[gmx-users] Performance test

[Javier E]

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*