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Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
Open accessAbstract
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.
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Cited by
Boyd, B. J., Bergström, C. A. S., Vinarov, Z., Kuentz, M., Brouwers, J., Augustijns, P., Brandl, M., Bernkop-Schnürch, A., Shrestha, N., Préat, V., et al. (2019) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2019.104967 · Cited by 367
Bioinspired hierarchical porous membrane for efficient uranium extraction from seawater
Yang, L., Xiao, H., Qian, Y., Zhao, X., Kong, X.-Y., Liu, P., Xin, W., Fu, L., Jiang, L., & Wen, L. (2021) · Nature Sustainability · doi:10.1038/s41893-021-00792-6 · Cited by 346
Kisalu, N. K., Idris, A. H., Weidle, C., Flores-Garcia, Y., Flynn, B. J., Sack, B. K., Murphy, S., Schön, A., Freire, E., Francica, J. R., et al. (2018) · Nature Medicine · doi:10.1038/nm.4512 · Cited by 293
Martinize2 and Vermouth provide a unified framework for molecular topology generation
Kroon, P. C., Grünewald, F., Barnoud, J., van Tilburg, M., Brasnett, C., Souza, P. C., Wassenaar, T. A., & Marrink, S. J. (2025) · eLife · doi:10.7554/elife.90627 · Cited by 124
Bhattacharyya, M., Stratton, M. M., Going, C. C., McSpadden, E. D., Huang, Y., Susa, A. C., Elleman, A., Cao, Y. M., Pappireddi, N., Burkhardt, P., et al. (2016) · eLife · doi:10.7554/elife.13405 · Cited by 112
Metadata
- Authors
- Páll, S., Abraham, M. J., Kutzner, C., Hess, B., & Lindahl, E.
- Venue
- Lecture Notes in Computer Science
- Publisher
- Springer International Publishing
- Published
- 2015
- Pages
- 3-27
- ISSN
- 0302-9743 (ISSN-L)
- 1611-3349
- OpenAlex
- W1624860839
- Cited by
- 1,208
- References
- 4
- FWCI
- 40.70
- Type
- conference paper
- Language
- en
- Open access
- green
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