The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS
Open accessAbstract
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these benefits, it has been necessary to reformulate some of the most fundamental algorithms, including the Verlet list, pair searching, and cutoffs. Here, we present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade. The setup involves a general cluster-based approach to pair lists and non-bonded pair interactions that utilizes both GPU and central processing unit (CPU) single instruction, multiple data acceleration efficiently, including the ability to load-balance tasks between CPUs and GPUs. The algorithm work efficiency is tuned for each type of hardware, and to use accelerators more efficiently, we introduce dual pair lists with rolling pruning updates. Combined with new direct GPU–GPU communication and GPU integration, this enables excellent performance from single GPU simulations through strong scaling across multiple GPUs and efficient multi-node parallelization.
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Self-citationGROMACS: Fast, flexible, and free
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Self-citationGROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
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Self-citationComputer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
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Self-citationSalomon-Ferrer, R., Götz, A. W., Poole, D., Le Grand, S., & Walker, R. C. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct400314y · Cited by 3,372
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Wang, K., Dagil, R., Lavstsen, T., Misra, S. K., Spliid, C. B., Wang, Y., Gustavsson, T., Sandoval, D. R., Vidal-Calvo, E. E., Choudhary, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23254-1 · Cited by 52
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Self-citationZhang, D., Qiao, L., Lei, X., Dong, X., Tong, Y., Wang, J., Wang, Z., & Zhou, R. (2023) · Nature Communications · doi:10.1038/s41467-023-39410-8 · Cited by 21
Metadata
- Authors
- Páll, S., Zhmurov, A., Bauer, P., Abraham, M., Lundborg, M., Gray, A., Hess, B., & Lindahl, E.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2020-10-05
- Volume
- 153
- Issue
- 13
- Pages
- 134110-134110
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W3035762603
- Cited by
- 940
- References
- 38
- FWCI
- 50.23
- Type
- journal article
- Language
- en
- Open access
- hybrid
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