molecular dynamics

Optimizing Legacy Molecular Dynamics Software with Directive-based Offload

Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines.

  • Developers
  • Linux*
  • lammps
  • molecular dynamics
  • many-core
  • Code Modernization
  • Intel® Many Integrated Core Architecture
  • LAMMPS* for Intel® Xeon Phi™ Coprocessor

    Purpose

    This code recipe describes how to get, build, and use the LAMMPS* code for the Intel® Xeon Phi™ coprocessor.

    Introduction

    Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS*) is a classical molecular dynamics code. LAMMPS has potentials for solid-state materials (metals, semiconductors), soft matter (biomolecules, polymers), and coarse-grained or mesoscopic systems. LAMMPS can be used to model atoms, or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.

  • Server
  • LAMMPS*
  • Intel® Xeon Phi™ Coprocessor
  • molecular dynamics
  • Intel® Many Integrated Core Architecture
  • GROMACS for Intel® Xeon Phi™ Coprocessor

     

    Purpose

    This code recipe describes how to get, build, and use the GROMACS* code with support for the Intel® Xeon Phi™ coprocessor with Intel® Many-Integrated Core (MIC) architecture.

  • Developers
  • Linux*
  • Server
  • Intermediate
  • biochemical molecules
  • molecular dynamics
  • Intel(R) Xeon Phi(TM) Coprocessor
  • GROMACS
  • Subscribe to molecular dynamics