frobnitzem / cabanamd

Molecular dynamics proxy application based on Cabana

CabanaMD

is a proxy application for molecular dynamics (MD) based on ExaMiniMD, modified to replace features with the CoPA Cabana Particle Toolkit: https://github.com/ECP-copa/Cabana

ExaMiniMD is a proxy app and research vehicle for MD using the Kokkos performance portability library ("KokkosMD"): https://github.com/ECP-copa/ExaMiniMD https://github.com/kokkos/kokkos

Build instructions

The following shows how to configure and build CabanaMD.

Dependencies

CabanaMD has the following dependencies:

Dependency	Version	Required	Details
CMake	3.9+	Yes	Build system
MPI	GPU Aware if CUDA Enabled	Yes	Message Passing Interface
Kokkos	3.0	Yes	Provides portable on-node parallelism
Cabana	0.3-dev	Yes	Performance portable particle algorithms
libnnp	1.0.0	No	Neural network potential utilities

Build Kokkos, followed by Cabana: https://github.com/ECP-copa/Cabana/wiki/Build-Instructions

Build instructions are available for both CPU and GPU. Note that Cabana with MPI is required (-D Cabana_ENABLE_MPI=ON)

CPU Build

After building Kokkos and Cabana for CPU:

# Change directories as needed
export KOKKOS_INSTALL_DIR=$HOME/kokkos
export CABANA_INSTALL_DIR=$HOME/Cabana

cd ./CabanaMD
mkdir build
cd build
pwd
cmake \
    -D CMAKE_PREFIX_PATH="$KOKKOS_INSTALL_DIR;$CABANA_INSTALL_DIR" \
    -D CabanaMD_ENABLE_Serial=OFF \
    -D CabanaMD_ENABLE_OpenMP=ON \
    -D CabanaMD_ENABLE_Cuda=OFF \
    \
    .. ;
make install
cd ../../

GPU Build

After building Kokkos and Cabana for GPU: https://github.com/ECP-copa/Cabana/wiki/Build-Instructions#GPU-Build

the GPU build is identical to that above except the options passed to CMake:

cmake \
    -D CMAKE_CXX_COMPILER=$KOKKOS_SRC_DIR/bin/nvcc_wrapper \
    -D CMAKE_PREFIX_PATH="$KOKKOS_INSTALL_DIR;$CABANA_INSTALL_DIR" \
    -D CabanaMD_ENABLE_Serial=OFF \
    -D CabanaMD_ENABLE_OpenMP=OFF \
    -D CabanaMD_ENABLE_Cuda=ON \
    \
    .. ;

Neural network potential build

If using the optional neural network potential, additional flags for the location of the libnnp library (https://github.com/CompPhysVienna/n2p2) and enabling the potential are needed for CMake:

    -D N2P2_DIR=$N2P2_INSTALL_DIR \
    -D CabanaMD_ENABLE_NNP=ON \