GROMACS performance on 8 cores workstation

alexmas
Fri, 14 Jan 2022 05:49:19 +0000
User discussions

GROMACS version: 2021.4
GROMACS modification: No

Hello,
I just completed a test run on a new installation and the performance was much lower then I expected: 0.661ns/day with a 41,175 Atoms system on an 8 cores CPU hardware.

Below I am listing more details about my simulation and my hardware.

The gromacs website showcase an example with ~50ns/day for a 24,000 atoms on a 6 cores CPU hardware (no GPU). Since my system is less than 2x larger, I would have expected to achieve at least 10ns/day.

I have not installed a GPU yet, and before I invest in it I would like to make sure I have the system optimally set up.

Is there something I am missing?

This is my simulation:
1ns NPT run, 50,000 steps, 2 fs/step
Total: 41,175 Atoms
Solvent: 12,580 water molecules (37,740 atoms)
Protein: 3,431 atoms (255 residues)
GROMACS version: 2021.4
Running on 1 node with total 8 cores, 16 logical cores
Using 1 MPI thread
Using 16 OpenMP threads
Using SIMD 4x4 nonbonded short-range kernels

Hardware:
AMD Ryzen 7 1700, 3.0GHz 8 cores (16 threads) non overclocked, 16M/AM4/65W
RAM: 16GB DDR4 2400UDIMM

During the simulation, all 16 threads engaged at ~3.1GHz with >95% load (according to Conky).

Thanks in advance for your help,

Al

9 posts - 4 participants