GROMACS 4.6 heterogenous CPU-GPU acceleration

Control and data-flow of the heterogeneus parallelization in GROMACS 4.6. The diagram illustrates both normal MD steps (black lines) as well as those steps in which the pair-search and domain-decomposition is carried out (blue). In the latter, the additional transfer of the pair list from the CPU to the GPU and a subsequent pruning done in the CUDA kernel is also indicated.

GROMACS 4.6的异构并行化控制与数据流。本示意图展示了常规分子动力学（Molecular Dynamics, MD）步骤（以黑色线条呈现），以及执行粒子对搜索与域分解的步骤（以蓝色线条呈现）。在后一类步骤中，成对列表从中央处理器（Central Processing Unit, CPU）传输至图形处理器（Graphics Processing Unit, GPU）的额外操作，以及在CUDA核函数中完成的后续剪枝过程也一并得到标注。