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8. Performance & scalability

LAMMPS performance on several prototypical benchmarks and machines is discussed on the Benchmarks page of the LAMMPS WWW Site where CPU timings and parallel efficiencies are listed. Here, the benchmarks are described briefly and some useful rules of thumb about their performance are highlighted.

These are the 5 benchmark problems:

  1. LJ = atomic fluid, Lennard-Jones potential with 2.5 sigma cutoff (55 neighbors per atom), NVE integration
  2. Chain = bead-spring polymer melt of 100-mer chains, FENE bonds and LJ pairwise interactions with a 2^(1/6) sigma cutoff (5 neighbors per atom), NVE integration
  3. EAM = metallic solid, Cu EAM potential with 4.95 Angstrom cutoff (45 neighbors per atom), NVE integration
  4. Chute = granular chute flow, frictional history potential with 1.1 sigma cutoff (7 neighbors per atom), NVE integration
  5. Rhodo = rhodopsin protein in solvated lipid bilayer, CHARMM force field with a 10 Angstrom LJ cutoff (440 neighbors per atom), particle-particle particle-mesh (PPPM) for long-range Coulombics, NPT integration

The input files for running the benchmarks are included in the LAMMPS distribution, as are sample output files. Each of the 5 problems has 32,000 atoms and runs for 100 timesteps. Each can be run as a serial benchmarks (on one processor) or in parallel. In parallel, each benchmark can be run as a fixed-size or scaled-size problem. For fixed-size benchmarking, the same 32K atom problem is run on various numbers of processors. For scaled-size benchmarking, the model size is increased with the number of processors. E.g. on 8 processors, a 256K-atom problem is run; on 1024 processors, a 32-million atom problem is run, etc.

A useful metric from the benchmarks is the CPU cost per atom per timestep. Since LAMMPS performance scales roughly linearly with problem size and timesteps, the run time of any problem using the same model (atom style, force field, cutoff, etc) can then be estimated. For example, on a 1.7 GHz Pentium desktop machine (Intel icc compiler under Red Hat Linux), the CPU run-time in seconds/atom/timestep for the 5 problems is

Problem: LJ Chain EAM Chute Rhodopsin
CPU/atom/step: 4.55E-6 2.18E-6 9.38E-6 2.18E-6 1.11E-4
Ratio to LJ: 1.0 0.48 2.06 0.48 24.5

The ratios mean that if the atomic LJ system has a normalized cost of 1.0, the bead-spring chains and granular systems run 2x faster, while the EAM metal and solvated protein models run 2x and 25x slower respectively. The bulk of these cost differences is due to the expense of computing a particular pairwise force field for a given number of neighbors per atom.

Performance on a parallel machine can also be predicted from the one-processor timings if the parallel efficiency can be estimated. The communication bandwidth and latency of a particular parallel machine affects the efficiency. On most machines LAMMPS will give fixed-size parallel efficiencies on these benchmarks above 50% so long as the atoms/processor count is a few 100 or greater - i.e. on 64 to 128 processors. Likewise, scaled-size parallel efficiencies will typically be 80% or greater up to very large processor counts. The benchmark data on the LAMMPS WWW Site gives specific examples on some different machines, including a run of 3/4 of a billion LJ atoms on 1500 processors that ran at 85% parallel efficiency.