## LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a software
application designed for molecular dynamics simulations. It has the potentials for solid-state materials (metals, semiconductor), soft matter (biomolecules, polymers), and  oarse-grained or mesoscopic systems. The main use case is atom scale particle modeling or, more generically, as a parallel particle simulator at the atomic, meson, or continuum scale.
LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. Read more on the [LAMMPS website](http://lammps.sandia.gov/).

## System requirements

Before running the NGC LAMMPS container please ensure your system meets the following requirements.

* One of the following container runtimes
  * [nvidia-docker](https://github.com/NVIDIA/nvidia-docker)
  * [Singularity](https://www.sylabs.io/docs/) >= 3.1
* One of the following NVIDIA GPU(s)
  * Pascal(sm60)
  * Volta (sm70)
  * Ampere (sm80)
  * Hopper (sm90)

### x86_64

* CPU with AVX2 instruction support
* One of the following CUDA driver versions
  * r520 (>=.61.05)
  * \>= 450.80.02

### arm64

* Marvell ThunderX2 CPU
* CUDA driver version >= r460

##### Examples

The following examples demonstrate using the NGC LAMMPS container to run a standard Leanard-Jones 3D melt experiment.

The input file must first be downloaded. The environment variable `BENCHMARK_DIR` will be used throughout the example to refer to the directory containing the input file, `in.lj.txt`. Throughout this example the container version will be referenced as `$TAG`, replace this with the tag you wish to run.

```bash
wget https://lammps.sandia.gov/inputs/in.lj.txt
export BENCHMARK_DIR=$PWD
```

Although the lammps executable, `lmp`, may be called directly within the NGC LAMMPS container this example will utilize a convenience script, run_lammps.sh. This script will set common command line arguments needed for the example experiment. This helper script should be placed within the benchmark data directory.

```bash
cd $BENCHMARK_DIR
wget https://gitlab.com/NVHPC/ngc-examples/-/raw/master/lammps/single-node/run_lammps.sh
chmod +x run_lammps.sh
```

## Running with nvidia-docker

```bash
cd $BENCHMARK_DIR
docker run --rm --gpus all --ipc=host -v $PWD:/host_pwd -w /host_pwd nvcr.io/hpc/lammps:$TAG ./run_lammps.sh
```

#### Note: Docker < v1.40

Docker versions below 1.40 must enable GPU support with `--runtime nvidia`.

```bash
docker run --rm --runtime nvidia --ipc=host -v $PWD:/host_pwd -w /host_pwd nvcr.io/hpc/lammps:$TAG ./run_lammps.sh
```

### Running with Singularity

```bash
cd $BENCHMARK_DIR
singularity run --nv -B $PWD:/host_pwd --pwd /host_pwd docker://nvcr.io/hpc/lammps:$TAG ./run_lammps.sh
```

#### Note: Singularity < v3.5

There is currently an issue in Singularity versions below v3.5 causing the `LD_LIBRARY_PATH` to be incorrectly set within the container environment. As a workaround The `LD_LIBRARY_PATH` must be unset before invoking Singularity:

```bash
LD_LIBRARY_PATH="" singularity run --nv -B $PWD:/host_pwd --pwd /host_pwd docker://nvcr.io/hpc/lammps:$TAG ./run_lammps.sh
```

### Running multi-node with Slurm and Singularity

Clusters running the Slurm resource manager and Singularity container runtime may launch parallel LAMMPS experiments directly through `srun`. The NGC LAMMPS container supports `pmi2`, which is available within most Slurm installations, as well as `pmix3`. A typical parallel experiment would take the following form.

```bash
srun --mpi=pmi2 [srun_flags] singularity run --nv [singularity_flags] lmp [lammps_flags]
```

An example Slrum batch script that may be modified for your specific cluster setup may be viewed [here](https://gitlab.com/NVHPC/ngc-examples/-/blob/master/lammps/multi-node/slurm/lammps.slurm).

## Suggested Reading

[LAMMPS Manual](http://lammps.sandia.gov/doc/Manual.html)

[LAMMPS Benchmarking](https://lammps.sandia.gov/doc/Speed.html)

[Nvidia Docker](https://github.com/NVIDIA/nvidia-docker/wiki)

lammps

Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a software application designed for molecular dynamics simulations.

LAMMPS

Description

Publisher

Latest Tag

Modified

Compressed Size

Multinode Support

Multi-Arch Support