The authors study the adaptation of an optimistic Time Warp kernel to cross-cluster computing on the Grid. Wide-area communication, the primary source of overhead, is offloaded onto dedicated routing processes. This a...
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The authors study the adaptation of an optimistic Time Warp kernel to cross-cluster computing on the Grid. Wide-area communication, the primary source of overhead, is offloaded onto dedicated routing processes. This allows the simulation processes to run at full speed and thus significantly decreases the performance gap caused by the wide-area distribution. Further improvements are obtained by employing message aggregation on the wide-area links and using a distributed global virtual time algorithm. The authors achieve many of their objectives for a cellular automaton simulation with lazy cancellation and moderate communication. High communication rates, especially with aggressive cancellation, present a challenge. This is confirmed by the experiments with synthetic loads. Even then, a satisfactory speedup can be achieved, provided that the computational grain of events is large enough.
Infection, replication and mutation govern the population dynamics of viruses and are the key mechanisms driving their evolution. In particular, RNA viruses (such as the causative agents of Ebola, Dengue, Zika, West N...
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ISBN:
(纸本)9780769561493
Infection, replication and mutation govern the population dynamics of viruses and are the key mechanisms driving their evolution. In particular, RNA viruses (such as the causative agents of Ebola, Dengue, Zika, West Nile, and SARS) have the highest mutation rates which enable them to form highly diverse populations within a single host, evade immune responses and develop resistances to drugs. Understanding the complexity of virus evolution is crucial for developing reliable countermeasures. We present an exploratory simulation model to study the evolution of heterogeneous virus populations in heterogeneous cell environments. This is a unique model that operates at three scales and captures the core mechanisms of the evolutionary process. To the best of our knowledge, this is the first HPC-based simulation of its kind.
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