MDACP (Molecular Dynamics code for Avogadro Challenge Project)

Summary

MDACP (Molecular Dynamics code for Avogadro Challenge Project) is an efficient implementations of classical molecular dynamics (MD) method for the Lennard-Jones particle systems.

This fork of MDACP is designed to support (1) the force calculation with GPU and MIC (2) pairlist construction using SIMD instructions.

The latest information of original MDACP is available at https://github.com/kaityo256/mdacp

How to compile

CPU only with AVX2

$ mkdir build
$ cd build
$ cmake ../ -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DUSE_AVX2=true
$ make

GPU & CPU with AVX2 @ ISSP System B

$ source env/sekirei.sh
$ mkdir build
$ cd build
$ cmake ../ -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=gcc -DUSE_AVX2=true -DUSE_GPU_CUDA=true -DGPU_ARCH=KEPLER
$ make

GPU & CPU with AVX2 @ Reedbush-L

$ source env/reedbush-l.sh
$ mkdir build
$ cd build
$ cmake ../ -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DUSE_AVX2=true -DUSE_GPU_CUDA=true -DGPU_ARCH=PASCAL
$ make

MIC @ Oakforest-PACS

$ mkdir build
$ cd build
$ cmake ../ -DCMAKE_CXX_COMPILER=mpiicpc -DCMAKE_C_COMPILER=mpiicc -DUSE_AVX512=true
$ make

Run

usage: mpiexec -np n ./mdacp [options] ...
options:
  -i, --in                      input file name (optional [default: input.cfg])
  -g, --num_gpus_per_node       number of gpus per one node (optional [default: # of GPUs available in one node])
  -p, --num_of_procs_per_gpu    number of processes per one gpu (mandatory when compiling with CUDA support)
  -?, --help                    print this message

CPU only @ ISSP System B

$ mpijob ./mdacp -i input.cfg

CPU + GPU @ ISSP System B

• Total number of MPI processes is 16.
• 8 MPI processes are assigned to each GPU.

$ mpijob ./mdacp -i input.cfg -p 8 -g 2