Exploit Innovative Computer Architectures with Molecular Dynamics

Exploit Innovative Computer Architectures with Molecular Dynamics

연구 분야: Strategies

학회: International Conference on Numerical Computations: Theory and Algorithms

Atomistic simulations are a powerful tool to analyse the structure and the behavior of various biological molecules and are widely used in biochemistry studies. Currently, there are several software packages available which provide the algorithms for the numerical resolution of the physical equation necessary for the simulations. Those softwares are demanding and need to handle a large amounts of resources, therefore the hardware in use has to be efficient in terms of performance and costs. Here we tested the Molecular Dynamics toolkit Gromacs on different platforms: Intel, AMD and ARM clusters are considered, also with the support of NVIDIA GPUs. During the tests energy consumption is measured in both idle and working case obtaining the energy to solution for every machine. While the highest performances are obtained with Intel we found that AMD and ARM servers are valid option if energy savings is considered alongside performance, the use of GPU gives a remarkable contribution to reduce consumption.