):
    gmx mdrun -ntmpi 1 -ntomp N -pin on -deffnm <md_job> &

Where N is the number of (logical) cores, and hardware is Intel(R) Core(TM)
i7-6700 @3.40 GHz, 16 GB RAM and no GPU. I tested two polymer chains of
different size (psu10= 552 atoms; psu36= 1956 atoms), 1ns NPT simulations
of the previously-equilibrated system, md settings were Berendsen
thermostat and barostat, V-rescale, time step 1fs, rcut-off 1.0 nm, PME for
coulombic computation. In this link the figures:
https://goo.gl/bVZKcU

And the table with the values if problems in opening the figures:
PSU10 (552 atoms)
N   wall-time  ns/day
1   1057.166   81.7025
2   631.117      136.908
3   461.265      187.448
4   352.821      244.886
5   440.070      196.393
6   386.782      223.346
7   348.273      248.083
8   389.243      255.187
------------------
PSU36 (1956 atoms)
N   wall-time  ns/day
1   2259.990  38.231
2   1254.619  68.870
3   875.394   99.267
4   672.042   128.570
5   822.385   105.056
6   712.061   121.338
7   628.172   137.551
8   576.145   149.963

Kind regards,
Javi

2017-11-21 13:50 GMT+01:00 Javier E <jluquedisalvo at gmail.com>:

> Dear users,
>
> I'm doing a performance analysis following this link
> http://manual.gromacs.org/documentation/5.1/user-guide/
> mdrun-performance.html and wanted to ask:
>
> Is there a "standard" procedure to test performance in gromacs (on single
> nodes, one multi-processor CPU)? Following there are some results, the
> system is a small polymeric chain of 542 atoms with no water and NPT 100 ps
> runs (if more information about md settings are needed please ask):
>
> Running on 1 node with total 4 cores, 8 logical cores
> Hardware detected:
>   CPU info:
>     Vendor: GenuineIntel
>     Brand:  Intel(R) Core(TM) i7-6700 CPU @ 3.40GHz
>     SIMD instructions most likely to fit this hardware: AVX2_256
>     SIMD instructions selected at GROMACS compile time: AVX2_256
>
>     GROMACS version: VERSION 5.1.4
>     Precision:                single
>     Memory model:        64 bit
>     MPI library:              thread_mpi
>     OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 32)
>     GPU support:           disabled
>     OpenCL support:      disabled
>
>
> gmx mdrun -ntmpi 1 -ntomp # -v -deffnm out.tpr
>
>
> _______________________________________________________________
> -ntomp  | MPI / OpenMP-     | Wall time (s)|    ns/day   |  % CPU   |
> Note?* |
> ------------------------------------------------------------
> -------------------------------------------------
>    1    |          1/1                 | 1075.764      |    80.315    |
> 100.0   |   No       |
>    2    |          1/2                 |  619.679       |   139.427   |
> 200.0   |   Yes     |
>    3    |          1/3                 |  458.721       |   188.350   |
> 299.9   |   Yes     |
>    4    |          1/4                 |  356.906       |   242.081   |
> 399.8   |   Yes     |
>    5    |          1/5                 |  433.572       |   199.275   |
> 499.0   |   Yes     |
>    6    |          1/6                 |  378.951       |   227.998   |
> 598.0   |   Yes     |
>    7    |          1/7                 |  355.785       |   242.844   |
> 693.1   |   Yes     |
>    8    |          1/8 (default)    |  328.520       |   262.081   |
> 779.0   |   No       |
> ------------------------------------------------------------
> -------------------------------------------------
>
> *NOTE: The number of threads is not equal to the number of (logical) cores
>       and the -pin option is set to auto: will not pin thread to cores.
>
>
> If (MPI-Threads)*(OpenMP-Threads) = number of threads, does mdrun uses
> number of cores= number of threads, and this can be seen in the %CPU usage?
>
> For example, as I installed GROMACS in default, the GMX_OpenMP_MAX_THREAD
> is set at 32 threads, but this will never happen with this hardware (4
> cores, 8 logical), is this correct? By now I'm re-running the exact same
> tests to have at least one replica, and extending the system size and the
> and run time. Any suggestions on how to deep further in this kind of tests
> are welcome,
>
> Best regards
> --
>
> ________________________________________
>
> *Javier Luque Di Salvo*
>
> Dipartamento di Ingegneria Chimica
>
> Universitá Degli Studi di Palermo
> *Viale delle Scienze, Ed. 6*
> *90128 PALERMO (PA)*
> *+39.09123867503 <+39%20091%202386%207503>*
>



-- 

________________________________________

*Javier Luque Di Salvo*

Dipartamento di Ingegneria Chimica

Universitá Degli Studi di Palermo
*Viale delle Scienze, Ed. 6*
*90128 PALERMO (PA)*
*+39.09123867503*