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Talks - Markus Höhnerbach

  1. High-Performance & Automatic Computing: Fast & portable code for complex molecular dynamics simulations
    Institute for Computational Engineering and Sciences, University of Texas at Austin, Babuska forum, November 2018.
    With the increase in complexity and heterogeneity of computing architectures, it is especially challenging and time consuming to devise algorithms that exploit the available computational power. Typically, scientific computing practitioners either invest in months-long cycles of software development --favoring computer efficiency at the expense of productivity and portability-- or resort to high-level languages --in favor of productivity, but entirely disregarding computer performance--. The High-Performance and Automatic Computing group aims to bridge the disconnect between application experts and computing architectures by providing tools that enable both productivity and performance. In this talk, we first give a short overview of our activities in the domanins of linear algebra and tensor operations, and then dive into the specific case of molecular dynamics (MD), an extremely popular technique to simulate the evolution of large systems of particles. We present a domain specific compiler that takes as input the mathematical description of the law that regulates how the particles attract each other, and returns optimized code. While code generation from an abstract representation of the target problem is a common technique for the solution of PDEs (e.g., the Fenics project), it is still largely unexplored in MD. We discuss different optimizations, both with respect to performance and portability, demonstrating efficiency on par to what achieved by human experts.
  2. Vectorization of Multi-Body Potentials: Performance and Portability
    SIAM Conference on Computational Science and Engineering.
    Atlanta, Georgia, February 2017.
    As today's supercomputers become more and more powerful, simulations can cover bigger length-scales and time-scales using more accurate, but also more expensive force fields. In the materials science community, many-body potentials are widely used for their predictive power with respect to certain material properties, at the expense of higher computational cost. The challenge lies in mapping the complex calculations necessary to evaluate such potentials onto the available computing devices. Since modern architectures concentrate the computational power in wide SIMD units, and compilers commonly have trouble generating efficient code for them, a dedicated optimization effort is necessary. Special care is needed to minimize the effort required to implement a potential on a new architecture, and to allow for portability at the algorithmic level. Our research provided insights in the vectorization of the Tersoff, REBO and AIREBO potentials, widely used for semiconductor, carbon material, and carbohydrate simuations. We target a diverse set of hardware ranging from x86 CPUs (Westmere to Skylake), to Xeon Phi accelerators of both generations, and even GPUs. The improvements typically double the simulation throughput in large-scale, parallel runs, and higher speedups are possible when deploying accelerators.
  3. IPCC @ RWTH Aachen University: Optimization of multibody and long-range solvers in LAMMPS
    IPCC Showcase November 2016.
    November 2016.
  4. The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability
    SC 2016.
    November 2016.
  5. Optimization of multibody and long-range solvers in LAMMPS
    Intel PCC EMEA Meeting.
    Ostrava, March 2016.
  6. The Tersoff many-body potential: Sustainable performance through vectorization
    SC15 Workshop: Producing High Performance and Sustainable Software for Molecular Simulation.
    November 2015.