TweTriS: Twenty trillion-atom simulation
@article{Tchipev2019TweTriSTT, title={TweTriS: Twenty trillion-atom simulation}, author={Nikola Tchipev and Steffen Seckler and M. Heinen and J. Vrabec and Fabio Alexander Gratl and M. Horsch and M. Bernreuther and C. Glass and Christoph Niethammer and N. Hammer and Bernd Krischok and Michael M. Resch and D. Kranzlm{\"u}ller and H. Hasse and H. Bungartz and Philipp Neumann}, journal={The International Journal of High Performance Computing Applications}, year={2019}, volume={33}, pages={838 - 854} }
Significant improvements are presented for the molecular dynamics code ls1 mardyn — a linked cell-based code for simulating a large number of small, rigid molecules with application areas in chemical engineering. The changes consist of a redesign of the SIMD vectorization via wrappers, MPI improvements and a software redesign to allow memory-efficient execution with the production trunk to increase portability and extensibility. Two novel, memory-efficient OpenMP schemes for the linked cell… CONTINUE READING
Figures, Tables, and Topics from this paper
14 Citations
From Molecular Dynamics towards a Node-Level Auto-Tuning Library for N-Body Simulations
- Computer Science
- 2018
- PDF
86 PFLOPS Deep Potential Molecular Dynamics simulation of 100 million atoms with ab initio accuracy
- Computer Science, Physics
- Comput. Phys. Commun.
- 2021
- 12
- PDF
Application and Evaluation of Auto-Tuning Tools in Molecular Dynamics Simulations
- Computer Science
- 2020
- PDF
Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation
- Computer Science
- 2020
- 10
Performance and Portability of State-of-Art Molecular Dynamics Software on Modern GPUs
- Computer Science
- PPAM
- 2019
- PDF
AutoPas: Auto-Tuning for Particle Simulations
- Computer Science
- 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)
- 2019
- 1
- PDF
References
SHOWING 1-10 OF 38 REFERENCES
ls1 mardyn: The massively parallel molecular dynamics code for large systems
- Computer Science, Medicine
- Journal of chemical theory and computation
- 2014
- 74
- PDF
Kernel optimization for short-range molecular dynamics
- Computer Science
- Comput. Phys. Commun.
- 2017
- 12
- PDF
Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure
- Computer Science
- Comput. Phys. Commun.
- 2017
- 10
Kernel Optimization on Short-Range Potentials Computations in Molecular Dynamics Simulations
- Computer Science
- 2015
- 3
Memory-Efficient Implementation of a Rigid-Body Molecular Dynamics Simulation
- Computer Science
- 2012 11th International Symposium on Parallel and Distributed Computing
- 2012
- 6
- PDF
Optimized Force Calculation in Molecular Dynamics Simulations for the Intel Xeon Phi
- Computer Science
- Euro-Par Workshops
- 2015
- 8