Optimizing Inter-Node Communication for Molecular Dynamics Simulations
With the trend in High Performance Computing (HPC) towards strong-scaling, HPC programs are no longer limited by the computational performance of the nodes but by the inter-node communication. Optimizing communication hence has become a topic of interest again. One way of optimizing communication lies with the exploration of problem-specific communication algorithms, which can reduce the overhead in communication. We are modeling different communication algorithms which are suitable for molecular dynamics simulations so that we can compare their time consumption based on the simulation parameters. This can be used to evaluate which algorithms will performe best under which conditions.
Publications
- Theresa Werner, Christof Päßler, Ivo Kabadshow, Andreas Beckmann, Matthias Werner, "A Communication Module for FMSolvr", 2023
- Theresa Werner, Christof Päßler, Martin Richter, Ivo Kabadschow, Matthias Werner, "A Petri-Net-Based Approach to Modeling Communication Algorithms for HPC Molecular Dynamics Simulations", in Proceedings of the International Workshop on Petri Nets and Software Engineering (PNSE'23), 1-16, 2023 @InProceedings{Th:Petri:2023,
author = {Theresa Werner and Christof Päßler and Martin Richter and Ivo Kabadschow and Matthias Werner},
title = {{A Petri-Net-Based Approach to Modeling Communication Algorithms for HPC Molecular Dynamics Simulations}},
year = {2023},
month = jun,
booktitle = {Proceedings of the International Workshop on Petri Nets and Software Engineering (PNSE'23)},
publisher = {CEUR Workshop Proceedings},
pages = {1-16},
isbn = {},
doi = {},
keywords = {fmsolvr}
- Theresa Werner, Ivo Kabadshow, Matthias Werner, "Optimizing Communication in Molekular Dynamics Simulations on HPC Clusters", in Simulation and Modeling Methodologies, Technologies and Applications, 86-100, 2023 @inproceedings{Th:Categorization:2023,
author = "Theresa Werner and Ivo Kabadshow and Matthias Werner",
editor = "Gerd Wagner and Frank Werner and Floriano De Rango",
title = "Optimizing Communication in Molekular Dynamics Simulations on HPC Clusters",
booktitle = "Simulation and Modeling Methodologies, Technologies and Applications",
publisher = "Springer International Publishing",
address = "Cham",
year = "2023",
pages = "86--100",
isbn = "978-3-031-43824-0",
doi = "10.1007/978-3-031-43824-0_5",
keywords = "fmsolvr"
- Theresa Werner, Christof Päßler, Ivo Kabadschow, Matthias Werner, "Analytical Model of Communication Algorithm for Simulations with Range-Limited Interactions", in Proceedings of the 13th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH'23), 311-317, 2023 @InProceedings{Th:Shift:2023,
author = {Theresa Werner and Christof Päßler and Ivo Kabadschow and Matthias Werner},
title = {{Analytical Model of Communication Algorithm for Simulations with Range-Limited Interactions}},
year = {2023},
month = jul,
booktitle = {Proceedings of the 13th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH'23)},
publisher = {SCITEPRESS},
pages = {311-317},
isbn = {978-989-758-668-2},
doi = {10.5220/0012085500003546},
keywords = {fmsolvr}
- Theresa Werner, Ivo Kabadschow, Matthias Werner, "Systematic Literature Review of Data Exchange Strategies for Range-limited Particle Interactions", in Proceedings of the 12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH'22), 218 - 225, 2022 @InProceedings{Th:SLR:2022,
author = {Theresa Werner and Ivo Kabadschow and Matthias Werner},
title = {Systematic Literature Review of Data Exchange Strategies for Range-limited Particle Interactions},
year = {2022},
month = jun,
booktitle = {Proceedings of the 12th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH'22)},
publisher = {SCITEPRESS},
pages = {218 - 225},
isbn = {978-989-758-578-4},
doi = {10.5220/0011144400003274},
keywords = {fmsolvr}
2023
2022