2022 High Performance Computing Practical Lecture 5.1 MPI Communicators & Data Structures Part1 👨💻
Practical Lecture 5.1 - Understanding MPI Communicators & Data Structures 👨💻 - Part One
Advanced Scientific Computing
16 university lectures with additional practical lectures for hands-on exercises in context
The University of Iceland, School of Engineering and Natural Sciences
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science
Spring 2022
Course Outline
1. High Performance Computing
2. Parallel Programming with MPI
3. Parallelization Fundamentals
4. Advanced MPI Techniques
5. Parallel Algorithms & Data Structures
6. Parallel Programming with OpenMP
7. Hybrid Programming & Patterns
8. Debugging & Profiling & Performance Analysis
9. Accelerators & Graphical Processing Units
10. Parallel & Scalable Machine & Deep Learning
11. HPC in Health & Neurosciences
12. Computational Fluid Dynamics & Finite Elements
13. Systems Biology & Bioinformatics
14. Molecular Systems & Material Sciences
15. Terrestrial Systems & Climate
16. Epilogue
Lecture Outline
Part One: Non-Blocking Communications & Communicator Examples
Blocking vs. Non-Blocking Communication – Revisited & Algorithms
Non-Blocking Communication with Isend/Irecv & Wait Functions
Understanding MPI Cartesian Communicator Dimensions & Shifts
Using Non-Blocking Communication with Cartesian Communicators
Simple Application Examples on Jötunn HPC System
Part Two: MPI Derived Data Types & Parallel I/O via HDF Examples
Simple Examples of MPI Derived Data Types with Applications
MPI I/O & Parallel Filesystems using HDF5 – Revisited
Data Science Example with Parallel & Scalable HPDBSCAN Algorithm
Understanding HDF5 Binary File Format & Using H5Dump Tool
HPDBSCAN Clustering of Point Cloud Data Set Bremen on Jötunn HPC System