Topic outline

• General
  

  General

     

  This course, a collaboration of Erlangen Regional Computing Center (RRZE) and Leibniz Supercomputing Center (LRZ), is targeted at students and scientists with interest in programming modern HPC hardware, specifically the large scale parallel computing systems available in Jülich, Stuttgart and Munich, but also smaller clusters in Tier-2 centers and departments.
  
  The exercises given below are suggestions - you are free to play with any code you like. If you are a beginner you will probably also not be able to complete all tasks.
  
  Note:

  • Topics 1-5 below refer to the February 25 - March 1 course phase (taking place at LRZ)
  • Topics 6-9 refer to the March 18-21 course phase ("Advanced Topics", taking place at LRZ)

  Course room:

  LRZ Building, Boltzmannstr. 1, D-85748 Garching bei Muenchen, Kursraum 2, H.U.010
  

  Contact:

  Dr. Georg Hager (georg.hager@fau.de)
  Dr. Volker Weinberg (weinberg@lrz.de)

  • Schedule for days 1-5 File
  • Useful links and references Page
• Day 1
  

  Day 1

  The lectures on day 1 cover general tools and practices that are useful for working in programming environments, and specifically when dealing with HPC systems.

  • Welcome and general remarks File
  • Introduction to HPC File
  • Programming Environment @ LRZ File
  • Using the IvyMUC Cluster at LRZ File
  • SSH, Modules and User Interfaces File
  • Exercise: Working with the LRZ IvyMUC system Page
  • Introduction to GNU make File
  • CMake Tutorial File
  • Basics of Software Engineering File
• Day 2
  

  Day 2

  Day 2 gives an introduction to the dominant HPC programming models (MPI and OpenMP) as well as to computer architecture on a general level.

  • Elementary MPI and OpenMP File
  • Exercise: π by the Monte Carlo method Page
  • Introduction to computer architecture File
  • Affinity by OpenMP places File
  • Exercise: Measuring the FP divide throughput Page
• Day 3
  

  Day 3

  On day 3 we cover the principles of serial code optimization, and in the afternoon we get an in-depth look at some features of MPI.

  • Principles of serial code optimization File
  • Exercise: General code optimization Page
  • Advanced MPI Programming File
  • Exercise: Parallelization of a raytracer code Page
  • Spoiler alert: Solution for MPI File
• Day 4
  

  Day 4

  The lectures of day 4 introduce parallelism on a theoretical level (parallel patterns, performance models) and the different variants and structures of parallel computer systems.

  We also cover some advanced correctness and performance issues with OpenMP. 

  • Parallel architectures in depth File
  • Parallel Algorithms File
  • Advanced OpenMP Programming File
  • Exercise: Parallel histogram computation Page
  • Exercise: Eliminating recursion Page
  • OpenMP performance and correctness File
  • How to pin threads and processes (HPC Wiki) URL
  • Evening event at LRZ Page
• Day 5
  

  Day 5

  Day 5 is deals with Intel tools for performance analysis, tuning and correctness checking of parallel programs. It also introduces the Scalasca tuning framework. In addition, version control with SVN and GIT is covered.
  

  • Performance analysis tools: Intel® VTuneTM Amplifier and Advisor File
  • Performance analysis tools: Intel® Application Performance Snapshot and ITAC File
  • Scalasca File
  • Score-P File
  • Managing software development with SVN and git File
  • Exercises File
  • Some exercises solutions as archive File
• Day 6
  

  Day 6

  PRACE Course: Advanced Topics in High Performance Computing

  This workshop is a PRACE Training Course courtesy the agreement of the Gauss Supercomputing Centre with PRACE with respect to Europe-wide HPC training. LRZ is obliged to PRACE for partial support of the costs for this event.

  
  

  Day A1 of the advanced topics course deals with node-level code optimisation.

  • Infos Advanced Course 2019 File
  • Schedule for days A1-A4 (advanced topics) 2019 File
  • Using the IvyMUC Cluster at LRZ File
  • Exercise: Working with the LRZ IvyMUC system Page
  • Processor Specific Optimisation Part 1 File
  • Processor Specific Optimisation Part 2 File
  • Exercise 1: Bandwidth benchmark Page
  • Processor Specific Optimisation Part 3 File
  • Exercise 2: Investigate instruction code Page
  • Processor Specific Optimisation Part 4 File
• Day 7
  

  Day 7

  Day A2 deals with MPI-I/O, I/O on LRZ's HPC systems, as well as introducing specialised I/O libraries.

  • Parallel I/O with MPI IO File
  • Exercises for MPI IO Page
  • Tuning I/O on LRZ's HPC systems File
  • I/O Profiling with the Darshan Tool File
  • Exercises I/O Profiling with Darshan File
• Day 8
  

  Day 8

  Day A3 continues with I/O libraries and provides a special public lecture about the Intel Xeon Scalable (Skylake) processor architecture.
  

  • SIONLib Library File
  • High-Level I/O Library: HDF5 File
  • I/O libraries Exercises File
  • Intel Xeon Scalable (Skylake) Processor Architecture File
  • Intel Xeon Scalable (Skylake) Processor Architecture (copy) File
• Day 9
  

  Day 9

  Parallel programming with PGAS languages
  

  • PGAS programming with Coarray Fortran and Unified Parallel C File
  • Exercises File

    Exercises including how to compile and run PGAS programs.

• Evaluation
  

  Evaluation

  Please fill out the course evaluation form before leaving the lecture room to help us and PRACE to increase the quality of PRACE trainings.

  https://events.prace-ri.eu/event/822/surveys/517
  

  http://tinyurl.com/LRZ-survey
  

  
  

  Thank you for your collaboration and thank you for joining our course!!