The HECBioSim benchmark suite consists of a set of simple benchmarks for a number of popular Molecular Dynamics (MD) engines, each of which is set at a different atom count. Our benchmarking suite has now been automated by making use of our job submission tool Longbow, this allows us to quickly benchmark new code versions or to benchmark HPC machines that we have not previously done this for. Having such a benchmarking suite enables us to provide guidelines about run-times that members of our community can expect when applying for time on HPC facilities and allows us to assess such applications at a technical level.

Our current benchmark results can be viewed on the following pages.

ARCHER Benchmarks

Jade Benchmarks

The Benchmark Systems

The benchmark suite currently contains benchmarks for the AMBER, GROMACS, LAMMPS and NAMD molecular dynamics packages. The following systems have currently been setup for each of the MD packages to represent examples of the sorts of simulations that biosimulation scientists would do in production. Currently we only have benchmarks for classical MD, however, we are working on new benchmarks to widen our benchmark suite to include other techniques.

 

20K Crambin thumb

 

20K atom system - 3NIR Crambin

Total number of atoms = 19,605

Protein atoms = 642  Water atoms = 18,963

 

 

 

61K GInBP thumb

 

61K atom system - 1WDN Glutamine-Binding Protein

Total number of atoms = 61,153

Protein atoms = 3,555  Water atoms = 57,957  Ions = 1

 

 

 

465K H1 H1 thumb

 

465K atom system - hEGFR Dimer of 1IVO and 1NQL

Total number of atoms = 465,399

Protein atoms = 21,749  Lipid atoms = 134,268  Water atoms = 309,087  Ions = 295

 

 

 

1400K H1 H1 thumb

 

1.4M atom system - A Pair of hEGFR Dimers of 1IVO and 1NQL

Total number of atoms = 1,403,182

Protein atoms = 43,498  Lipid atoms = 235,304  Water atoms = 1,123,392  Ions = 986

 

 

 

3000K H1 H1 thumb

 

3M atom system - A Pair of hEGFR tetramers of 1IVO and 1NQL

Total number of atoms = 2,997,924

Protein atoms = 86,996  Lipid atoms = 867,784  Water atoms = 2,041,230  Ions = 1,914

 

 

The Benchmark Files

The following files make up our benchmarking suite, the files for each MD package are provided on an individual basis so that we can update for compatibiltity issues per each package release cycle.

AMBER - compatible with versions 16 and 18

GROMACS - compatible with versions 5.1.x, 2016.x and 2018.x

LAMMPS - compatible with versions release in years 2016, 2017 and 2018

NAMD -  compatible with versions 2.9 - 2.12.