I am trying to run MD of a single atomistic polymer chain. The simulation is exceedingly slow, apparently due to long-range charge interaction calculations (kspace). I have read about the following techniques for speeding up the simulation:
- Using intel acceleration suffix (suffix intel)
- Running on GPUs and using associated acceleration packages
- Partitioning processors (partition command with run_style verlet/split)
- Changing kspace order (kspace_modify)
I have run a simulation using all of these techniques except the GPUs, which I am still working on. The attachments are the lammps input and log files for this simulation running 9 MPI tasks on two partitions (8x1). While CPU efficiency was >90% for both partitions, kspace accounted for >99% of the MPI task time in both cases.
After 7 days, only ~35,000 time steps had elapsed.
I have tried running a similar simulation with more processors, which was “faster” but efficiency suffered. I realize that this is in part due to the density gradient through the simulation box (a single chain stretched diagonally through a cube) which could be helped in part with the balance command (which I have not tried yet).
Any pointers would be appreciated.