  GROMACS is one of the most widely used HPC software packages using the
Molecular Dynamics (MD) simulation technique. In this work, we quantify GROMACS
parallel performance using different configurations, HPC systems, and FFT
libraries (FFTW, Intel MKL FFT, and FFT PACK). We break down the cost of each
GROMACS computational phase and identify non-scalable stages, such as MPI
communication during the 3D FFT computation when using a large number of
processes. We show that the Particle-Mesh Ewald phase and the 3D FFT
calculation significantly impact the GROMACS performance. Finally, we discuss
performance opportunities with a particular interest in developing GROMACS for
the FFT calculations.
