ArticleJournal of computational chemistry2025
Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster.
Article in Journal of computational chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Accelerating molecular dynamics simulations using fast Ewald summation with prolates.Nature communications · 2026Article
- Structural flexibility of the human vault particle revealed by high-resolution cryo-EM and molecular dynamics simulations.Nature communications · 2026Article
- Coarse-Grained Martini 3 Model of Chondroitin Sulfate A.Journal of chemical theory and computation · 2026Article
- Lignin-Derived Oligomers as Promising mTOR Inhibitors: Insights from Dynamics Simulations.International journal of molecular sciences · 2025Article
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7 authors.
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Abstract
We benchmarked the performance of the GROMACS 2024 molecular dynamics (MD) code on a modern high-performance computing (HPC) cluster with AMD CPUs on up to 65,536 CPU cores. We used five different MD systems, ranging in size from about 82,000 to 204 million atoms, and evaluated their performance using two different Message Passing Interface (MPI) libraries, Intel-MPI and Open-MPI. The largest system showed near-perfect strong scaling up to 512 nodes or 65,536 cores, maintaining a parallel efficiency above 0.9 even at the highest level of parallelization. Energy efficiency for a given number of nodes was generally equal to or slightly better than parallel efficiency. We achieved peak performances of 687 ns/d for the 82k atom system, 116 ns/d for the 53M atom system, and about 35 ns/d for the largest 204M atom system. These results demonstrate that highly optimized software running on a state-of-the-art HPC cluster provides sufficient computing power to simulate biomolecular systems at the mesoscale of viruses and organelles, and potentially small cells in the near future.
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