[gmx-users] Slow MDRUN performance

[Syed Azeem]

Hi all,

I installed gromacs 5.1.2 on a new machine.
Config: Intel Core i5 6500 3.20 GHz Quad Core Skylake with 8 GB DDR4.

Then I started a NVT simulation for 500ps with ~250000 atom system.
Surprisingly, the estimated time was 4 days and 3 hours.

There was a note stating consider rebuilding gmx with the
GMX_USE_RDTSCP=ON CMake option, as follows:

GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Command line:
  gmx mdrun -v -deffnm nvt


Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: None

Compiled SIMD instructions: None, GROMACS could use AVX2_256 on this
machine, which is better


The current CPU can measure timings more accurately than the code in
gmx was configured to use. This might affect your simulation
speed as accurate timings are needed for load-balancing.
Please consider rebuilding gmx with the GMX_USE_RDTSCP=ON CMake option.

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads


WARNING: Using the slow plain C kernels. This should
not happen during routine usage on supported platforms.

Then, I rebuilt gromacs with the CMAKE GMX_USE_RDTSCP=ON, as suggested.

Again the performance is slow with the same note being generated.

PS: For comparison, I ran 500 ps NVT simulation of the same ~250000
atom system on another machine of the same config and finished within
7 hours.

What mistake am I making in the installation?

Thanks in advance,

Azeem