http://www.ccs.uky.edu/~douglas/cs521

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Course Description

    Study of computer science techniques and tools that support computational sciences and engineering.  Emphasis will be on visualization, performance evaluation, parallel computing, and distributed computing.  Prerequisites: CS-115, CS/EE-380, and engineering standing.  CS/MA/EGR 537 is about to or has become a prerequisite.  All graduate students should take 537 before taking this course.

(Picture courtesy of CSEP)

Requirements and Goals

    Students need a knowledge of programming in a modern object oriented language and a basic knowledge of machine organization and architecture. You need to know how to make presentations in either PowerPoint or Acrobat.

    Students will learn about hardware and software support for high performance computing. They will learn to select algorithms and develop code for computing in a parallel (or distributed computing) environment. They will learn about benchmarking, optimization, and visualization.  The course will include a hands on component utilizing a parallel computing environment.

Textbook and Course Outline

    The course will follow, where still appropriate, the lecture notes of the Computational Science Educational Project (CSEP).  The lectures will cover some or all of the topics below.  I may allow swapping of team members on a one for one basis as long as I approve it well in advance.

  • An Overview of Computational Science (Douglas) 1/15-17
       
    PowerPoint    PDF
  • MPI and OpenMP (T1) 1/24
       
    PowerPoint    PDF
  • Cache Designs and Tricks (Douglas)  2/5-12
        PowerPoint    PDF
  • Computer Architecture (T2)  2/19-21
        PowerPoint    PDF
  • Networks (T5)  2/26-28
       PowerPoint    PDF
  • Scientific Visualization in High Performance Computing (T1)  3/19-21
       PowerPoint    PDF
  • Numerical Linear Algebra (T4) 4/2
       PowerPoint    PDF
  • Some High Performance Computing Issues in PDEs (T1) 4/9
       PowerPoint    PDF
  • Random Number Generators (T3)  3/4-6
       PowerPoint    PDF
  • Monte Carlo Methods (T4)  3/6-19
       PowerPoint    PDF
  • Case Study: Dust Particle Movement (Douglas) 1/22
        PowerPoint    PDF
  • Case Study: Ocean Models (Douglas) 1/29-31
        Part 1:
    PowerPoint    PDF    Part 2: PDF
  • Case Study: Chaos from Nonlinear Mappings (NTY)
  • Case Study: Monte Carlo Surface to Surface Particle Transport (NTY)
  • Case Study: Seismic Wave Propagation and Inversion (T2) 4/4
       PowerPoint    PDF
  • Case Study: Direct and Inverse Bioelectric Fields Problems (T3) 4/11
       PowerPoint    PDF
  • Case Study: Mutational Meltdown of Endangered Species (NTY)
  • Case Study: Semiconductor Modeling (T5) 4/16
       PowerPoint    PDF
  • Sports Lighting (Douglas) 4/23-25
        PowerPoint    PDF    Report

We will cover as many of these topics as time permits.  Which case studies we consider will depend on the class' interests.

Homework

    We begin with a simple starter assignment:  HW1 that is due January 17th.  Each student should do this assignment independently.  NO GROUPS ON THIS ONE.

    We will produce a high quality package this semester to compute a triple sparse matrix multiply.  This will be done in groups with full disclosure of algorithms and code by the groups.  In the end, we will have several implementations that might converge.

  • General reading on the topic
        PostScript    PDF
  • First part, due January 22
        HTML
  • Second part, due February 14
        HTML
  • Third part, due February 19
        HTML
  • Fourth part, due February 28
        HTML
  • Fifth part due March 8
        HTML
  • Sixth part, due April 11
        HTML
  • Seventh part, due April 25
        HTML

Your options are PostScript and PDF, I have produced the PDF file using ps2pdf, which looks best using Ghostview, not Acrobat.  We will have teams in this assignment, which will be in several parts.  The sparse matrix teams are the following:

Team Web P=RT Members
SM1 SM1 web No Hui Tan, Chunfang Chen, Lei You and Chao Shen.
SM2 SM2 web Yes Christopher Cprek, Ben Pullen, Ryan McKenzie, and Ben Schrooten
SM3 SM3 web Yes Guojin Chen, George Landon, Eddie Willett, and Shawn Borchardt
SM4 SM4 web No Vandana Chopra, Chengdong Li, Chris Rambicure, Danny Thorne, and Adam Zornes

 

Teams

    I am assigning teams.  There is a prime number of students in the class, which means there is no possibility of dividing the class evenly.  You should exchange email (click on the team name) with your talking team (T? in the table below) as soon as possible and arrange to meet and start planning how to work together.

Team Members
T1 Danny Thorne, Chunfang Chen, Adam Zornes
T2 Vandana Chopra, Ben Schrooten, Shawn Borchardt, Eddie Willett
T3 Chengdong Li, George Landon, Chao Shen
T4 Christopher Cprek, Chris Rambicure, Guojin Chen
T5 Hui Tan, Benjamin Pullen, Ryan McKenzie, Lei You

Office Hours and Contact Information

    My office hours will be reached by class consensus during the first class and posted as part of the electronic syllabus.  Office hours will be on Tuesday through Thursday.

Day Time
Tuesday 3:15-4:00
Wednesday 9:00-10:00
Thursday 9:00-10:00

or by appointment.

    My office is 321A McVey Hall.  My office telephone number is 257-2326 and the FAX is 323-1029. Feel free to telephone my office as late as 11:00pm.  In a pinch, I can be reached at home on weekends at 203-625-9449.  Please do not call me at home before 8:30am or after 9:00pm.  I respond to e-mail (douglas@ccs.uky.edu or douglas-craig@cs.yale.edu) fairly quickly (always include a phone number where I can call you back).  If you are stuck on something, please do not hesitate to contact me.

    Warning:  The entrance to my office is inside another office (321 McVey).  I really do not hear knocking on the outer office's door.  Please just walk in and continue right into 321A and let me know that you are present.  Do not assume that I will know that you are in the outer office.  If I am not in my office, go straight to 325 McVey and ask where am I.  I may well be in there and have to be extracted from another inner office.  Please be utterly brazen.

Grading

    Your grade will be based on the homework and class participation.  Only letter grades will be given (no +/-'s).  Homework assignments usually have a presentation associated with them.  You will be expected to use overhead transparencies and/or a computer to make the presentation.  Our lecture hall has both projection and computer equipment to do both styles of presentations including in parallel.  I would prefer that you use PowerPoint for your presentations, however.

    From a legal viewpoint, I am allowed to change the grading system anytime in the course as long as I give adequate notice to the class.  The university ombud issues memorandums that cover this and many more topics. However, you should watch the class web page for any changes in the grading policy.

    It is very difficult to either cheat or plagiarize in this course.  However, either can be done.  I ask that you not copy, verbatim, presentations given in earlier years.  Seeing them twice will put me to sleep and then you will not get a very good grade since I will not have noticed that you did the project.  There are plenty of interesting things on the web on any of these topics that will be different from before and you will learn more by doing some research on the topics.  Getting caught cheating or plagiarizing will result in a grade of E and possibly much worse, including expulsion from the university and legal proceedings against you.

    The projects are done in small groups in which everyone gets the same mark.  If one fails, the whole group fails on the assignment.  A lot of the information is available through CSEP and other web resources.  It is considered good academic form to cite others' work that you use.  A simple mechanism is to include a set of references at the end of a presentation with pointers to interesting places to visit to get more information.

327 McVey

    The lecture hall is normally locked.  The staff (Teresa Moody and Sandy Leachman) in 325 McVey have a key and can let you in.  The systems staff (Vikram, Yuan, Satosh, and Satish) also have keys and can answer technical questions about the computers, but are usually very busy.  The room is in use MWF 9-10, Tu 12-1, W 3-5.  During working hours (M-F 8:30-4:30) you can usually get in by asking.  You can prepare your lectures on the computers in the room using PowerPoint.  Be sure to keep a copy someplace else.

 

Cheers,
Craig C. Douglas

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