LAMMPS¶

LAMMPS is a large scale classical molecular dynamics code, and stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers), solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

Availability and Supported Architectures¶

LAMMPS is available at NERSC as a provided support level package. LAMMPS runs at NERSC are currently supported on Haswell, KNL, and GPU nodes.

Application Information, Documentation and Support¶

The official LAMMPS is available at LAMMPS Online Manual. LAMMPS has a large user base and a good user support. Question related to using LAMMPS can be posted to the LAMMPS User forum. Archived user mailing list are also useful to resolve some of the common user issues.

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Using LAMMPS at NERSC¶

NERSC uses modules to manage access to software. To use the default version of LAMMPS, type:

module load lammps

Using LAMMPS on Cori¶

There are two ways of running LAMMPS on Cori: submitting a batch job, or running interactively in an interactive batch session.

#!/bin/bash
#SBATCH -J test_lammps
#SBATCH -C haswell
#SBATCH -q debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j

module load lammps

srun -n 64 -c 2 --cpu-bind=cores lmp_cori -in test.in

#!/bin/bash
#SBATCH -J test_lammps
#SBATCH -C knl
#SBATCH -q debug
#SBATCH -N 2
#SBATCH -t 30:00
#SBATCH -o test_lammps.o%j

module load lammps

srun -n 136 -c 2 --cpu-bind=cores lmp_cori -in test.in

These job scripts request two nodes in the debug partition, and run for up to 30 minutes. The first example runs 64 MPI processes across 64 cores on 2 nodes of Cori Haswell. The second example runs 136 MPI processes across 136 cores on 2 nodes of Cori KNL.

Then submit the job script using the sbatch command, e.g., assuming the job script name is test_lammps.slurm:

sbatch test_lammps.slurm

If running LAMMPS with Kokkos package, please review the Kokkos package page to add appropriate flags to the job submission line as well as modify the input script.

Building LAMMPS from source¶

Some users may be interested in building LAMMPS from source to enable more specific LAMMPS packages. The source files for LAMMPS can be downloaded as either a tar file or from the LAMMPS Github repository.

module purge
module load esslurm
module load gcc/11.2.0
module load openmpi/4.1.2
module load cmake

git clone https://github.com/lammps/lammps.git
cd lammps
mkdir build
cd build

cmake -DCMAKE_INSTALL_PREFIX=$PWD/../install_hsw -DCMAKE_CXX_COMPILER=mpicxx \
            -DCMAKE_BUILD_TYPE=Release -D BUILD_MPI=yes -DKokkos_ENABLE_OPENMP=ON \
            -DKokkos_ARCH_HSW=ON -DCMAKE_CXX_STANDARD=17 -D PKG_MANYBODY=ON \
            -D PKG_MOLECULE=ON -D PKG_KSPACE=ON -D PKG_REPLICA=ON -D PKG_ASPHERE=ON \
            -D PKG_RIGID=ON -D PKG_KOKKOS=ON -D DOWNLOAD_KOKKOS=ON \
            -D CMAKE_POSITION_INDEPENDENT_CODE=ON -D CMAKE_EXE_FLAGS="-dynamic" ../cmake
make -j16
make install

module load cudatoolkit
module load craype-accel-nvidia80

git clone https://github.com/lammps/lammps.git
cd lammps
mkdir build
cd build

cmake -DCMAKE_INSTALL_PREFIX=$PWD/../install_pm -D CMAKE_BUILD_TYPE=Release \
            -D CMAKE_Fortran_COMPILER=ftn -D CMAKE_C_COMPILER=cc -D CMAKE_CXX_COMPILER=CC \
            -D MPI_C_COMPILER=cc -D MPI_CXX_COMPILER=CC -D LAMMPS_EXCEPTIONS=ON \
            -D BUILD_SHARED_LIBS=ON -D PKG_KOKKOS=yes -D Kokkos_ARCH_AMPERE80=ON -D Kokkos_ENABLE_CUDA=yes \
            -D PKG_MANYBODY=ON -D PKG_MOLECULE=ON -D PKG_KSPACE=ON -D PKG_REPLICA=ON -D PKG_ASPHERE=ON \
            -D PKG_RIGID=ON -D PKG_MPIIO=ON \
            -D CMAKE_POSITION_INDEPENDENT_CODE=ON -D CMAKE_EXE_FLAGS="-dynamic" ../cmake
make -j16
make install

Related Applications¶

• NAMD

User Contributed Information¶