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Area of Science:

  • Computational Chemistry
  • Molecular Dynamics
  • High-Performance Computing

Background:

  • Quantum mechanics/molecular mechanics (QM/MM) methods are crucial for simulating complex molecular systems.
  • Efficient implementation on graphics processing units (GPUs) is key to accelerating these simulations.
  • Optimization for diverse GPU architectures, including AMD, expands accessibility and computational power.

Purpose of the Study:

  • To port and optimize the GPU-accelerated QUICK and AMBER QM/MM implementation on AMD GPUs.
  • To enhance the performance of the entire Fock matrix build and force calculation within the QUICK code.
  • To benchmark the performance on both NVIDIA and AMD GPUs and compare with previous versions.

Main Methods:

  • Porting and optimization of QUICK and AMBER QM/MM code for AMD GPUs.
  • Inclusion of Fock matrix build and force calculation optimizations (one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, linear algebra).
  • Performance benchmarking on NVIDIA V100 and AMD MI100 GPUs for standalone HF/DFT and QM/MM molecular dynamics.

Main Results:

  • Achieved similar performance for standalone HF/DFT and QM/MM simulations on NVIDIA and AMD GPUs.
  • Observed significant speedups for QM/MM molecular dynamics simulations compared to QUICK/AMBER version 21.
  • Demonstrated general performance improvements in the QUICK GPU code.

Conclusions:

  • The optimized QM/MM implementation on AMD GPUs provides comparable performance to NVIDIA hardware.
  • Significant speedups enhance the feasibility of complex simulations using open-source QM/MM software.
  • This advancement broadens the scope of scientific inquiry addressable with modern computational resources.