High Performance Computing for Science and Engineering (HPCSE) I – HS 2019

Lecturer

Prof. Petros Koumoutsakos

Teaching Assistants

Class Room

ML H44

Class Times

Lecture: Friday, 10:15 – 12:00 (ML H44)
Exercise: Friday, 08:15 – 10:00 (ML H44)

Computer Rooms

HG E26.1, E26.3, E27

The environment provided by these computers is similar to the exam environment.

Class Material

Mailing List: hpcse_hs19@sympa.ethz.ch
Git repository: https://gitlab.ethz.ch/hpcse19/lecture.git
Exercise submission: Moodle
Piazza discussion board: Piazza

Schedule and Lecture Slides

20.09.2019	Introduction, Architectures, Performance (> Additional Slides <)
27.09.2019	Shared Memory, Concurrency, Threads
04.10.2019	OpenMP, part 1
11.10.2019	OpenMP, part 2, Linear algebra: BLAS
18.10.2019	SVD and Neural Networks, lecture notes PCA
25.10.2019	Neural Networks and Matrix Vector multiplication, lecture notes Perceptron
01.11.2019	Instruction Set Architecture and Pipelining
08.11.2019	MPI, part 1
15.11.2019	MPI, part 2 and strong / weak scalings
22.11.2019	MPI, part 3 I/O + hybrid MPI-OpenMP
29.11.2019	Structured grids and Finite differences (Diffusion)
06.12.2019	Particles and N-Body Solvers (Diffusion) , lecture notes
13.12.2019	Vectorization
20.12.2019	Particle-Grid Algorithms (Remeshing, Semi-Lagrangian) , blackboard

Exercises

The exercises begin in the second week of the semester.

Date	Exercise	Handout	Solution
27.09.2019	Set 1	PDF, skeleton code (Suppl.: SSH for Windows)	Solution
11.10.2019	Set 2	PDF, skeleton code, slides, tutorial	Solution
25.10.2019	Set 3	PDF, skeleton code, slides	Solution
08.11.2019	Set 4	PDF, skeleton code, slides	Solution
22.11.2019	Set 5	PDF, skeleton code, slides	Solution
06.12.2019	Set 6	PDF, skeleton_code, slides	Solution

Tutorial sessions

Date	Session	Handout
04.10.2019	Tutorial 1: C/C++ Basics for Science And Engineering	Exercise Files
18.10.2019	Tutorial 2: BLAS & Optimizations	Exercise Files
01.11.2019	Tutorial 3: Oja’s rule & PCA, blackboard	Exercise Files
15.11.2019	Tutorial 4: Name mangling, debugging, memory leaks, profiling	Exercise Files
29.11.2019	Tutorial 5: Parallel data storage and visualization	Exercise Files
13.12.2019	Tutorial 6: Cell-lists	Exercise Files

Exam

Updated 20.12.2019: PDF summary for Exam info/tips discussed in the Q&A session of the last exercise: exam info

Computer based session examination involving theoretical questions and coding problems. You are allowed to bring a handwritten summary of 4 A4 sheets, written on the front and back pages (8 pages total). In addition, we will provide you with the following material:

Lecture slides
Exercise solutions
Additional lecture notes distributed during the lecture
OpenMP specification and reference card (pdf)
MPI standard and reference card (pdf)
Offline version of cppreference.com
Offline version of the Intel intrinsics guide
The book by Victor Eijkhout

Textbooks

An Introduction to Parallel Programming, P. Pacheco, Morgan Kaufmann, 2011
Introduction to High Performance Computing for Scientists and Engineers, G. Hager and G. Wellein, CRC Press, 2011
Parallel Programming in MPI and OpenMP, V. Eijkhout. (Will be available in the exam) List of chapters
Computer Organization and Design, D.H. Patterson and J.L. Hennessy

Additional Material

Old Exam Sheets

Exam Sheet (2012): It included some topics that are NOT part of this semester’s lecture.
Exam Sheet (2015): It included some topics that are NOT part of this semester’s lecture. (skeleton codes)
Documentation: Lecture slides and exercise solutions, Manuals for C++, OpenMP, MPI and SIMD. Available in the 2016 exam. Sample cover sheet

Useful Links

General links on HPC and clusters

Bash tutorial
cheat.sh, multi-purpose command line reference
Command Reference
Euler wiki
CSCS users page
www.hpc-ch.org