Abstract: GROMACS is one of the most popular Molecular Dynamic (MD) applications and is widely used in the field of chemical and biomolecular system study. Similar to other MD applications, it is computationally demanding. Therefore, many high-performance platforms have been employed to accelerate it, such as the KNL, Cell Processor, GPU and so on. As the third fastest supercomputer in the world, the TaihuLight contains 40,960 SW26010 processors, and every processor is a typical many-core processor. To make full use of the superior computation ability of the TaihuLight, we port the GROMACS to the SW26010. Finally, we not only achieved the 60× speedup in the hot spot kernel but also came up with a new useful strategy to accelerate the short-range interaction computation. This strategy could deal with the update conflict in the many-core processor acceleration without much performance hit. Besides SW26010, it could also be used in many other processors.
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