SCIENTIFIC COMPUTING & VISUALIZATION
Lecture Notes
- Introduction;
slides;
computational-research survival guide
- 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; additional slides;
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
- Pair distribution computation with CUDA;
see also B. G. Levine et al.,
J. Comput. Phys. 230, 3556 (2011)
- Hybrid MPI+OpenMP+CUDA computing
- Intel Xeon Phi programming
- Grid computing
- MapReduce;
using Hadoop at USC-HPC
- Virtual-reality programming
- Optimizing molecular dynamics; see Berkeley CS267 lecture on
Single processor machines: memory hierarchies and processor features by Prof. Kathy Yelick;
for BLAS-ification, see K. Nomura et al.,
Metascalable quantum molecular dynamics simulations of hydrogen-on-demand,
Prof. Supercomputing, SC14 (IEEE/ACM, '14); for MD optimization, see
J. Mellor-Crummey et al.,
Improving memory hierarchy performance for irregular applications using data and computation reorderings,
Int'l J. Par. Prog. 29, 217 ('01)
- 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: