High Performance Computing

High Performance Computing

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Utah State University

Fall 2020

HPC
Days

Tue, Thu

Time

3:00-04:15 PM

Location

RWST 306 or Web Broadcast

Office hours

Wed 4.30-5.30PM, Fri 2.00-3.00PM on Zoom (Canvas)

This course is an introduction to high-performance computing. High-performance computing (HPC) is the practice of leveraging parallel computing power, from computer clusters and supercomputers, to solve complex computational problems faster. In this course students will learn the main programming models, such as openMP and MPI, to write highly optimized code for modern multi-core processors, clusters, and modern computing architecture (e.g., GPUs). Furthermore, this course will explore the concepts and challenges of performance scalability, portability, and energy efficiency of HPC applications and systems.

Lecturer: Dr. Steve Petruzza TA: Kohl Kennedy

Topics include: multithread programming, openMP, distributed programming, MPI, performance profiling, parallel and distributed algorithms, parallel I/O, in situ analytics, GPU programming.

Prerequisites: a good C/C++ programming background. Most of the assignment will be in C/C++. In particular, a student needs to have knowledge of data structures, arrays, pointers and memory allocation in C/C++. If you are not too familiar with C/C++ here is a tutorial that could be useful, the “C++ basic” section is a good place to start. If you are not familiar with the Unix terminal:

  • you can try it online or install it on your machine (see here )
  • some basic commands that you can use can be found here
  • if you use Windows you can install a Linux subsystem following this guide here.

Resources

  • [IPP] An Introduction to Parallel Programming. Peter Pacheco
  • [UMPI] Using MPI: Portable Parallel Programming with the Message-Passing Interface. Anthony Skjellum, William Gropp, and Ewing Lusk
  • [GPU] Programming Massively Parallel Processors, 2nd Edition. David B. Kirk, Wen-mei W. Hwu
  • [CHPC] Accessing CHPC Resources

Gradings

  • Homework (30%), 7 assignments
  • Mid-term exam (25%)
  • Final exam (25%)
  • Project (20%)

Class schedule

Day Topic References Homework
Sep 1 Introduction IPP Ch. 1  
Sep 3 Computing architecture and memory IPP Ch. 2  
Sep 8 Parallel hardware and interconnects IPP Ch. 2  
Sep 10 Parallel software and scalability IPP Ch. 2 HW1
Sep 15 Shared memory programming: PThreads IPP Ch. 4  
Sep 17 Shared memory programming: PThreads (2) IPP Ch. 4  
Sep 22 Shared memory programming: PThreads (3) IPP Ch. 4  
Sep 24 C++11 Threads and running on an HPC system CHPC HW2
Sep 29 OpenMP (1) IPP Ch. 5  
Oct 1 OpenMP (2) IPP Ch. 5  
Oct 6 Distributed programming: basics IPP Ch. 3  
Oct 8 Distributed programming: MPI IPP Ch. 3  
Oct 13 Mid-term exam   Mid-term
Oct 15 Reviews, more MPI (2)   HW3
Oct 20 Applications (1)    
Oct 22 Applications (2)    
Oct 27 Projects, Parallel I/O   HW4
Oct 29 Introduction to GPU Programming and CUDA GPU Ch.1,2,3  
Nov 3 GPU: execution and memory model GPU Ch.4,5  
Nov 5 GPU: tiling and matrix multiplication GPU Ch.6,7 HW5
Nov 10 GPU: convolution GPU Ch.8  
Nov 12 GPU: applications GPU Ch.9  
Nov 17 Review   HW6
Nov 19 Python for HPC    
Nov 24 In situ analytics    
Nov 26 Thanksgiving    
Dec 1 Parallel programming languages   HW7
Dec 3 Review    
Dec 8 Project presentations    
Dec 10 Project presentations    
Dec 15 Final exam   Final
Dec 17 Project presentations and final review    


The schedule above is subject to change

Assignments

  • You will submit your assignment using the Canvas System. Assignment is due by 11:59 p.m. on the due date. No late assignment will be accepted. However, I will grant one gift (e.g., turn in the assignment up to 2 days beyond the submission deadline) for the entire semester with an email request to grader (name: Kohl Kennedy; email: kohl.kennedy@aggiemail.usu.edu) before the due date.
  • You are required to do your own work. You will be responsible to ensure that your assignment is submitted correctly. If you have multiple files to submit, you need to zip multiple files into one file before submission. Please verify the information in the confirmation email. If the assignment is submitted incorrectly, you can resubmit it. The system keeps track of the last file submitted for each assignment. If you do not get the confirmation information within a few minutes, you can assume the assignment has not been submitted.
  • Homeworks, mid-term and final exams are a mix of quiz, open questions and short programming assignments. Most of the programming assignments are in C/C++.
  • At the top of each assignment, please include comments that consist of your name, your contact email, and assignment name or number. For programming assignments please clearly add comments for each important variable and section.

Projects

Selection/proposal deadline: Nov 8, 2020 Submission deadline: Dec 6, 2020

More details to come

Grading Scheme

A [93%, 100%] A- [87%, 93%) B+ [81%, 87%) B [75%, 81%) B- [70%, 75%) C+ [65%, 70%) C [60%, 65%) C- [58%, 60%) D+ [55%, 58%) D [53%, 55%) F Below 53%

Grading Policy and Grades

  • Each programming assignment is graded based on the following factors: code efficiency, code structure, technique difficulty, code readability, etc.
  • Your scores for each assignment and exam will be available through the Canvas System. You will be shown each individual score, your percent to date, and any comments. You will be notified via email whenever you receive a score or when a change is made to a score.
  • If you want to dispute a score, contact Kohl (kohl.kennedy@aggiemail.usu.edu) within two days of having received the original score. If the disagreement is not resolved after communicating with the TA, contact me by email (steve.petruzza@usu.edu). I will review your submission, talk to the TA and then respond to you. I will not consider changes in scores if you do not contact me within one week of when the score is sent to you.

Important dates

  • Late Adds: The last day to add this class is September 21 (Monday). Attending this class beyond that date, without being officially registered, will not be approved by the Dean’s Office. Students must be officially registered for this course. No assignments or tests of any kind will be graded for students whose names do not appear on the class list.
  • Drop Date: The last day to drop classes is:
    1. Monday, September 21 - without a “W” notation on transcript.
    2. Monday, November 2 - with a “W” notation on transcript.

Withdrawal Policy, “I” Grade Policy, and Dropping Courses

If a student does not attend a class during the first week of the term or by the second class meeting, whichever comes first, the instructor may submit a request to have the student dropped from the course. (This does not remove responsibility from the student to drop courses which they do not plan to attend.) Students who are dropped from courses will be notified by the Registrar’s Office through their preferred e-mail account. Students may drop courses without notation on the permanent record through the first 20 percent of the class. If a student drops a course following the first 20 percent of the class, a W will be permanently affixed to the student’s record (check General Catalog for exact dates). Students with extenuating circumstances should refer to the policy regarding Complete Withdrawal from the University and the Incomplete (I) Grade policy in the General Catalog.

COVID-19 Classroom Protocols

In order to continue to provide various forms of face-to-face instruction at USU, and to limit the spread of COVID-19 during the pandemic, students are asked to follow certain classroom protocols during the fall 2020 semester. These protocols are based on CDC, state, and local health department guidelines and requirements are in place not only for your safety but also the safety of the entire campus community.

  • Face coverings are required in all classrooms and teaching laboratories. Students will not be permitted to remain in class without a face covering, as per University Policy 20T.3. Students that do not adhere to the face covering policy will be referred to the Office of Vice President for Student Affairs for a possible violation of the Student Code of Conduct. There may be individual medical circumstances that prevent some students from using face coverings. If you require this exemption, contact the Disability Resource Center prior to the start of classes to investigate alternative instruction. These circumstances will be rare, but if they do exist, we ask that everyone be respectful.
  • Follow faculty instructions regarding social distancing and entering/exiting classrooms.
  • Stay home when you are sick, however mild your symptoms.
  • Wash your hands frequently with soap and water.

Academic Freedom and Professional Responsibilites

Academic freedom is the right to teach, study, discuss, investigate, discover, create, and publish freely. Academic freedom protects the rights of faculty members in teaching and of students in learning. Freedom in research is fundamental to the advancement of truth. Faculty members are entitled to full freedom in teaching, research, and creative activities, subject to the limitations imposed by professional responsibility. USU Policy 403 further defines academic freedom and professional responsibilities.

Academic Integrity – “The Honor System”

The University expects that students and faculty alike maintain the highest standards of academic honesty. The Code of Policies and Procedures for Students at Utah State University (Student Conduct) addresses academic integrity and honesty and notes the following:

Academic Integrity

Students have a responsibility to promote academic integrity at the University by not participating in or facilitating others’ participation in any act of academic dishonesty and by reporting all violations or suspected violations of the Academic Integrity Standard to their instructors.

The Honor Pledge

To enhance the learning environment at Utah State University and to develop student academic integrity, each student agrees to the following Honor Pledge: “I pledge, on my honor, to conduct myself with the foremost level of academic integrity”. Violations of the Academic Integrity Standard (academic violations) include, but are not limited to cheating, falsification, and plagiarism.

Plagiarism and Cheating

Plagiarism includes knowingly “representing by paraphrase or direct quotation, the published or unpublished work of another person as one’s own in any academic exercise or activity without full and clear acknowledgment. It also includes the unacknowledged use of materials prepared by another person or agency engaged in the selling of term papers or other academic materials.” The penalties for plagiarism are severe. They include warning or reprimand, grade adjustment, probation, suspension, expulsion, withholding of transcripts, denial or revocation of degrees, and referral to psychological counseling.

This course adheres to the cheating policy for courses in the Department of Computer Science.

Students with Disabilities

USU welcomes students with disabilities. If you have, or suspect you may have, a physical, mental health, or learning disability that may require accommodations in this course, please contact the Disability Resource Center (DRC) as early in the semester as possible (University Inn # 101, 435797‐2444, drc@usu.edu). All disability related accommodations must be approved by the DRC. Once approved, the DRC will coordinate with faculty to provide accommodations.

Sexual Harassment

Utah State University is committed to creating and maintaining an environment free from acts of sexual misconduct and discrimination and to fostering respect and dignity for all members of the USU community. Title IX and USU Policy 339 address sexual harassment in the workplace and academic setting.

The university responds promptly upon learning of any form of possible discrimination or sexual misconduct. Any individual may contact USU’s Affirmative Action/Equal Opportunity (AA/EO) Office for available options and resources or clarification. The university has established a complaint procedure to handle all types of discrimination complaints, including sexual harassment (USU Policy 305), and has designated the AA/EO Director/Title IX Coordinator as the official responsible for receiving and investigating complaints of sexual harassment.

Grievance Process

Students who feel they have been unfairly treated [in matters other than discipline, admission, residency, employment, traffic, and parking - which are addressed by procedures separate and independent from the Student Code] may file a grievance through the channels and procedures described in the Student Code: Article VII Grievances.

Assumption of Risk

All classes, programs, and extracurricular activities within the University involve some risk, and some involve travel. The University provides opportunities to participate in these programs on a voluntary basis. Therefore, students should not participate in them if they do not care to assume the risks. Students can ask the respective program leaders/sponsors about the possible risks a program may generate, and if students are not willing to assume the risks, they should not select that program. By voluntarily participating in classes, programs, and extracurricular activities, students do so at their own risk. General information about University Risk Management policies, insurance coverage, vehicle use policies, and risk management forms can be found at http://www.usu.edu/riskmgt/.

Mental Health

Mental health is critically important for the success of USU students. As a student, you may experience a range of issues that can cause barriers to learning, such as strained relationships, increased anxiety, alcohol/drug problems, feeling down, difficulty concentrating and/or lack of motivation. These mental health concerns or stressful events may lead to diminished academic performance or reduce your ability to participate in daily activities. Utah State University provides free services for students to assist them with addressing these and other concerns. You can learn more about the broad range of confidential mental health services available on campus at Counseling and Psychological Services (CAPS).

Students are also encouraged to download the “SafeUT App” to their smartphones. The SafeUT application is a 24/7 statewide crisis text and tip service that provides real-time crisis intervention to students through texting and a confidential tip program that can help anyone with emotional crises, bullying, relationship problems, mental health, or suicide related issues.