Dataset containing raw CP2K output logs produced by running benchmarks from the BioExcel QM/MM benchmark suite (https://doi.org/10.5281/zenodo.6591692), provided as part of BioExcel-2 project deliverable D1.6. An analysis of (a subset of) these benchmark results can be found in https://doi.org/10.5281/zenodo.6591574 Machines used for benchmarking: Cirrus@EPCC (HPE SGI ICE XA): https://www.cirrus.ac.uk Infiniband interconnect CPU compute nodes: 2 x 18-core Intel Xeon (Broadwell) E5-2695, 2.1 GHz 256GB RAM GPU compute nodes: 2 x NVIDIA Tesla V100 (Volta) SXM2-16GB 2 x 20-core Intel Xeon (Cascade Lake) Gold 6248, 2.4 GHz 384GB RAM ARCHER2@EPCC (HPE CRAY EX): https://www.archer2.ac.uk/ Interconnect: HPE Cray Slingshot Compute nodes: 2 x 64-core AMD EPYC (Zen2 Rome) 7742, 2.25GHz 256GB RAM Benchmarking protocol Repeated runs to rule out machine noise variability were performed for each benchmark on each machine for both 1 MD step and 6 MD steps. Subsequent analysis and visualisation of parallel scaling of average runtime per MD step and subroutine-level profiling was performed using our analysis script available from: https://doi.org/10.5281/zenodo.6591681 Results on Cirrus CPU nodes are for CP2K release version 8.1, whilst results on Cirrus GPU nodes and ARCHER2 are with CP2K version 8.2.