MOLECULAR DYNAMICS PERFORMANCE GUIDE - COMPUTE CANADA

FIND THE OPTIMAL
SUBMISSION PARAMETERS

SPEED UP SIMULATION

  • Finding optimal resources
    A poor choice of job submission or simulation parameters leads to poor performance and a waste of computing resources. However, finding optimal MD engines and submission parameters in a complex HPC environment with heterogeneous hardware is a daunting and time-consuming challenge. We developed this web portal to simplify this task.
  • How fast will a simulation run?
    Chart of the maximum simulation speed of all tested MD executables attained on CC systems provides a quick idea of how long a simulation will take.
  • Finding balance between speed and efficiency
    The fastest simulations may be inefficient due to poor parallel scaling to many CPUs or GPUs. Inefficient simulations consume more resources and impact priority, resulting in longer times in queue and less work done. Color-coded by efficiency chart allows choosing an optimal combination of speed and efficiency.
  • Exploring the database
    All benchmarks are available from the Explore menu . This menu offers tools for querying, filtering, and viewing benchmark data.
  • Viewing QM/MM benchmarks
    To view QM/MM benchmarks select simulation system 4cg1 in the Explore window .

Best Performance Of Each MD Engine Among All Clusters