davidpoliakoff/examinimd

ExaMiniMD

ExaMiniMD is a proxy application and research vehicle for particle codes, in particular Molecular Dynamics (MD). Compared to previous MD proxy apps (MiniMD, COMD), its design is significantly more modular in order to allow independent investigation of different aspects. To achieve that the main components such as force calculation, communication, neighbor list construction and binning are derived classes whose main functionality is accessed via virtual functions. This allows a developer to write a new derived class and drop it into the code without touching much of the rest of the application.

These modules are included via a module header file. Those header files are also used to inject the input parameter logic and instantiation logic into the main code. As an example, look at modules_comm.h in conjunction with comm_serial.h and comm_mpi.h.

In the future the plan is to provide focused miniApps with a subset of the available functionality for specific research purposes.

This implementation uses the Kokkos programming model, which you can clone from github via:

git clone https://github.com/kokkos/kokkos ~/kokkos

Current Capabilities

Force Fields:

• Lennard-Jones Cell List
• Lennard-Jones Neighbor List
• SNAP Full Neighbor List

Neighbor List:

• 2D NeighborList creation
• CSR NeighborList creation

Integrator:

• NVE (constant energy velocity-Verlet)

Communication

• Serial
• MPI

Binning:

• Kokkos Sort Binning

Input:

• Restricted LAMMPS input files

Compilation

ExaMiniMD utilizes the standard GNU Make build system of Kokkos. For detailed information about the Kokkos build process please refer to documentation of Kokkos at github.com/kokkos/kokkos ExaMiniMD requires Kokkos version 2.6.00 (March 2018) as a minimum. ExaMiniMD requires a C++11 compiler. Here is some quickstart information which assume that Kokkos was cloned into ${HOME}/kokkos (see above) and you are in the "src" directory:

Intel Sandy-Bridge CPU / Serial / MPI:

  make -j KOKKOS_ARCH=SNB KOKKOS_DEVICES=Serial CXX=mpicxx MPI=1

Intel Haswell CPU / Pthread / No MPI:

  make -j KOKKOS_ARCH=HSW KOKKOS_DEVICES=Pthread CXX=clang MPI=0

IBM Power8 CPU / OpenMP / MPI

  make -j KOKKOS_ARCH=Power8 KOKKOS_DEVICES=OpenMP CXX=mpicxx

IBM Power8 CPU + NVIDIA P100 / CUDA / MPI (OpenMPI)

  export OMPI_CXX=[KOKKOS_PATH]/bin/nvcc_wrapper
  make -j KOKKOS_ARCH=Power8,Pascal60 KOKKOS_DEVICES=Cuda CXX=mpicxx

Running

Currently ExaMiniMD can only get input from LAMMPS input files with a restricted set of LAMMPS commands. An example input file is provided in the input directory. Assuming you build in the src directory:

To run 2 MPI tasks, with 12 threads per task:

mpirun -np 2 -bind-to socket ./ExaMiniMD -il ../input/in.lj --comm-type MPI --kokkos-threads=12

To run 2 MPI tasks, with 1 GPU per task:

mpirun -np 2 -bind-to socket ./ExaMiniMD -il ../input/in.lj --comm-type MPI --kokkos-ndevices=2

To run in serial, writing binary output every timestep to ReferenceDir

./ExaMiniMD -il ../input/in.lj --kokkos-threads=1 --binarydump 1 ReferenceDir 

To run in serial with 2 threads, checking correctness every timestep against ReferenceDir

./ExaMiniMD -il ../input/in.lj --kokkos-threads=2 --correctness 1 ReferenceDir correctness.dat