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Scaling a Biological Simulator Platform to the Cloud

Kanellis, Konstantinos; Rademakers, Fons; Breitwieser, Lukas


A distributed middleware early prototype has been designed for the BioDynaMo project, which aims to be a general platform for computer simulations of biological tissue dynamics. The middleware’s functionality has been implemented keeping in mind the diversity of the performance and reliability characteristics of highperformance clusters and cloud environments. It currently, exposes a transparent and straightforward API to the simulation engine, hiding most of the internal low-level communication details, and it is also capable of sending ROOT objects over the network. By making use of a robust message-oriented library, called ZeroMQ, and by extending its flexible network node organization patterns, we believe it will be able to speed-up the execution of large-scale simulations when many computational nodes are employed. This claim, however, needs to be investigated using benchmarking and profiling techniques under real-world systems and network infrastructures.

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