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arXiv · 2306.11544

Lessons learned from a performance analysis and optimization of a multiscale cellular simulation

Marc Clascà·Marta Garcia-Gasulla·Arnau Montagud·Jose Carbonell Caballero·Alfonso Valencia
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Abstract

This work presents a comprehensive performance analysis and optimization of a multiscale agent-based cellular simulation. The optimizations applied are guided by detailed performance analysis and include memory management, load balance, and a locality-aware parallelization. The outcome of this paper is not only the speedup of 2.4x achieved by the optimized version with respect to the original PhysiCell code, but also the lessons learned and best practices when developing parallel HPC codes to obtain efficient and highly performant applications, especially in the computational biology field.

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Marc Clascà, Marta Garcia-Gasulla, Arnau Montagud, Jose Carbonell Caballero, Alfonso Valencia. 2023-06-20. Lessons learned from a performance analysis and optimization of a multiscale cellular simulation. https://doi.org/10.1145/3592979.3593403

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