U.C. Berkeley CS267 Home Page

Applications of Parallel Computers

Spring 2015

T Th 9:30-11:00, 306 Soda Hall

Instructor:

  • Jim Demmel
  • Offices:
    564 Soda Hall ("Virginia", in ParLab), (510)643-5386
    831 Evans Hall
  • Office Hours: (subject to change) MWF 10-11 (starting Jan 21)
  • (send email)
  • Teaching Assistants:

  • Evangelos Georganas
  • Office: 5th Floor Soda Hall (ASPIRE Lab)
  • Office Hours: T/Th 1-2pm, in 283E Soda Hall (updated Jan 19)
  • (send email)
  • Forrest Iandola
  • Office: 5th Floor Soda Hall (ASPIRE Lab)
  • Office Hours: F 3-5pm, in 580 Soda (updated Jan 20)
  • (send email)
  • Penporn Koanantakool
  • Office: 5th Floor Soda Hall (ASPIRE Lab)
  • Office Hours: T/Th 4-5pm, in 580 Soda Hall (updated Jan 19)
  • (send email)
  • Administrative Assistants:

  • Tammy Johnson
  • Office: 565 Soda Hall
  • Phone: (510)643-4816
  • (send email)
  • Roxana Infante
  • Office: 563 Soda Hall
  • Phone: (510)643-1455
  • (send email)
  • Syllabus and Motivation

    CS267 was originally designed to teach students how to program parallel computers to efficiently solve challenging problems in science and engineering, where very fast computers are required either to perform complex simulations or to analyze enormous datasets. CS267 is intended to be useful for students from many departments and with different backgrounds, although we will assume reasonable programming skills in a conventional (non-parallel) language, as well as enough mathematical skills to understand the problems and algorithmic solutions presented. CS267 satisfies part of the course requirements for the Designated Emphasis ("graduate minor") in Computational Science and Engineering.

    While this general outline remains, a large change in the computing world started in the mid 2000's: not only are the fastest computers parallel, but nearly all computers are becoming parallel, because the physics of semiconductor manufacturing will no longer let conventional sequential processors get faster year after year, as they have for so long (roughly doubling in speed every 18 months for many years). So all programs that need to run faster will have to become parallel programs. (It is considered very unlikely that compilers will be able to automatically find enough parallelism in most sequential programs to solve this problem.) For background on this trend toward parallelism, click here.

    This is a huge change not just for science and engineering but the entire computing industry, which has depended on selling new computers by running their users' programs faster without the users having to reprogram them. Large research activities to address this issue are underway at many computer companies and universities, including Berkeley's ASPIRE project, and its predecessor the ParLab. A summary of the ParLab's research agenda, accomplishments, and remaining challenges may be found here.

    While the ultimate solutions to the parallel programming problem are far from determined, students in CS267 will get the skills to use some of the best existing parallel programming tools, and be exposed to a number of open research questions.

  • Tentative Detailed Syllabus
  • Grading

    There will be several programming assignments to acquaint students with basic issues in memory locality and parallelism needed for high performance. (Note: plan to redesign the third programming assignment to solve a different problem, a graph problem arising in genomics.) Most of the grade will be based on a final project (in which students are encouraged to work in small interdisciplinary teams), which could involve parallelizing an interesting application, or developing or evaluating a novel parallel computing tool. Students are expected to have identified a likely project by mid semester, so that they can begin working on it. We will provide many suggestions of possible projects as the class proceeds.

    Asking Questions

    Outside of lecture, you are welcome to bring your questions to office hours (posted at the top of this page). If you cannot physically attend office hours, you may contact the instructor team via the instructor email. We encourage you to post your questions to the CS267 Piazza page (you need to sign up first). If you send a question to the instructor email, we may answer your question on Piazza if we think it might help others in the class. During lecture, remote students can also email their questions to instructor email, which the teaching assistants will be monitoring during lecture. Depending on the question, the teaching assistants will either answer by email, or ask the instructor to answer during the lecture. You will also submit homeworks via the instructor email; please check with assignment-specific submission instructions first.

    Class Projects

    You are welcome to suggest your own class project, but you may also look at the following sites for ideas:

  • the ParLab webpage,
  • the ASPIRE webpage,
  • the BEBOP webpage,
  • the Computational Research Division and NERSC webpages at LBL,
  • class posters and their brief oral presentations from CS267 in Spring 2009.
  • class posters from CS267 in Spring 2010
  • Brief oral poster presentations from CS267 in Spring 2012
  • Brief oral poster presentations from CS267 in Spring 2013
  • Brief oral poster presentations from CS267 in Spring 2014
  • Announcements

  • (Apr 17) Poster presentations of final projects (possibly including recording a short video presentation) will occur in the morning of May 7 (Thursday of RRR week) in the Wozniak Lounge. Final report writeups are due Monday May 11 at midnight (11:59pm). For more details, see Class Project Suggestions, in pptx and pdf (updated May 3, 6:45am).
  • (Apr 2) Prof. Demmel will hold extra office hours on Th, Apr 2, 2-3pm; Fr, Apr 3, 1-2pm; M, Apr 6, 11-12am
  • (Feb 3) Results of Homework 0 are now posted near the bottom of the Class Resources Web Page.
  • (Feb 3) Homework 1, including assigned student teams, is now posted near the bottom of the Class Resources Web Page.
  • (Jan 26) Please create an XSEDE User Portal account and let us know of your account usernames here by Jan 30, 2015.
  • (Jan 18) For students who want to try some on-line self-paced courses to improve basic programming skills, click here. You can use this material without having to register. In particular, courses like CS 9C (for programming in C) might be useful.
  • (Jan 18) Please complete the following class survey.
  • (Jan 18) Homework Assignment 0 has been posted here, due Jan 30 by midnight.
  • (Jan 18) Fill out the following form to allow us to create a NERSC account for you.
  • (Jan 18) Please read the NERSC Computer Use Policy Form so that you can sign a form saying that you agree to abide by the rules state there.
  • (Jan 18) This course satisfies part of the course requirements for the Designated Emphasis ("graduate minor") in Computational Science and Engineering.
  • Class Resources and Homework Assignments.

  • This will include, among other things, class handouts, homework assignments, the class roster, information about class accounts, pointers to documentation for machines and software tools we will use, reports and books on supercomputing, pointers to old CS267 class webpages (including old class projects), and pointers to other useful websites.
  • Lecture Notes and Video

  • Live video streaming of the lectures may be seen here here.
  • Archived video of the lectures may be seen here here. The final video shows student introducing posters about their final projects.
  • To ask questions during live lectures, you can email them to instructor email, which the teaching assistants will be monitoring during lecture. Depending on the question, the teaching assistants will either answer by email, or ask the instructor to answer during the lecture.
  • The class web page from the 1996 offering has detailed, textbook-style notes available on-line which are up-to-date in their presentations of some parallel algorithms. The slides to be posted during this semester will contain a number of more recently invented algorithms as well.

  • Lectures from Spr 2015 will be posted here.
  • Lecture 1, Jan 20, Introduction, in ppt and pdf
  • Lecture 2, Jan 22, Single Processor Machines: Memory Hierarchies and Processor Features in ppt and pdf
  • Lecture 3: Jan 27, Complete Lecture 2 (updated Jan 27, 5:36am), begin Parallel Machines and Programming Models in ppt and pdf
  • Lecture 4: Jan 29, Complete Lecture 3 (updated Jan 29, 8:40am), begin Sources of Parallelism and Locality in Simulation (Part 1) in ppt and pdf
  • Lecture 5: Feb 3, Complete Lecture 4 (updated Feb 3, 5:50am), then Sources of Parallelism and Locality in Simulation (Part 2) in ppt and pdf
  • Lecture 6: Feb 5, Complete Lecture 5, then Shared Memory Programming with Threads and OpenMP, in ppt and pdf, and Tricks with Trees, in ppt and pdf.
  • Lecture 7: Feb 10, Complete Lecture 6, then Distributed Memory Machines and Programming, in ppt and pdf.
  • Lecture 8: Feb 12, Complete Lecture 7, then Partitioned Global Address Space Programming with Unified Parallel C (UPC) and UPC++, in pptx and pdf. by Kathy Yelick.
  • Lecture 9: Feb 17, Debugging and Optimization Tools, by Richard Gerber, in pptx and pdf; and
    Performance Debugging Techniques for HPC Applications, by David Skinner, in pptx and pdf.
  • Lecture 10, Feb 19, Cloud Computing and Big Data Processing, by Shivaram Venkataraman, in pdf.
  • Lecture 11: Feb 24, An Introduction to CUDA/OpenCL and Graphics Processors (GPUs), by Forrest Iandola, in pptx and pdf.
  • Lecture 12: Feb 26, Dense Linear Algebra (Part 1), in ppt and pdf.
  • Lecture 13: Mar 3, Complete Lecture 12, then Dense Linear Algebra (Part 2): Communication Avoiding Algorithms, by Laura Grigori, in ppt and pdf.
  • Lecture 14: Mar 5, Complete Lecture 13, then Graph Partitioning, by Laura Grigori, in ppt and pdf.
  • Lecture 15: Mar 10, Complete Lecture 14, then Sparse Linear Solvers, by Laura Grigori, in pdf.
  • Lecture 16: Mar 12, Complete Lecture 15, updated (Mar 12), then Sparse Iterative Solvers, in pdf, by Laura Grigori.
  • Lecture 17: Mar 17, Homework #3 Presentation, in pptx and pdf, then Class Project Suggestions, in pptx and pdf (updated May 3, 6:45am), then Structured Grids, in ppt and pdf.
  • Lecture 18: Mar 19, Parallel Graph Algorithms, in pptx and pdf, by Aydin Buluc
  • Lecture 19: Mar 31, Architecting Parallel Software with Patterns, in pptx and pdf, by Kurt Keutzer
  • Lecture 20: Apr 2, Frameworks in Complex Multiphysics HPC Applications, in pptx and pdf, by John Shalf
  • Lecture 21: Apr 7, Hierarchical Methods for the N-body problem, in pptx and pdf.
  • Lecture 22: Apr 8, complete Hierarchical Methods for the N-body problem, (updated Apr 9, 7:15am)
  • Lecture 23: Apr 14, Fast Fourier Transform, in ppt and pdf.
  • Lecture 24: Apr 16, Big Bang, Big Data, Big Iron: High Performance Computing and the Cosmic Microwave Background, by Julian Borrill, in pptx and pdf
  • Lecture 25: Apr 21, Dynamic Load Balancing, in ppt and pdf.
  • Lecture 26: Apr 23, Modeling and Predicting Climate Change, by Michael Wehner, in ppt and pdf.
  • Video of NASA Projections of Temperature and Precipitation in the 21st Century
  • Video of Preliminary CAM5 hi-resolution simulations
  • Video of fvCAM5.1 Simulated Atmospheric River
  • Lecture 27, Apr 28, Accelerated Materials Design through High-throughput First-Principles Calculations and Data Mining, by Kristin Persson, in pptx and pdf
  • Lecture 28, Big Data, Big Iron and The Future of HPC, by Kathy Yelick. in pptx and pdf
  • Sharks and Fish

  • "Sharks and Fish" are a collection of simplified simulation programs that illustrate a number of common parallel programming techniques in various programming languages (some current ones, and some old ones no longer in use).
  • Basic problem description, and (partial) code from 1999 class, written in Matlab, CMMD, CMF, Split-C, Sun Threads, and pSather, available here.