Compiling LAMMPS

Last updated on 2025-11-11 | Edit this page

Estimated time: 15 minutes

Overview

Questions

“How can I compile LAMMPS using CMake”
“How do I build LAMMPS with its shared libraries?”

Objectives

“Know how to compile LAMMPS on ARCHER2 (and what to look for when compiling elsewhere).”

Building LAMMPS with Python

For this course, we will be using a version of LAMMPS that has been built with the “Python” package and with shared libraries. These will help us ensure that we can run LAMMPS through Python.

The build instructions used can be found in the hpc-uk github and were:

BASH

# select centrally installed modules needed for compilation
module load cpe/22.12
module load cray-fftw/3.3.10.3
module load cmake/3.21.3
module load cray-python

# Add cray library paths to the LD_LIBRARY_PATH variable
export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH

# clone the chosen version of LAMMPS
git clone --depth=1 --branch stable_15Dec2023 https://github.com/lammps/lammps.git lammps-src-2023-12-15

# create and source a virtual environment
python -m venv --system-site-packages  /work/y07/shared/apps/core/lammps/15_Dec_2023/venv/lammps-python-15-Dec-2023
source /work/y07/shared/apps/core/lammps/15_Dec_2023/venv/lammps-python-15-Dec-2023/bin/activate

# creata folder for configuration and compilation
cd lammps-2023-12-15 && mkdir build_cpe && cd build_cpe

# use cmake to configure LAMMPS
cmake -C ../cmake/presets/most.cmake                                       \
      -D BUILD_MPI=on                                                      \
      -D BUILD_SHARED_LIBS=yes                                             \
      -D CMAKE_CXX_COMPILER=CC                                             \
      -D CMAKE_CXX_FLAGS="-O2"                                             \
      -D CMAKE_INSTALL_PREFIX=/path/to/install  \
      -D FFT=FFTW3                                                         \
      -D FFTW3_INCLUDE_DIR=${FFTW_INC}                                     \
      -D FFTW3_LIBRARY=${FFTW_DIR}/libfftw3_mpi.so                         \
      -D PKG_MPIIO=yes                                                     \
      ../cmake/

make -j 8
make install
make install-python

Of note here:

-D CMAKE_INSTALL_PREFIX=/path/to/install defines the path into which your LAMMPS executables and libraries will be built. You will need to change /path/to/install to whatever you like.
-D BUILD_SHARED_LIBS=yes will build the shared LAMMPS library required to run LAMMPS in Python.
-D PKG_PYTHON=yes will build the Python packages.
The -C ../cmake/presets/most.cmake command adds the packages that we are installing. Not all of them are required for this course, but it includes all packages that don’t need extra libraries.
The rest of the instructions are to ensure that the correct compiler is used, the MPI version of LAMMPS is built, and that it has access to the correct fast Fourier transform (FFTW) and Eigen3 libraries.

Once this is built, you should be able to run LAMMPS from the compute nodes by loading the appropriate module.

Building LAMMPS with VTK - local linux system

To vuild LAMMPS with VTK on an Ubuntu/Debian system (or virtual machine), you will need to install the following pre-requesites:

Compiler (gcc or clang)
MPI
VTK
FFTW3
Optionally, python

To do this, you can use the aptitude package manager:

BASH

sudo apt install libvtk9-dev openmpi-bin openmpi-common python3-dev libfftw3-dev

Download LAMMPS

Clone the latest stable version of LAMMPS from the GitHub repository:

BASH

git clone --depth=1 --branch stable_22Jul2025_update1 https://github.com/lammps/lammps.git lammps-2025-09-02

Optional - for Python support

BASH

# create
python -m venv --system-site-packages /path/to/venv/lammps-2025-09-02
# and source a virtual environment
source /path/to/venv/lammps-2025-09-02/bin/activate

Regular MPI executable and python wrappers

Create and go into a build directory:

BASH

cd lammps-2025-09-02 && mkdir build_cpe && cd build_cpe

Build using:

BASH

cmake -C ../cmake/presets/most.cmake            \
      -D PKG_VTK=yes                            \
      -D BUILD_MPI=on                           \
      -D BUILD_SHARED_LIBS=yes                  \
      -D CMAKE_CXX_FLAGS="-O2"                  \
      -D CMAKE_INSTALL_PREFIX=/path/to/install  \
      -D FFT=FFTW3                              \
      ../cmake/


make -j 8
make install
make install-python

BASH

export LD_LIBRARY_PATH=/path/to/install/lib:$LD_LIBRARY_PATH
export PATH=/path/to/install/bin:$PATH

Building LAMMPS with VTK on ARCHER2

These instructions are for building LAMMPS version 13Feb2024, also known as 07Feb2024 update 1, on ARCHER2 using the Cray clang compilers 15.0.2 // cpe 22.12 with support for VTK files.

Path setup

BASH

# base-path for download and source files
export DWNLD_DIR="/work/ta215/ta215/shared/download"
export INSTALL_DIR="/work/ta215/ta215/shared/"
export LAMMPS_DWNLD=${DWNLD_DIR}/lammps-2024-02-13
export LAMMPS_BUILD=${LAMMPS_DWNLD}/build
export LAMMPS_INSTALL=${INSTALL_DIR}/lammps
export VTK_DWNLD=${DWNLD_DIR}/vtk
export VTK_BUILD=${VTK_DWNLD}/build
export VTK_INSTALL=${INSTALL_DIR}/vtk-9.5.2

Setup your environment

Load the correct modules:

BASH

module load cpe/22.12
module load cray-fftw/3.3.10.3
module load cmake/3.21.3
module load cray-python

export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH

# create and source a virtual environment
python -m venv --system-site-packages ${LAMMPS_INSTALL}/venv/lammps-python-13-Feb-2024
source ${LAMMPS_INSTALL}/venv/lammps-python-13-Feb-2024/bin/activate

Download and compile the VTK library

BASH

mkdir -p ${VTK_DWNLD}
cd ${VTK_DWNLD}
wget https://vtk.org/files/release/9.5/VTK-9.5.2.tar.gz
tar -xvf VTK-9.5.2.tar.gz
mv VTK-9.5.2 source
mkdir -p ${VTK_BUILD}
cd ${VTK_BUILD}
cmake -DVTK_USE_MPI:BOOL=ON -DVTK_SMP_IMPLEMENTATION_TYPE:STRING=OpenMP -DCMAKE_BUILD_TYPE:STRING=Release ${VTK_DWNLD}/source
cmake --build . -j8
cp -r ${VTK_DWNLD} ${VTK_INSTALL}

Download LAMMPS

Clone the latest stable version of LAMMPS from the GitHub repository:

BASH

cd $DWNLD_DIR
git clone --depth=1 --branch patch_7Feb2024_update1 https://github.com/lammps/lammps.git ${LAMMPS_DWNLD}

Regular MPI executable and python wrappers

Create and go into a build directory:

BASH

mkdir -p ${LAMMPS_BUILD}
cd ${LAMMPS_BUILD}

Build using:

BASH

cmake -C ../cmake/presets/most.cmake                \
      -D BUILD_MPI=on                               \
      -D BUILD_SHARED_LIBS=yes                      \
      -D CMAKE_CXX_COMPILER=CC                      \
      -D CMAKE_CXX_FLAGS="-O2"                      \
      -D CMAKE_INSTALL_PREFIX=${LAMMPS_INSTALL}     \
      -D FFT=FFTW3                                  \
      -D FFTW3_INCLUDE_DIR=${FFTW_INC}              \
      -D FFTW3_LIBRARY=${FFTW_DIR}/libfftw3_mpi.so  \
      -D PKG_MPIIO=yes                              \
      -D PKG_VTK=yes                                \
      -D VTK_DIR=${VTK_INSTALL}                     \
      ../cmake/

make -j 8
make install
make install-python

Callout

To run LAMMPS from python

LD_PRELOAD needs to be modified (this is done in the module file, but if running the text below without loading a module, it needs to be done explicitly):

BASH

export LD_PRELOAD=/opt/cray/pe/lib64/libsci_cray_mp.so.5:$LD_PRELOAD

Testing LAMMPS from python

BASH

python -i
>>> import lammps
>>> lmp = lammps.lammps()
LAMMPS (07 Feb 2024 - Update 1)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
  using 1 OpenMP thread(s) per MPI task

Key Points

“Compiling LAMMPS with CMake is easy and quick on ARCHER2”