Computer Science 335
Parallel Processing and High Performance Computing

Fall 2024, Siena College

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Disclaimer

Everything on this syllabus is subject to change. Changes will be announced in class and updated in the online version of the syllabus.

Mission Statements and Learning Goals

• The Siena College mission statement can be found on the College web site
• Siena College learning goals can be found on the College web site
• The School of Science mission statement can be found on the School of Science web site.
• The Department of Computer Science learning goals can be found on the Department of Computer Science web site.
• The Department of Computer Science mission statement can be found on the Department of Computer Science web site.

Course Objectives

Once available only in supercomputers, parallel hardware is now pervasive, right down to our personal computers and mobile devices. To harness the full power of these computers programmers must understand parallel processing, which introduces challenges at many levels. This course examines methods and techniques to support parallel programming in a variety of parallel computing environments, performance analysis, effciency and complexity of parallel algorithms, and applications of parallel computation.

Our specific learning objectives for CSIS 335 include the following:

• reinforce general programming skills acquired in previous course work (see "Prerequisites") and expand problem solving skills
• learn specifics of parallel processing, including problem decomposition, language tools to specify that decomposition, and run problems of relevance within a range of modern parallel computing environments

Prerequisites

• Computer Science 210, Data Structures, or equivalent.
• C programming including pointers and memory management is required. Students with insufficient C programming experience should take the 1-credit half-semester course Computer Science 301, C Programming in Unix, offered concurrently with this course.

Texts

The required text for the course is An Introduction to Parallel Programming, First Edition (Morgan Kaufmann, 2011, ISBN 9780123742605) by Peter Pacheco. This is available from the Siena Bookstore (and elsewhere). If you buy elsewhere, be sure to get the correct edition.

Other readings will also be assigned from freely available sources, made available as needed.

Lecture/Lab Meetings

A significant fraction of our class time to be used for lab activities. To minimize the need for traditional lectures, it is important to do any pre-lab tasks and readings before coming to class. This will permit more of our class time to be used for hands-on work. Come to class prepared and on time. Assigned readings are listed on the lecture and reading schedule. Everyone is expected to attend class and participate in discussions and to complete in-class exercises.

Assignments

Assignments will be made regularly, and will include several types of items. Different requirements apply to each, as described below. It is important that you adhere to file format and naming requirements to facilitate grading. Submissions that do not meet these requirements will not be accepted.

Lab Questions

The answers to all "lab questions" for a particular lab will normally be entered in the provided response areas in the shared lab document.

Note: for lab questions that ask you to draw a memory diagram, you have a few options. You may attempt to represent the memory with plain text, but that is difficult to construct and read. Ideally, you would use a drawing program and submit in your shared document, but you are also permitted to draw the diagram on paper and submit a scan or photograph, as long as the diagram is legible in that form.

Practice Programs

Your submissions for practice programs are graded primarily on correctness, but you will be required to include your name at the top of the program, and you must use the file name specified. You are of course encouraged to practice good documentation, formatting, and style for these programs, but the grade will depend only on correctness (and having your name in a properly-named file).

Programming Assignments

These are the most formal submissions and will be graded on design, documentation, style, correctness, and efficiency (where appropriate). A good design will use an appropriate algorithm, data structures, and language constructs to solve the problem. A well-documented program will include a comment at the top of each file that includes your name, the assignment, and a description of the contents of the file. There should also be comments for each constructor or method definition (including a brief description of the method's purpose, its parameters, and return value), each variable or group of related variables, and any section of code whose purpose and/or behavior is not obvious from context or the code itself. Style requirements include appropriate formatting (sufficient and consistent indentation, spacing, and punctuation, wrapping long lines of code), good use of named constants, and meaningful and appropriate names for variables, methods, constants, and parameters. Correctness, of course, requires the expected output be produced for a set of test inputs (which will normally not be provided in advance). Efficiency will be more important in some assignments than others, and requires that the program does not do any unnecessary computation or use any more memory than needed. And, of course, you must use the file name(s) specified.

The number of points available will vary with the size and complexity of the assignment.

You may develop your programs on any platform that has the necessary hardware and software, but grading will be done on the platform specified in each assignment. It is your responsibility to ensure that your program works on the grading platform. Programming projects will be graded on design, documentation, style, correctness, and efficiency. All assignments and projects are to be submitted electronically unless otherwise specified. Please submit plain text where appropriate and PDF otherwise. Please avoid other formats such as Word documents. If in doubt about a file format, please check with me first.

In-class exercises must be submitted in class to earn credit. Most assignments, unless otherwise specified, may be turned in late with a penalty computed as 1.08^h%, where h is the number of hours late. Extensions will only be granted in serious situations and requests must be accompanied by appropriate written documentation from the appropriate college office. You can find a C program that prints out a table of the late penalties here. Work turned in after solutions have been made available cannot receive credit.

Final Project

For the last part of the semester, the workload of the regular assignments will be reduced and you will focus your efforts on a large project on a relevant topic of your own choosing. The project will include a proposal, a progress report, a paper and a presentation. Most projects will also involve significant software development. Details will be made available around mid-semester, but you should expect a series of intermediate due dates during the last few weeks of the semester and a minisymposium where you will present your projects to your classmates. The final project submission will be due on the last day of classes.

Exams

There will a midterm exam during the semester, tentatively scheduled for October 14, and a final at the end of the semester at a time as scheduled by the Registrar's office. Details will be announced as the exams approach.

Grading

Grades for individual exams and assignments are not scaled. Any scaling deemed appropriate will take place at the end of the semester by adjusting the above thresholds. The following thresholds may be adjusted downward (thereby raising grades) but will never be adjusted upward.

Attendance

Please be sure you are familiar with the Siena College Student Class Attendance Policy.

Every college student should be motivated to attend every class meeting for all the right reasons (e.g., desire for knowledge, getting your money's worth, etc.). You surely understand that regular attendance is essential to your ability to master the course material.

Therefore, there is no formal attendance policy. You are expected to attend regularly, and should contact the instructor about any absences. Absences for which accommodations may be provided include any of the following:

1. A documented athletic or academic event that conflicts with a class meeting. The required paperwork must be presented in person at least one week prior to the event.
2. Bereavement or other family emergency. These must be documented through the Office of Academic Affairs, who will then contact your instructors.
3. Medical leave. Health Services or the Counseling Center will submit a recommendation to the Dean of Students Office and a medical leave will be initiated for absences of five or more days. The Dean's Office will contact your instructors.
4. Other personal illness. You should not attend class when you are ill, especially if you may be contagious.

If you must miss a class meeting, you can request that a meeting be live-streamed and/or recorded on Zoom. These options are better than missing the meeting altogether, but are a poor substitute for in-person attendance.

While there is no formal penalty, missing class regularly, frequent tardiness, or being distracted in class (e.g., checking your phone) will be considered a sign that you are not taking the course seriously. Attendance is taken daily, with late arrivals and evidence of distraction or inattention noted as needed. Common sense suggests and experience validates that students who are frequently absent, late, or inattentive do not learn the material, and this is reflected in poor grades. Do not expect compassion when final grades are assigned or extensive extra help if you do not understand a topic that was covered while you were absent without good reason.

Disability Accommodations

In compliance with the Americans with Disabilities Act and with Section 504 of the Rehabilitation Act, Siena College is committed to ensuring educational access and accommodations for all its registered students.

The Office of Accessibility allocates reasonable academic accommodations to students with documented disabilities. If you need assistance due to a disability, please contact accessibility@siena.edu or drop by Foy Hall 109A to discuss further.

Complaints about services provided or not provided may be brought to the attention of Public Safety at 518-783-2376 or Ms. Lois Goland, JD, Title IX Coordinator and Equal Opportunity Specialist (SSU 235, 518-782-6673).

Academic Integrity

You are encouraged to discuss the concepts related to course assignments and exams with your classmates. This is an essential part of a healthy academic environment. However, work submitted for grading must be your own (or the combined work of group members, for group assignments). Any unauthorized copying, collaboration, or use of generative artificial intelligence, such as ChatGPT and other platforms that generate text, code, artwork, etc. (except where explicitly permitted on an assignment or exam), is considered a breach of academic integrity and will not be tolerated. Academic dishonesty cases are unpleasant and uncomfortable for everyone involved. You are responsible for reading and understanding the College's Academic Integrity Policy and the Computer Science Department's Academic Integrity statement. The minimum penalties for a first violation will include failure (0 grade) for the assignment or exam in question and the filing of an Academic Integrity Violation Accusation Form. A second violation will result in failure of the course and a formal letter describing your misconduct will be sent to the head of the Computer Science Department and the Office of Academic Affairs. Students suspected of violating academic integrity will be referred to the Academic Integrity Committee for final determination.

If there is any doubt about the degree of collaboration allowed or the permitted sources for a particular assignment, please ask for clarification before collaborating or consulting the source. Any such collaborations or sources must be cited properly.

Additional College Policies

The following are College policies that apply to all courses at Siena.

Accommodations Policy

In compliance with the Americans with Disabilities Act and with Section 504 of the Rehabilitation Act, Siena College is committed to ensuring educational access and accommodations for all its registered students.

The Office of Accessibility allocates reasonable academic accommodations to students with documented disabilities. If you need assistance due to a disability, please contact accessibility@siena.edu or drop by Foy Hall 109A to discuss further.

Complaints about services provided or not provided may be brought to the attention of Public Safety at 518-783-2376 or Ms. Lois Goland, JD, Title IX Coordinator and Equal Opportunity Specialist (SSU 235, 518-782-6673).

Mental Health and Counseling Resources

For any number of reasons, you may become overwhelmed during your time at Siena. It is very common to experience symptoms of anxiety, depression or other mental health conditions. Fortunately, the Counseling Center, located in Foy Hall Room 110, is a resource to help overcome those potential challenges. You can make an appointment by stopping by, calling 518-783-2342, or requesting one online on the Siena Counseling Center webpage. In addition, for urgent matters after 4PM, there is an on-call therapist who may be accessed by calling Public Safety at 518-783-2376.

Inclusive Classroom

In our Franciscan community, diversity is an invitation to celebrate the uniqueness of each individual, as well as the cultural differences that enrich us all. In this course, I will do my best to ensure that students from all backgrounds and perspectives will be served equitably. The diversity that students bring to this class will be viewed as a resource, strength and benefit. It is my intent to present materials and activities that are respectful and inclusive of the many identities of students in terms of gender, sexual orientation, disability, age, socioeconomic status, ethnicity, race, culture, perspective, and other background characteristics. Your suggestions about how to improve the value of diversity and inclusiveness in this course are encouraged and appreciated.

Preferred Pronouns

Students are asked to indicate their preferred pronouns by updating their profile in Canvas. The use of preferred pronouns is important to show respect for students' gender identities, and to recognize and validate students' right to choose their own names and forms of address. Please use preferred pronouns that other students display in oral and written comments to them during class discussions.

Reporting a Bias Incident or Sexual Misconduct

In any case of possible bias or sexual misconduct, either in the classroom or anywhere on campus, you are encouraged to file a report online (Search: Siena College Bias Report) or in person with Lois Goland, Sienas Title IX/Title VII Officer, SSU 235, 518-782-6673, lgoland@siena.edu. Any Siena community member, who experiences or observes an incident of bias or misconduct, including faculty, staff and students, can file a report through this system. More information and resources around procedures dealing with sexual misconduct and discrimination and harassment are available online.

Emergency Preparedness

Take your text and a copy of the syllabus home with you along with your electronic devices in the event of a college closure. Continue with readings and assignments according to the course schedule; some assignments may be posted on Canvas or sent to you via e-mail. Check your email and Canvas pages for instructions about course delivery, for example, whether the course will be resumed online. If possible, online office hours will be established. Information regarding the Colleges status and reopening schedule may be monitored on the Siena website, www.siena.edu.