# High-Performance Scientifc Computing

What Value
Class Time/Location Wednesday 5:10-7pm, Room 101 Warren Weaver Hall (NYU)
Instructor Andreas Kloeckner, Marsha Berger
Email kloeckner@cims.nyu.edu, berger@cims.nyu.edu
Office Courant Institute, Warren Weaver Hall, Rooms 1105A, 1121
Office Hours Andreas: Wednesdays, 2-4pm WWH 1105A
Class Webpage http://bit.ly/hpc12
Email Listserv Info page

## Lecture Material

Lecture # Date Topics Slides Video Code Extra Info
1 Sep 5 Intro, why parallel, Vector-add in seq, OpenMP, CL Slides Video Code
2 Sep 12 Vector-add in MPI, Intro to OpenMP Slides Video Code
3 Sep 19 HW2, OMP subtleties Slides Video
4 Sep 26 Make, Intro to OpenCL Slides Video Code
5 Oct 3 Git, OpenCL sync/local, Intro to MPI Slides Video Code
6 Oct 10 Gdb, MPI point-to-point Slides Video Code
7 Oct 17 Valgrind, MPI collectives, Intro perf. Slides Video Code
8 Oct 24 Software installation, tmux, single-thread perf. Slides Video Code
Oct 31 NYU closed, no class because of Hurricane Sandy aftermath
9 Nov 7 Shell scripting, single/multi-thread perf. Slides Video Code
10 Nov 14 Profilers, parallel perf. Slides Video Code
11 Nov 21 Advanced git, GPU perf. Slides Video Code
12 Nov 28 GPU perf., patterns Slides Video Code GPU mem access patterns
12 Dec 5 Parallel patterns, 3D vis. Slides Video Code
Dec 12 No class, NYU legislative day. Runs on a Monday schedule.
13 Dec 18 Project Presentations (part 1) /Projects Video /Projects
14 Dec 19 Project Presentations (part 2) Video

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.

As far as the videos are concerned, Internet Explorer and Safari are not supported, because they do not understand the video format we're using. And Chrome behaves _much_ better than Firefox with the new lecture video player, to the point of Firefox not even starting up properly. We're currently [investigating](https://bugzilla.mozilla.org/show_bug.cgi?id=795686). In the meantime, please use Chrome.

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!

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

• 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

Book Where
OpenCL in Action: How to Accelerate Graphics and Computation from NYU net
OpenCL Programming Guide from NYU net
Heterogeneous Computing with OpenCL from NYU net

### 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:

### 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:

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.