GROMACS benchmark
GROMACS is a free and open-source software suite for high-performance molecular dynamics and output analysis.
This directory includes a data file, gromacs_1400k_atoms.tpr
, which can be used to benchmark both GPU and CPU machines. This data file was taken from https://www.hecbiosim.ac.uk/access-hpc/benchmarks.
The benchmarks are designed as strong scaling tests which run across multiple full nodes for a given system.
Usage
From the top-level directory of the repository, you can run the benchmarks with
Filtering the benchmarks
Note that, since we are running strong scaling tests over multiple nodes, the benchmarks may need to be filtered if usage rules restrict the size of jobs which can be run on any given system. To do this filtering, use the -n
option like so
reframe --system <your_system> -c benchmarks/apps/gromacs -r --performance-report -n '.*num_nodes_param=<2|4|8|16>.*'
Again, depending on the system's rules/machine size, further filtering may be needed for GPU tests i.e.
reframe --system <your_system> -c benchmarks/apps/gromacs -r --performance-report -n '.*num_nodes_param=<2|4|8|16>.*num_gpus_per_node_param=<1|2|4>'
Figure of Merit
The figure of merit captured by these benchmarks is the performance metric Rate, measured in ns/day. Here, ns/day refers to the number of nanoseconds of simulation that you can do in a day of computation.
This output can be found in the md.log
file within the output directory produced by Reframe. If the end of this file resembles what is shown below, the Rate 4.892
would be captured.