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.
If after checking the above forum, if you believe that there is an issue with the NERSC module, please file a ticket with our help desk
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.
Sample Batch Script to Run LAMMPS on Cori Haswell
#!/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
Sample Batch Script to Run LAMMPS on Cori KNL
#!/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
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.
Building on Cori
The following procedure was used to build LAMMPS on Cori Haswell. In the terminal:
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=$PWD/../install_hsw -DCMAKE_CXX_COMPILER=mpicxx \ -DCMAKE_BUILD_TYPE=Release -D BUILD_MPI=yes -DKokkos_ENABLE_OPENMP=ON \ -DKokkos_ARCH_HSW=ON -DCMAKE_CXX_STANDARD=17 -D PKG_MANYBODY=ON \ -D PKG_MOLECULE=ON -D PKG_KSPACE=ON -D PKG_REPLICA=ON -D PKG_ASPHERE=ON \ -D PKG_RIGID=ON -D PKG_KOKKOS=ON -D DOWNLOAD_KOKKOS=ON \ -D CMAKE_POSITION_INDEPENDENT_CODE=ON -D CMAKE_EXE_FLAGS="-dynamic" ../cmake make -j16 make install
Building on Perlmutter
The following procedure was used to build LAMMPS on Perlmutter GPU with Kokkos. In the terminal:
module load cudatoolkit module load craype-accel-nvidia80 git clone https://github.com/lammps/lammps.git cd lammps mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=$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
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