论文标题
分解Gromacs的平行性能，Gromacs是一种高性能分子动力学软件
Breaking Down the Parallel Performance of GROMACS, a High-Performance Molecular Dynamics Software
论文作者
论文摘要
Gromacs是使用分子动力学（MD）模拟技术使用最广泛使用的HPC软件包之一。在这项工作中，我们使用不同的配置，HPC系统和FFT库（FFTW，Intel MKL FFT和FFT Pack）量化Gromacs并行性能。我们分解了每个gromacs计算阶段的成本，并确定了不可算的阶段，例如使用大量过程时3D FFT计算过程中的MPI通信。我们表明，粒子网埃瓦尔德阶段和3D FFT计算显着影响gromacs的性能。最后，我们讨论了对FFT计算开发gromacs特别兴趣的绩效机会。
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.
