CIS5930-02 High performance computing for scientific applications

Spring 2003, 3 Credit hours

Instructor: Ashok Srinivasan Office hours: TF 1:00 pm - 2:00 pm, or by appointment. Location: 169, Love Building Phone: 644-0559, Email: asriniva@cs.fsu.edu Course web site: Access through blackboard http://campus.fsu.edu

Lecture hours: MW 3:35 pm - 4:50 pm, LOV 103

Text book: Parallel Programming in C with MPI and OpenMP, M.J. Quinn, McGraw-Hill publishing, manuscript (for use in this course only).

Reference books:

1. Designing and Building Parallel Programs, by Ian Foster. Available on-line at: http://www-unix.mcs.anl.gov/dbpp.
2. Parallel computer architecture -- A hardware/software approach, D. E. Culler and J. P. Singh, Morgan Kaufmann, 1999.
3. Using MPI -- Portable parallel programming with the Message-Passing Interface, second edition, W. Gropp, E. Lusk, and A. Skjellum, The MIT press, 1999.

Prerequisites:

Course rationale:

Course objectives:

Course description:

Sequential computing: Computer architectural features to support high performance computing, use of standard libraries, programming techniques, compiler optimization, exploiting the memory hierarchy, other algorithmic issues. Parallel computing: parallel machine and programming models, parallel algorithms, performance models, MPI, OpenMP. Applications: Numerical linear algebra, Molecular dynamics, Monte Carlo, etc. Project: You will also work on a project involving parallel programming. You are encouraged to chose your research project as the topic, if you are already involved in research.

Grading criteria:

Class participation	5
Project	20
Paper presentation	10
Homework assignments	15
Midterm	25
Final Exam	25

Your grade will be based on the scores obtained in the above categories, with weights as given above.

Course average	Letter grade
90 - 100	A
87 - 90	A-
80-87	B
70-80	C
60 - 70	D
0 - 60	F

Attendance

While you will not be explicitly graded for attendance, you will be graded for class participation, and you will need to attend class in order to participate in it!

Course policies:

• Deadlines: If your assignment is late, you will get a 20% reduction in points for up to one day late (ignoring weekends and university holidays), and 30% more for each subsequent day. Please do not depend on our watches being exactly synchronized; do submit a few minutes early. A submission that is late by 1 minute will still get the entire 20% penalty! (In order to help you deal with emergencies, your first late submission will be excused from the 20% penalty, provided it is not late by more than one working day.)

• Cheating: You should not collaborate with anyone in any way while working on assignments. Copying others' homework, replacing variable names in their code with different names, altering indentation, or making modifications to others' code, and submitting it as your own will all be considered forms of cheating. Students are expected to uphold the academic honor code published in "The Florida State University Bulletin" and the "Student Handbook". Please read the provisions of the Academic Honor Code: http://www.fsu.edu/Books/Student-Handbook/codes/honor.html. Also read the section on "Honor code" below.

• ADA: Students with disabilities needing academic accommodation should (1) register with and provide documentation to the Student Disability Center, and (2) bring a letter to the instructor indicating the need for accommodation and what type. This should be done during the first week of class. This syllabus and other class materials will be made available in alternative format upon request.

Honor code:

Plagiarism is "representing another's work or any part thereof, be it published or unpublished, as one's own. . . . For example, plagiarism includes failure to use quotation marks or other conventional markings around material quoted from any source" (Florida State University General Bulletin 1998-1999, p. 69). Failure to document material properly, that is, to indicate that the material came from another source, is also considered a form of plagiarism. Copying someone else's program, and turning it in as if it were your own work, is also considered plagiarism.

What I expect from the student:

• I am particularly strict about deadlines and following instructions. Please read instructions carefully, and schedule your activities so that you submit assignments well in time. You should check your garnet email account and the class web page regularly, and note other announcements, on-line and in class.

• I expect you to complete any reading assignments when you come to class, since I will assume you have learned the material.
• You should participate in the class by asking questions, suggesting ideas, etc.

• In exams, I test knowledge, understanding, and creativity. When you learn some topic, you should not just try to understand the material, but also analyze what would happen if some things were different.

Lecture plan:

Useful links:

• Reading assignments and review questions: www.cs.fsu.edu/~asriniva/courses/hpcsa/lectures.html
• MPI: www-unix.mcs.anl.gov/mpi
• NCSA: www.ncsa.uiuc.edu
• SDSC: www.sdsc.edu
• OpenMP: www.openmp.org
• Ultrascale simulation: www.ultrasim.info