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Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations.

Jaewoon Jung1,2, Akira Naurse3, Chigusa Kobayashi2

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|September 16, 2016
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This study introduces a new scheme for large-scale molecular dynamics (MD) simulations using graphics processing units (GPUs). The method accelerates biomolecular simulations on supercomputers by optimizing computations between GPUs and central processing units (CPUs).

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Area of Science:

  • Computational Biology
  • Biophysics
  • Materials Science

Background:

  • Graphics Processing Units (GPUs) accelerate molecular dynamics (MD) simulations for small to medium biomolecular systems.
  • Scaling MD simulations for large systems (millions of atoms) on GPU-accelerated supercomputers is challenging due to GPU memory limitations and inter-node communication.

Purpose of the Study:

  • To develop a new computational scheme within the GENESIS software to accelerate large-scale molecular dynamics (MD) simulations on GPU-accelerated supercomputers.
  • To overcome limitations in GPU memory and inter-GPU communication for simulating large biological systems.

Main Methods:

  • Implemented a hybrid computation scheme assigning real-space nonbonded interactions to GPUs and bonded/reciprocal-space interactions to CPUs.
  • Developed a single particle interaction list based on the midpoint cell method to reduce GPU memory usage.
  • Utilized RESPA multiple time-step integration to minimize CPU idle time by offloading nonbonded interactions to CPUs and GPUs.

Main Results:

  • The new scheme effectively reduces computational time for large-scale MD simulations.
  • GPU memory usage was reduced, enabling simulations of systems with millions of atoms.
  • MD simulations of a million-atom system demonstrated scalability up to 256 GPU nodes on the TSUBAME supercomputer.

Conclusions:

  • The developed computational scheme significantly enhances the efficiency of large-scale biomolecular simulations on GPU-accelerated supercomputers.
  • GENESIS software with the new scheme enables scalable and efficient simulations of large biological systems.
  • This advancement facilitates in-depth studies of complex biomolecular systems previously limited by computational power.