The HECToR Service is now closed and has been superceded by ARCHER.

Implementing dynamic load balancing and rigid body dynamics within DL_POLY_3

DL_POLY is a general purpose package for classical molecular dynamics simulations developed by I.T. Todorov and W. Smith at STFC Daresbury Laboratory. The main purpose of this software is to enable the exploitation of large scale MD simulations on multi-processor platforms.

The DL_POLY_2 (DL_POLY_CLASSIC) classical molecular dynamics package uses a full force field and molecular description. However, the parallelisation employs replicated data structures and is therefore only scalable up to tens of processes with up to 30,000 atoms. DL_POLY_3 has improved parallelisation, based on a static/equi-spatial domain decomposition and is scalable for up to 512 processes with 1,000,000 atoms. DL_POLY_3 also provides a full force field, although no rigid body description.

The overall aims of this project were to:

  • Implement rigid body (RB) dynamics in the DL_POLY_3 framework. This will improve the modelling of large bio-molecules and solvents by a faster time to solution, due to better efficiency in calculating atomic forces and integrating the equations of motion.
  • Adapt a prototype dynamic load-balancing scheme to the DL_POLY_3 framework. This will address the challenging problem of modelling spatially non-uniform systems evolving in time through more intelligent load balancing.
  • After a thorough testing of the new code on a realistic physical system, it will be released as DL_POLY_4.

The outcomes of the project are:

  • A stand alone load balancing implementation was developed around a rudimentary MD time stepping loop in which only 2-body interactions are considered and the atom trajectories are non-physical. This will minimise the spatial variations in atom density throughout the computational domain.
  • Performance tests carried out on HECToR Phase 2b (XE6) show good speed ups for a number of simple test systems. The largest test run consisted of around 5 million atoms with a maximum of 2744 cores. However, due to the overall complexity of the task, the new code was not implemented within the DL_POLY_4 framework, but with further work this should be possible in the near future.
  • Rigid body dynamics was implemented successfully, although this is not documented in the final report. This functionality is now available in DL_POLY_4.

Please see PDF or HTML for a report which summarises this project.