Foundations of HPC, 2021/2022

This repository collects the materials from the course "Foundations of HPC" at Data Science and Scientific Computer, University of Trieste, year 2021/2022

Teachers:

Stefano Cozzini, Area Science Park, Trieste

Luca Tornatore, INAF - National Institute for Astrophysics, Astronomical Observatory of Trieste

Lab session are helped by: Federico Barone, Area Science Park, Trieste

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-- DSSC -- Data Science and Scientific Computing @ University of Trieste

-- Master in HPC @ SISSA/ICTP, Trieste

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Welcome to the "Foundations of HPC" course at (i) DSSC Department of the University of Trieste and (ii) Master in HPC program at SISSA/ICTP in Trieste.

The scope of the course is to give you:

• an introduction to basic concepts of the High Performance Computing
• an introduction to the modern computer architecture and the techniques to exploit it to maximize performance
• an introduction to parallel/multi-threading programming with MPI and OpenMP
• an introduction to basic and advanced techniques for code optimisation for single- and multi-threaded codes

The lectures will be both in presence (this may change in the future according to the evolution of the COVID pandemic) and in streaming; each lecture will also be recorded and available to be viewed asynchronously. The lectures (the precise calendar is shown in the table below) will be held in Aula Morin, building H2bis

The lectures will start on Monday, 4th October 2020.

DAY	11.00 - 11.55	12.00 - 12.55	16.00 - 16.55	17.00 - 17.55
Monday			first part	second part
Tuesday	first part	second part
Thursday	first part	second part
Friday	first part	second part

HOw to get an account on ORFEO

Please fill in with your details this google table:

https://docs.google.com/spreadsheets/d/1UFZMffMRBDp-tXRxOwdH2rzRGyib6-ZpeFguXleTEEA/edit#gid=1853927763

To learn how to generate a private/public keys on windows here a link: https://www.maketecheasier.com/generate-ssh-public-private-keys-windows/

Units's Microsoft Teams

Link for today lecture

https://teams.microsoft.com/l/meetup-join/19:6HsghqYmJTd3mXlRuhDl9EZV5vX9imECoBk8VBWbQXk1@thread.tacv2/1633960864011?context=%7B%22Tid%22:%22a54b3635-128c-460f-b967-6ded8df82e75%22,%22Oid%22:%22d7c26965-1813-464f-b1dd-239b179a37e8%22%7D

https://teams.microsoft.com/l/meetup-join/19%3ae7d09041acca41b9aa856b32db205960%40thread.tacv2/1639477577427?context=%7b%22Tid%22%3a%22a54b3635-128c-460f-b967-6ded8df82e75%22%2c%22Oid%22%3a%22d7c26965-1813-464f-b1dd-239b179a37e8%22%7d

slack Channel link:

https://join.slack.com/t/fhpc2021/shared_invite/zt-wp3dpcsn-CtRi3ICKavfjWiisEdPXWg

Contact details:

Stefano Cozzini: stefano.cozzini@areasciencepark.it

Luca Tornatore: luca.tornatore@inaf.it

EVALUATION

The final grade of the exam will be the result of a set of assignments during course, or alternatevely a project, and an oral examination based on the work done by students.

During the course, the students have been asked to carry out two assignments. It will be required to submit the code developed and the results written in a given format (so to allow automatic checking) on a repo that we will indicate. Each assignment will have a due date of either 1 or 2 weeks.

If the two assignments have been submitted and will be successful, the student will be directly admitted to a final oral examination. The oral examination will focus on the topics covered in the lessons, and it will start from the examination of some of the assignments.

If the either the two assignments will not have been submitted, or they are not successful, a written exam will be required. This test will consist in a project that must be submitted at least 1 week before taking the oral examination.

CALENDAR

DATE	LECTURES	TUTORIALS	ASSIGNEMENTS
Mon, Oct 4	[1] Introduction to course/ introduction to HPC
Tue, Oct 5	[2] Introduction to HPC: part 2
Thu, Oct 7	[3] HPC Hardware and HPC software stack and tools
Fri, Oct 8			Assignment 0: enable your account on ORFEO
Mon, Oct 11		[1] Using an HPC infrastructure
Tue, Oct 12	[5] Single Core Optimization (SCO) / 1 Modern Architecture + Opt. Intro + Stack & Heap + Memory allocation
Thu, Oct 14	[6] SCO / 2 How to use the Compiler + Cache hierarchy
Fri, Oct 15	[7] SCO / 3 loops
Mon, Oct 18		[2] Tools for profiling
Tue, Oct 19	[8] SCO / 4 Pipelines +branch predictions
Thu, Oct 21	[9] SCO / 5 Prefetching + vectorization
Fri, Oct 22		[3] Debugging
Mon, Oct 25	[10] Parallel programming concepts and performance
Tue, Oct 26	[11] Message Passing and MPI programminng
Thu, Oct 28	[12] Collective MPI operations and virtual topology
Fri, Oct 29	[13] Domain Decomposition with MPI	[4] Exercises on MPI
Thu, Nov 4	[14] Network basic for MPI application
Fri, Nov 5	[15] MPI libraries and performance model
Mon, Nov 8		[5] short tutorial on measuring MPI performance on ORFEO nodes
Tue, Nov 9	[16] Performance Evaluation for MPI
Thu, Nov 11			Assignment 1
Fri, Nov 12		[6] short tutorial on using ORFEO at best for the assignment
Mon, Nov 15	[17] OpenMP / 1
Tue, Nov 16	[18] OpenMP / 2
Thu, Nov 18	[19] OpenMP / 3
Fri, Nov 19	[20] OpenMP / 4	[7] Exercises on openMP	Assigment 2
Mon, Nov 22	[21] OpenMP / 5
Tue, Nov 23	[22] OpenMP / 6
Thu, Nov 25	[23] OpenMP / 7
Fri, Nov 26	[23] OpenMP / 8
Mon, Nov 29	[24] OpenMP / 9
Tue, Nov 30	[25] Parallel HPC libraries
Thu, Dec 2	[26] Benchmarking HPC systems
Fri, Dec 3		[9] Exercises on benchmarking
Mon, Dec 6	[27] Parallel I/O
Tue, Dec 7	[28] exercise on parallel I/O
Thu, Dec 9	[29] roof model + parallel performance analysis /1
Fri, Dec 10	c[30] Parallel Performance Analysis /2	(PerformanceAnalysis/README.md)
Mon, Dec 13	[31] Parallel Performance Analysisscalasca
Tue, Dec 14		[10] [exercise on parallel performance analysis]
Thu, Dec 16	[32] GPU programming/1
Fri, Dec 17	[33] GPU programming/2

PRACTICAL ADVICES

As you will experiment, having a Linux is always the most adequate solution (Linux is running on the vast majority - possible the 100% - on HPC facilities and brings native tools and utilities for programming).

So, our advice is that on your laptop you run a Linux (of course, it is not needed that you run only Linux: you may a have a multi-boot machine with any other OS you want).

As a second option, you can install a Linux machine in a Virtual box under your preferred OS.

For Windows users, a third option is running Linux under the W10 WSL, that seems to be enough for our course needs.

REFERENCES & BOOKS

Ref 1: High Performance Computing Modern Systems and Practices

Available at ICTP library Authors: Thomas Sterling Matthew Anderson Maciej Brodowicz eBook ISBN: 9780124202153 Paperback ISBN: 9780124201583

Some of the materials of this book are presented during some lectures.

Ref 2: Introduction to High-Performance Scientific Computing,by Victor Eijkhout

The source and pdf of the book (as well as lecture slides) can be found at this link: https://pages.tacc.utexas.edu/~eijkhout/istc/istc.html, DOI: 10.5281/zenodo.49897

Some of the materials presented in classes are taken from this book.

Ref 3: Computer Organization and Design

by D. A. Patterson and J. L. Hennessy The Morgan Kaufmann Series in Computer Architecture and Design easily available as pdf on the net.

Ref 4: Introduction to High Performance Computing for Scientists and Engineers

by Georg Hager and Gerhard Wellein Paperback: 356 pages Publication date July 2, 2010 Editors (Chapman & Hall/CRC Computational Science)

Ref 5: Optimizing HPC Applications with Intel Cluster Tools

Paperback – October 15, 2014 by Alexander Supalov (Author), Andrey Semin (Author), Michael Klemm (Author), & 1 more ISBN-13: 978-1430264965 ISBN-10: 1430264969 Edition: 1st

Ref 6: High Performance Parallelism Pearls, 1st Edition

Multicore and Many-core Programming Approaches by Reinders & Jeffers Morgan Kaufmann, Print Book ISBN :9780128021187