Skip to content

Installation on Midway3

Jump to bottom
Pablo Zubieta edited this page Oct 13, 2023 · 10 revisions

These are the specific instructions on how to build LAMMPS and lammps-dlext on Midway3.

Build and install LAMMPS

Load the necessary modules

module load python/anaconda-2021.05 openmpi/4.1.2+gcc-7.4.0 cuda/11.2 cmake/3.19 clang ffmpeg/5.1 fftw3

Activate the pysages3 virtual environment

source activate pysages3

Non-admin users should clone the pysages3 environment instead

conda config --set pip_interop_enabled false  # the cloning step below may fail otherwise
conda create --clone pysages3 --prefix=/path/to/pysages3-dev
source activate /path/to/pysages3-dev

Clone the LAMMPS repository

git clone https://github.com/lammps/lammps.git
cd lammps
git checkout stable_23Jun2022  # or any other branch you want to build

Configure LAMMPS with KOKKOS and PYTHON packages, and install LAMMPS to the same location as the pysages3 virtual environment

BUILD_PATH=build
PYTHON_EXECUTABLE=$CONDA_PREFIX/bin/python
INSTALL_PREFIX=$(${PYTHON_EXECUTABLE} -c "import sys; print(sys.prefix)")

cmake -S cmake -B $BUILD_PATH \
    -C cmake/presets/most.cmake \
    -C cmake/presets/nolib.cmake \
    -C cmake/presets/kokkos-cuda.cmake \
    -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
    -DBUILD_SHARED_LIBS=ON \
    -DFFT=KISS \
    -DKokkos_ARCH_PASCAL60=OFF \
    -DKokkos_ARCH_AMPERE80=ON \
    -DLAMMPS_EXCEPTIONS=ON \
    -DPKG_MPI=ON \
    -DPKG_OPENMP=ON \
    -DPython_EXECUTABLE=${PYTHON_EXECUTABLE}

cmake --build $BUILD_PATH --target install -j8

cd $BUILD_PATH
make install-python

If the build succeeds, the shared library liblammps.so is installed into $INSTALL_PREFIX/lib64.

To test the installation of the LAMMPS python module

${PYTHON_EXECUTABLE} -c "from lammps import lammps; p = lammps()"

You can also check if lammps is listed in the python environment via ${PYTHON_EXECUTABLE} -m pip list.

Build and install lammps-dlext

Clone the lammps-dlext repository

git clone https://github.com/SSAGESLabs/lammps-dlext.git
cd lammps-dlext

With the same python environment as above active, configure and build lammps-dlext

BUILD_PATH=build
cmake -S . -B $BUILD_PATH -DCMAKE_PREFIX_PATH=$CONDA_PREFIX/lib64/cmake
cmake --build $BUILD_PATH --target install -j4

Alternatively to setting CMAKE_PREFIX_PATH you can directly set the following:

  • The path to LAMMPS_ROOT (most likely $CONDA_PREFIX/lib64/cmake/LAMMPS if you installed LAMMPS as above).
  • When compiling with Kokkos support, the path to Kokkos_ROOT (likely to be $CONDA_PREFIX/lib64/cmake/Kokkos). See also the Kokkos documentation.

If during compilation you encounter an error stating that dlpack/dlpack.h cannot be found, try adding -DFETCH_DLPACK=ON at the end of the first cmake command above.

Clone this wiki locally