Optimierung der Kommunikation zwischen Rechenknoten für Molekulardynamik-Simulationen
Durch den strong-scaling Trend im High Performance Computing (HPC) sind manche HPC-Programme mittlerweile zeitlich limitiert durch die Kommunikation zwischen den Knoten statt wie bisher durch die Rechenleistung auf den Knoten. Kommunikationsoptimierung ist daher wieder ein interessantes Thema. Ein Weg die Kommunikationszeit zu optimieren ist die Anwendung problemspezifischer Kommunikationsalgorithmen, die den Overhead der Kommunikation reduzieren können. Wir befassen uns mit der Modellierung verschiedener Kommunikationsalgorithmen, die vorrangig in der Molekulardynamiksimulation Anwendung finden, sodass wir deren durch die Simulationsparameter bedingten Zeitverbrauch vergleichen können. Die Ergebnisse können genutzt werden, um zu entscheiden, welcher Algorithmus unter welchen Konditionen bessere Zeiten erzielt.
Veröffentlichungen
- Theresa Werner, Christof Päßler, Ivo Kabadshow, Matthias Werner, "Effects of the FMM Tree Mapping on MDS Communication Algorithms (Poster)", 2024
@misc{Th:JLESC24:2024,
title = {{Effects of the FMM Tree Mapping on MDS Communication Algorithms (Poster)}},
author = {Theresa Werner and Christof Päßler and Ivo Kabadshow and Matthias Werner},
year = 2024,
month = april,
location = {Kobe, Japan},
doi = {10.13140/RG.2.2.18996.05765},
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, 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, Christof Päßler, Ivo Kabadshow, Andreas Beckmann, Matthias Werner, "A Communication Module for FMSolvr (Poster)", 2023
@misc{Th:JLESC23:2023,
title = {{A Communication Module for FMSolvr (Poster)}},
author = {Theresa Werner and Christof Päßler and Ivo Kabadshow and Andreas Beckmann and Matthias Werner},
year = 2023,
month = mar,
location = {Bordeaux, France},
doi = {10.13140/RG.2.2.20292.30080},
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}
2024
2023
2022