Welcome

  • “The course will be flexible to best meet the learning needs of the attendees.”
  • “Feedback is an essential part of our training to allow us to continue to improve and make sure the course is as useful as possible to attendees.”

Connecting to ARCHER2 and transferring data

  • “ARCHER2’s login address is login.archer2.ac.uk.”

An introduction to LAMMPS on ARCHER2

  • “LAMMPS is a versatile software used in a wide range of subjects to run classical molecular dynamics simulations.”
  • “Running jobs on ARCHER2 requires a submission to the Slurm batch system using specific account, budget, queue, and qos keywords.”
  • “Adding more cores is not always the most effective way of increasing performance.”

Setting up a simulation in LAMMPS

  • “LAMMPS can simulate systems of many particles that are allowed to interact, using any of a number of contact models.”
  • “A LAMMPS input file is a an ordered collection of commands with both mandatory and optional arguments.”
  • “To successfully run a LAMMPS simulation, an input file needs to cover basic simulation setup, read/create a system topology, force-field, and type/frequency of outputs.”

Understanding the logfile

  • “Thermodynamic information outputted by LAMMPS can be used to track whether a simulations is running OK.”
  • “Performance data at the end of a logfile can give us insights into how to make a simulation faster.”

Advanced input and output commands

  • “Using compute and fix commands, it’s possible to calculate myriad properties during a simulation.”
  • “Variables make it easier to script several simulations.”

Measuring and improving LAMMPS performancePerformance inprovements

  • “LAMMPS offers a number of built in methods to improve performance.”
  • “It is important to spend some time understanding your system and considering its performance.”
  • “Where possible, always run a quick benchmark of your system before setting up a large run.”

Compiling LAMMPS

  • “Compiling LAMMPS with CMake is easy and quick on ARCHER2”

Running LAMMPS through Python

  • “Running LAMMPS through Python can have certain advantages.”
  • “However, finding the root cause of problems when things go wrong is harder to do when running LAMMPS through Python rather than through a LAMMPS executable.”