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- Introduction; slides
- Basic molecular dynamics algorithm; linked-list cell MD algorithm; slides
- Message Passing Interface; slides
- Parallel computation of Pi
- Parallel MD algorithm;
introduction;
slides;
in situ analysis of MD simulation data using communicators;
Shaw's NT algorithm;
see
A fast, scalable method for the parallel evaluation of distance-limited pairwise particle interactions,
D. E. Shaw,
*J. Comput. Chem***26**, 1318 (2005) and A scalable parallel algorithm for dynamic range-limited n-tuple computation in many-body molecular dynamics simulation, M. Kunaseth et al.,*Proc. of Supercomputing, SC13*(ACM/IEEE, 2013) - OpenMP
- Hybrid MPI+OpenMP parallel MD;
see
Performance characteristics of hardware transactional memory for molecular dynamics application on Blue Gene/Q:
toward efficient multithreading strategies for large-scale scientific applications,
M. Kunaseth et al., best paper of
*Proc. of PDSEC13*(IEEE, 2013); MPI+X, M. Wolfe,*HPC Wire*(2014); MPI+MPI, T. Hoefler et al.,*Computing***95**, 1121 (2013). - Visualizing molecular dynamics; slides; how to use OpenGL and GLUT with Microsoft Visual Studio
- VMD animation of molecular dynamics;
see Parallel in situ visualization with a fully featured visualization system,
B. Whitlock et al.,
*Proc. of PGV11*(Eurographics, 2011) and Biological electron transfer pathway analysis plugin for VMD, I. A. Balabin et al.,*J. Comput. Chem.***33**, 906 (2012); A framework for stochastic simulations and visualization of biological electron-transfer dynamics, C. M. Nakano et al.,*Comput. Phys. Commun.***193**, 1 (2015) and an associated movie - Massive dataset visualization
- CUDA
- Hybrid MPI+CUDA computing
- Pair distribution computation with CUDA;
see also B. G. Levine et al.,
*J. Comput. Phys.***230**, 3556 (2011) - Intel Xeon Phi programming
- Grid computing
- MapReduce; using Hadoop at USC-HPC
- Optimizing molecular dynamics
- Advanced topics in parallel molecular dynamics
- Metascalable divide-conquer-recombine algorithmic framework;
Quantum molecular dynamics in the post-petaflop/s era,
N. A. Romero et al.,
*IEEE Computer***48(11)**, 33-41 (2015) - Miscellaneous lectures:
- MSCS-HPCS: Master of Science in Computer Science specialized in High Performance Computing and Simulations; see also MSCS-HPCS information
- Taylor's expansion
- Least square fit of a line
- Arithmetic implementation of sqrt()
- Introduction to HPC cluster computing by Avalon Johnson at USC Center for High Performance Computing (HPC)
- Distributed-memory parallel computing
- Virtual reality as a research tool by Erick Moen
- 20 years of Beowulf; see Frontiers in Massive Data Analysis (National Research Council, 2013) and our Beowulf14 paper
- Parallel quantum dynamics
- Parallel computing using Matlab by Raymond Norris (MathWorks)