Optimizing fine-grained communication in a biomolecular simulation application on Cray XK6


Achieving good scaling for fine-grained communication intensive applications on modern supercomputers remains challenging. In our previous work, we have shown that such an application --- NAMD --- scales well on the full Jaguar XT5 without long-range interactions; Yet, with them, the speedup falters beyond 64K cores. Although the new Gemini interconnect on… (More)
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