The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a classical molecular dynamics code for materials modeling. It is capable of modeling 2d or 3d systems composed of only a few up to billions of particles. The code is primarily designed to run in parallel computers that support the Message Passing Interface (MPI) library and spatial decomposition of the simulation domain.
This document provides build recipes for running LAMMPS on AMD Instinct GPUs via the Kokkos backend.
LAMMPS is distributed as an open source code under the terms of the GPLv2. The current version of LAMMPS can be downloaded here. Links to older versions are also included. All LAMMPS development is done via GitHub, so all versions can also be accessed there. Periodic releases are also posted to SourceForge.
More information about LAMMPS can be found in the LAMMPS Website and in the LAMMPS Manual.
In this section, we provide a couple of examples from the set of LAMMPS standard benchmarks, intended to guide users when constructing their own run commands tailored to their specific workload(s).
In these examples, the input to the run command is provided via an input file. Other inputs may have additional parameters that can be modified and may change performance.
Additionally, we have supplied several arguments such as cuda/aware on which modify the behavior of LAMMPS, in this case, forcing enablement of GPU-aware communications. For additional run options, see Running LAMMPS with the KOKKOS package.
Note that the use of `neigh full' in the run command triggers the use of full neighbor-lists, as described here.
For convenience, we also added the installed binary path (install/bin) to the PATH environment variable (see bare metal build instructions above) so that the lmp binary can be found when running the benchmark examples.
- Run EAM benchmark on eight GPUs
The following command runs the EAM benchmark using a x/y/z size of 1/1/1, as defined by the input file.
mpirun --mca pml ucx --mca btl ^vader,tcp,openib,uct -np 8 lmp -k on g 8 -sf kk -pk kokkos cuda/aware on neigh half comm device -v x 1 -v y 1 -v z 1 -in in.eam -nocite -log log.lammps
- Run LJ benchmark on one GPU
The following command runs the LJ benchmark using a x/y/z of size 8/8/8. Note that we have chosen to run a larger problem size than specified in the sample input file. The user may wish to experiment with problem sizes and other run options to achieve optimal performance.
mpirun --mca pml ucx --mca btl ^vader,tcp,openib,uct -np 1 lmp -k on g 1 -sf kk -pk kokkos cuda/aware on neigh full -v x 8 -v y 8 -v z 8 -in in.lj -nocite -log log.lammps
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The application is provided in a container image format that includes the following separate and independent components:
| Package | License | URL |
|---|---|---|
| Ubuntu | Creative Commons CC-BY-SA Version 3.0 UK License | Ubuntu Legal |
| CMAKE | OSI-approved BSD-3 clause | CMake License |
| OpenMPI | BSD 3-Clause | OpenMPI License OpenMPI Dependencies Licenses |
| OpenUCX | BSD 3-Clause | OpenUCX License |
| ROCm | Custom/MIT/Apache V2.0/UIUC OSL | ROCm Licensing Terms |
| LAMMPS | GPLv2.0 | LAMMPS LAMMPS License |
| NumPy | BSD 3-clause | NumPy License |
| PANDAS | BSD 3-clause | PANDAS license |
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