MDBenchmark — quickly generate, start and analyze benchmarks for your molecular dynamics simulations.

MDBenchmark is a tool to squeeze the maximum out of your limited computing resources. It tries to make it as easy as possible to set up systems on varying numbers of nodes and compare their performances to each other.

You can also create a plot to get a quick overview of the possible performance (and also show of to your friends)! The plot below shows the performance of a molecular dynamics system on up to five nodes with and without GPUs.

You can install mdbenchmark via pip, conda or pipenv:

pip install mdbenchmark

conda install -c conda-forge mdbenchmark

pipenv install mdbenchmark

After installation MDBenchmark is accessible on your command-line via mdbenchmark:

$ mdbenchmark
Usage: mdbenchmark [OPTIONS] COMMAND [ARGS]...

  Generate and run benchmark jobs for GROMACS simulations.

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  analyze   analyze finished benchmark.
  generate  Generate benchmark queuing jobs.
  submit    Start benchmark simulations.

• Generates benchmarks for GROMACS and NAMD simulations (contributions for other MD engines are welcome!).
• Automatically detects the queuing system on your high-performance cluster and submits jobs accordingly.
• Grabs performance from the output logs and creates a fancy plot.
• Benchmarks systems on CPUs and/or GPUs.

The following shows a short usage reference for MDBenchmark. Please consult the documentation for a complete guide.

Assuming you want to benchmark GROMACS version 2016.4 and your TPR file is called protein.tpr, run the following command:

mdbenchmark generate --name protein --module gromacs/2016.4

To run benchmarks on GPUs simply add the --gpu flag:

mdbenchmark generate --name protein --module gromacs/2016.4 --gpu

After you generated your benchmarks, you can submit them at once:

mdbenchmark submit

As soon as the benchmarks have been submitted you can run the analysis via mdbenchmark analysis. When at least one system has finished, the script will produce a .csv output file or a plot for direct usage (via the --plot option).

Note: The plotting function currently only allows to plot a CPU and GPU benchmark from the same module. This will be fixed in an upcoming version and is already implemented in the develop branch. If you want to compare different modules with each other, either use the --directory option to generate separate plots or create your own plot from the provided CSV file.

$ mdbenchmark analyze
                   gromacs  nodes  ns/day  run time [min]    gpu        host  ncores
0  gromacs/5.1.4-plumed2.3      1  10.878              15  False       draco      32
1  gromacs/5.1.4-plumed2.3      2   21.38              15  False       draco      64
2  gromacs/5.1.4-plumed2.3      3  34.033              15  False       draco      96
3  gromacs/5.1.4-plumed2.3      4  40.274              15  False       draco     128
4  gromacs/5.1.4-plumed2.3      5   51.71              15  False       draco     160

Contributions to the project are welcome! Information on how to contribute to the project can be found in CONTRIBUTING.md and DEVELOPER.rst.