HIGH PERFORMANCE COMPUTING AND SIMULATIONS

• Introduction: HPCS courses; slides
• Deterministic particle simulation algorithms
  • Survey of molecular dynamics (MD): notes and slides
  • Fast multipole method--multiresolution in space: slides; minimal complex analysis; electrostatic potential around a charged line; multipole expansion of 2d Coulomb potential; fast multipole method algorithm in 2d
  • Multiple time stepping--multiresolution in time: slides
• Parallel computing frameworks
  • Parallel computing basics and parallel molecular dynamics: message passing interface (MPI) notes and slides; parallel MD algorithms notes and slides; scalability analysis of parallel molecular-dynamics and fast-multipole-method algorithms; multithreading using OpenMP; hybrid MPI+OpenMP programming; MD machines; Shaw's MD algorithm
  • Divide-and-conquer parallelism: notes and slides; reproducible global sum
  • Load balancing: slides; Lanczos method for eigensystems (slides and supplementary notes) used in spectral bisection load balancer
  • Optimizing parallel MD: slides; lecture note by Prof. Kathy Yelick (UC Berkeley) on memory hierarchies and matrix multiplication
  • New architectures: graphics processing unit (GPU) programming using CUDA; running a hybrid MPI+OpenMP+CUDA program at HPC; OpenMP target offload for heterogeneous devices; OpenMP 4.5 specification; Data parallel C++; Data Parallel C++ by J. Reinders et al. (Apress, 2020); lattice-Boltzmann fluid simulation on a Playstation3 cluster; MD simulation on GodsonT
• Deterministic continuum simulation algorithms
  • Survey of quantum dynamics (QD): QD basics; spectral QD and fast Fourier transform (FFT); parallelizing QD (slides)
  • Multiresolution numerical methods: slides; wavelets (Numerical Recipes, Sec. 13.10); multiresolution analysis using wavelets; multigrid method (Numerical Recipes, Sec. 19.6); Fermi-operator expansion for linear-scaling electronic structure calculations
• Hybrid particle/continuum simulation methods
  • Multiscale simulation methods: slides
• Scientific data analysis and visualization
  • Visualization basics--OpenGL programming and visualizing particles: notes and slides; how to use OpenGL and GLUT with Microsoft Visual Studio; for the visualization of quatum wave functions, see Visualizing quantum scattering on the CM-2 supercomputer, J. L. Richardson, Comput. Phys. Commun. 63, 84 (1991)
  • Massive dataset visualization: slides
  • Scientific data mining and machine learning: slides; ATPESC lectures on deep learning basics and data parallel deep learning
• Stochastic simulation methods
  • Monte Carlo (MC) simulation basics: MC basics; parallel MC; parallel kinetic MC simulation; kinetic MC simulation of electron transfer
  • Long time dynamics and global optimization
  • Stochastic continuum simulations
• Distributed scientific computing
  • Grid computing basics for application scientists: slides
  • Grid-enabling scientific applications
  • MapReduce for cloud computing
• Quantum computational science
  • Quantum computing
  • Quantum gates and circuits: hands-on
  • Transverse-field Ising model: hands-on
• Miscellaneous lectures
  • GitHub
  • Arithmetic implementation of sqrt() & floating-point performance