  Molecular dynamics (MD) is an important research tool extensively applied in
materials science. Running MD on a graphics processing unit (GPU) is an
attractive new approach for accelerating MD simulations. Currently, GPU
implementations of MD usually run in a one-host-process-one-GPU (OHPOG) scheme.
This scheme may pose a limitation on the system size that an implementation can
handle due to the small device memory relative to the host memory. In this
paper, we present a one-host-process-multiple-GPU (OHPMG) implementation of MD
with embedded-atom-model or semi-empirical tight-binding many-body potentials.
Because more device memory is available in an OHPMG process, the system size
that can be handled is increased to a few million or more atoms. In comparison
with the CPU implementation, in which Newton's third law is applied to improve
the computational efficiency, our OHPMG implementation has achieved a
28.9x~86.0x speedup in double precision, depending on the system size, the
cut-off ranges and the number of GPUs. The implementation can also handle a
group of small boxes in one run by combining the small boxes into a large box.
This approach greatly improves the GPU computing efficiency when a large number
of MD simulations for small boxes are needed for statistical purposes.
