High-Performance Scientifc Computing

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Lecture Material

You'll need an up-to-date version of Google Chrome to play the videos. You'll also need decent internet bandwidth to do streaming (2 MBit/s should be sufficient). If your internet accesss is too slow, you can always right click and download the video.

Updates

Apr 26, 2013 : I just gave a talk on my HPC-related work in the Graduate Student and Postdoc Seminar at Courant. I recorded slides and audio. (should play in Firefox and Chrome)

Dec 13, 2012 : I've posted the /ProjectPresentationsSchedule, now in its final form. See you next week!

Sep 9, 2012 : We're moving to a bigger room! We'll be meeting in room 101 of Warren Weaver Hall from September 12 onward.

Aug 21, 2012 : If you're from outside of Courant, you may encounter some difficulty registering for the class. We're fighting with the NYU administration to make this better. In the meantime, please get in touch with us. This class is most definitely open to students from other departments, NYU Albert apparently just hasn't gotten the memo.

Aug 9, 2012 : Less than a month to go! Class starts on September 5, 2012, from 5-7pm. We've also been assigned a room. We will be meeting in Warren Weaver Hall, room 512 (but check back here just in case there are changes in the meantime). See you then!

Grading/Evaluation

If you will be taking the class for credit, there will be

• Weekly homework (60% of your grade)
• A more ambitious final project, which may be inspired by your own research needs (40% of your grade) (also see /ProjectSubmissionGuidelines) If you're planning on auditing or just sitting in, you are more than welcome.

Homework

• Homework 1 due September 12
• Homework 2 due September 19 September 23
• Homework 3 due October 3 (updated 9/30 for sign bug in formula)
• Homework 4 due October 10
• Homework 5 due October 17
• Homework 6 due November 1 November 4 because of the storm November 7 because of protracted power outage
• Final project presentations in class around Dec 17--19

Material

Books

• Parallel Programming: for Multicore and Cluster Systems (available for in PDF form free online from within the NYU network, also from off-campus via this EZProxy link) For OpenCL and GPU programming, we will also be referring to the following sources:

Update 9/12: Fixed ezproxy links.

Primary source material

These are the technical standards on which this class will be based. While sometimes a bit technical, these documents define whether the programs you write are correct (or not) or, perhaps result in undefined behavior:

• C99 specification
• OpenMP 3.1 specification (tutorial)
• MPI 3.0 specification (tutorial /!\ not up-to-date, teaches functions removed from MPI 3)
• OpenCL 1.2 specification

Secondary Sources

• Is Parallel Programming Hard, And, If So, What Can You Do About It?, edited by Paul Mc``Kenney
• Parallel Programming Lecture slides (and book) by Karypis et al. More theory-heavy (less practical? :) ) than this class
• CS267 Spring '12 Lecture by Jim Demmel et al, Berkeley
• DGEMM optimization
• Parallel Computer Architecture and Programming
• Learn C the hard way by Zed Shaw
• Memory Cache Optimizations from the libtorrent authors
• Introduction to High-Performance Scientific Computing by Victor Eijkhout
• Parallel Computing for Science and Engineering by Victor Eijkhout

Collected Wisdom

• ToolCheatSheet

Virtual Machine Images

This information has moved to ComputeVirtualMachineImages.

Installing MPE into the virtual machine

MPE and Jumpshot for visualization of MPI execution were demonstrated during lecture 7. If you'd like to have those in your own virtual machine, download the following script:

install-mpe.sh

Change into the directory where the script resides and start the installation:

sudo bash install-mpe.sh

If the script says

*** SUCCESSFULLY INSTALLED MPE

then you should be able to use mpecc and jumpshot from now on. Note that jumpshot seems to have a habit of creating its main window title bar underneath the top panel, so that you can't move it. A solution is to right-click the task bar entry for Jumpshot, and click "Move".

Notes:

• You need to be online for the entire run time of the script.
• Depending on your machine and internet connection, the script may take around half an hour to finish. (10 minutes just now on my laptop, but that's a fairly fast machine on a fast connection)
• It is best to leave the computer alone while it is processing the script.
• This script is only intended for the class virtual machine, and even then you are using it at your own risk. I highly recommend that you use Virtualbox to create a system restore point before you attempt the installation, in case something goes awry. Do not attempt to use this on a Mac or another Linux machine.

Links

• Code from lectures and homework
• Class collaboration space ("forge")
• NYU HPC systems group

Previous Editions of the Class

• Fall '10
• Fall '08