COSC 365: High Performance Computing

Fall 2024

Course Resources

General	Syllabus Textbook: Our textbook (should be available in the bookstore). Example code from the book
Software and Other Resources	PuTTY: An ssh client for Windows machines. Cyberduck: A graphical server/cloud browser (use this to move files to/from LittleFe Note: You should just need to change the protocol to sftp, enter LittleFe’s IP address as the server, and type your username. Top500: The world’s top 500 supercomputers PicoCluster & LittleFe Tutorial: Instructions for logging into and using the PicoCluster and LittleFe clusters. Ookami Ookami Tutorial: Instructions for logging into and using the Ookami supercomputer at Stony Brook University in New York. You will need to complete the instructions found here. Ookami Website Ookami: Getting Started Guide Ookami: Frequently Asked Questions Example SLURM scripts mpi_example.slurm openmp_example.slurm To set up Duo, log in here Anvil Note: Our allocation account is cis240453-gpu, which you will need for submitting jobs. Anvil User Guide Follow instructions in welcome email first Set up SSH keys (required) Logging in
Videos	Supercomputer Tour at University of Wisconsin-Eau Claire Take a Tour of the Supercomputer Fugaku Take a Tour of One of Australia’s Most Powerful Supercomputers Timelapse: Constructing Australia’s Fastest Supercomputer
C Tutorials	Crash Course in C learn-c.org Tutorials Point Programiz w3schools Books from Amazon
Unix/Linux Command Line Tutorials	command-line-tutorial.readthedocs.io Tutorial from Ubuntu Tutorials Point Books from Amazon Linux Journey
Terminal-Based Text Editor Tutorials	vim-adventures openvim tutorialspoint (Vim) How to learn Emacs Emacs Tutorial The Beginner’s Guide To Nano
Projects	Project 1 (Introduction to C) Project 2 (Estimating Pi Using MPI) Project 3 (Timing MPI Communication Using Ping-pongs) Project 4 (Estimating Pi Using Pthreads) Project 5 (Estimating Pi Using OpenMP) Project 6 (Running Jobs on Ookami) Project 7 (Counting Primes with MPI and OpenMP)

Course Schedule

Week	Date	Topics	Due
1	Aug 29th (Thursday)	Course Introduction For next time: Read the syllabus, obtain the textbook and read Chapter 1, practice logging into LittleFe and navigating around. Try compiling a basic C program on LittleFe.
2	Sept 3rd (Tuesday)	The C Programming Language / Why Parallel Computing For next time: Practice logging into LittleFe and navigating around the Linux command line. Compile basic C programs on LittleFe. Start working on Project 1. Read Chapter 1.
	Sept 5th (Thursday)	The C Programming Language / Parallel Hardware and Parallel Software For next time: Keep working on Project 1. Read Chapter 2.1 and 2.2	Read Chapter 1
3	Sept 10th (Tuesday)	Distributed Memory Programming with MPI For next time: Finish Project 1. Read Chapter 3.1.	Project 1 (Introduction to C) Read Chapter 2.1 and 2.2
	Sept 12nd (Thursday)	Distributed Memory Programming with MPI For next time: Start working on Project 2. Start reading Chapter 3.2.	Read Chapter 3.1
4	Sept 17th (Tuesday)	Distributed Memory Programming with MPI For next time: Keep working on Project 2. Finish reading Chapter 3.2.
	Sept 19th (Thursday)	Distributed Memory Programming with MPI For next time: Keep working on Project 2. Start reading Chapter 3.3 and 3.4.	Read Chapter 3.2
5	Sept 24th (Tuesday)	Shared-Memory Programming with Pthreads	Read Chapter 3.3
	Sept 26th (Thursday)	Shared-Memory Programming with Pthreads For next time: Start reading Chapter 4.1 and 4.2.	Project 2 Read Chapter 3.4
6	Oct 1st (Tuesday)	HURRICANE - NO CLASS
	Oct 3rd (Thursday)	HURRICANE - NO CLASS
7	Oct 8th (Tuesday)	Shared-Memory Programming with Pthreads / PicoCluster Overview For next time: Start working on Project 3. Start reading Chapters 4.3, 4.4, and 4.5.	Read 4.1
	Oct 10th (Thursday)	Introduction to PicoCluster For next time: Keep working on Project 3. Start reading Chapters 4.6 and 4.7.	Read 4.2 and 4.3
8	Oct 15th (Tuesday)	Shared-Memory Programming with Pthreads / PicoCluster Overview For next time: Finish Project 3 (due date moved to next Tuesday). Start reading 4.8 and 4.9.	Read 4.4 and 4.5
	Oct 17th (Thursday)	FALL ACADEMIC HOLIDAY - NO CLASS
9	Oct 22nd (Tuesday)	Shared-Memory Programming with OpenMP For next time: Work on Project 4. Read 5.1 and 5.2.	Project 3 Read 4.6 and 4.7
	Oct 24th (Thursday)	Shared-Memory Programming with OpenMP For next time: Keep working on Project 4. Start reading 5.3, 5.4, and 5.5.	Read 4.8 and 4.9
10	Oct 29th (Tuesday)	Shared-Memory Programming with OpenMP For next time: Finish Project 4 (due date moved to next Tuesday). Start reading 5.6 and 5.7.	Project 4 Read 5.1 and 5.2
	Oct 31st (Thursday)	Introduction to Ookami For next time: Catch up on reading. Complete the instructions found in the Ookami tutorial posted above.	Read 5.3, 5.4, and 5.5
11	Nov 5th (Tuesday)	Running Jobs on Ookami For next time: If you still do not have Ookami access, complete the instructions ASAP, as they could take a couple days to complete.	Read 5.6 and 5.7
	Nov 7th (Thursday)	Running Jobs on Ookami For next time: You should now be able to access Ookami and run jobs. I will be able to track Ookami use, so please experiment with running various types of jobs (MPI, OpenMP), and know how to request an interactive session.	Project 5
12	Nov 12th (Tuesday)	Running Jobs on Ookami For next time: Project 6 is now posted.
	Nov 14th (Thursday)	Running Jobs on Ookami For next time: Finish Project 6.
13	Nov 19th (Tuesday)	Introduction to Anvil For next time: Project 7 is posted. Finish setting up your account on Anvil so that you can log in.	Project 6
	Nov 21st (Thursday)
14	Nov 26th (Tuesday)	THANKSGIVING HOLIDAY - NO CLASS
	Nov 28th (Thursday)	THANKSGIVING HOLIDAY - NO CLASS
15	Dec 3rd (Tuesday)
	Dec 5th (Thursday)		Project 7
16	Dec 11th (Wednesday)	Final Exam (3:00PM - 5:00PM)