Benchmarking of GPU Performance Saturation on Accelerated Cluster Nodes via Molecular Dynamics Software Packages
摘要
The fast development of Graphics processing units (GPUs) and the software libraries needed for their usage in scientific computing allows highly efficient calculations using not only a single but also multiple GPUs per task. One of the fields in which graphic cards are widely used is molecular dynamics (MD). By including a large number of GPUs in a single MD simulation, systems with the size of several millions of atoms can be simulated. However, the most common sizes of systems studied via MD rarely exceed 300 k atoms. The computational resources of a single GPU might not be fully occupied by such systems, making the use of further graphic cards inefficient. To estimate at which system size the resources of a given GPU are saturated, in this work, we studied the performance of data center-class graphic cards from different vendors as a function of the number of atoms in the simulated system. We found out that for all graphic cards, the resource saturation is reached at system sizes of approximately 250 k atoms, confirming the initial assumption that the computational capabilities of a single GPU are sufficient for the most commonly studied system sizes.