KoMD

Small MD framework

The intention is to provide a full MD framework for non-rigid multi-site molecular models. Portability is provided by using Kokkos. Currently, OpenMP and Cuda backends are supported.

Prequisites

• vtk Library: sudo apt install libvtk<version>-qt-dev minimum version: 7
• For CUDA support: Install CUDA Toolkit, follow the instructions on the official CUDA Toolkit page.
• For OpenMP support: Install OpenMP lib and runtime

Compilation

• Create build directory mkdir build && cd build
• Configure CMake cmake .. <options> or ccmake ..
• CMake options:
  • ENABLE_VTK:BOOL=ON|OFF
  • CUDA options:
    • CUDA_TOOLKIT_ROOT_DIR:FILEPATH=<path to cuda installation>
    • CUDAToolkit_INCLUDE_DIRECTORIES:FILEPATH=<path to cuda installation>/targets/x86_64-linux/include
    • CUDA_CUDART:FILEPATH=<path to cuda installation>/targets/x86_64-linux/lib
  • Kokkos options:
    • Kokkos_ENABLE_<backend>:BOOL=ON backend options are CUDA and OpenMP
    • Kokkos_ARCH_NATIVE:BOOL=ON
    • Kokkos_NVCC_WRAPPER:FILEPATH=<path to KoMD repo>/dependencies-external/kokkos-4.3.01/bin/nvcc_wrapper
    • Kokkos_ARCH_<arch>:BOOL=ON set arch to used GPU architecture
• Compile with make all

Troubleshooting

• When installing CUDA Toolkit, make sure it is fully installed and sourced. If it is not, then many CUDA tools and libs need to be symlinked into PATH directories.
• Recommendation: Use ccmake to configure CMake. There all options will be visible.

Input File format

• see examples/inp.dat

Running KoMD

• KoMD <path to input file>
• When running with OpenMP, set these env variables: OMP_PROC_BIND=spread;OMP_NUM_THREADS=8