Supplementary Materials for "High-Performance and Scalable Agent-Based Simulation with BioDynaMo"

This repository contains all Supplementary Materials for the paper "High-Performance and Scalable Agent-Based Simulation with BioDynaMo" and received the Best Artifact Award at PPoPP '23.

The paper is available at https://doi.org/10.1145/3572848.3577480 and https://doi.org/10.48550/arXiv.2301.06984.

We provide detailed instructions to reproduce all results of the paper in file: SF1-readme.pdf

Citation:

If you find this repository useful, please cite the following works:

Lukas Breitwieser et al., High-Performance and Scalable Agent-Based Simulation with BioDynaMo. 2023, In Proceedings of the 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming (Montreal, QC, Canada) (PPoPP ’23). Association for Computing Machinery, New York, NY, USA, 174–188. https://doi.org/10.1145/3572848.3577480 arXiv:2301.06984 [cs.DC]

@inproceedings{breitwieser_biodynamo_2023,
  author = {Breitwieser, Lukas and Hesam, Ahmad and Rademakers, Fons and Luna, Juan G\'{o}mez and Mutlu, Onur},
  title = {High-Performance and Scalable Agent-Based Simulation with BioDynaMo},
  year = {2023},
  isbn = {9798400700156},
  publisher = {Association for Computing Machinery},
  address = {New York, NY, USA},
  url = {https://doi.org/10.1145/3572848.3577480},
  doi = {10.1145/3572848.3577480},
  booktitle = {Proceedings of the 28th ACM SIGPLAN Annual Symposium on Principles and Practice of Parallel Programming},
  pages = {174–188},
  numpages = {15},
  keywords = {NUMA, HPC, performance evaluation, parallel computing, space-filling curve, high-performance simulation, performance optimization, agent-based modeling, memory layout optimization, memory allocation, scalability},
  location = {Montreal, QC, Canada},
  series = {PPoPP '23},
  archivePrefix = "arXiv",
  eprint        = "2301.06984",
  primaryClass  = "cs.DC"
}

Lukas Breitwieser et al., BioDynaMo: a modular platform for high-performance agent-based simulation, Bioinformatics, Volume 38, Issue 2, 15 January 2022, Pages 453–460, https://doi.org/10.1093/bioinformatics/btab649

@article{breitwieser_biodynamo_2022,
    author = {Breitwieser, Lukas and Hesam, Ahmad and de Montigny, Jean and Vavourakis, Vasileios and Iosif, Alexandros and Jennings, Jack and Kaiser, Marcus and Manca, Marco and Di Meglio, Alberto and Al-Ars, Zaid and Rademakers, Fons and Mutlu, Onur and Bauer, Roman},
    title = "{BioDynaMo: a modular platform for high-performance agent-based simulation}",
    journal = {Bioinformatics},
    volume = {38},
    number = {2},
    pages = {453-460},
    year = {2021},
    month = {09},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btab649},
    url = {https://doi.org/10.1093/bioinformatics/btab649}
}

License

License information for the code repositories in SF2-code.tar.gz can be found in the files:

• biodynamo/LICENSE
• bdm-paper-examples/LICENSE