Class Notes

The Web pages that will be posted here are not always a full or complete set of lecture notes. If you miss a class, be sure to check with other students for what went on. The definitive set of material for the course is that which is presented or referred to in the notes, and any explicitly identified topics in these web notes.

First day: a minor puzzle.
Some general software tools of interest and use.
1. Much of your work will involve writing code that is used to generate some results: timings of different approaches, etc. Using makefiles will ease the job of this writing and running, and I will in some cases require this. Makefiles are the standard mechanism for building complex software systems, not just in scientific computing.
2. Accessing remote machines is dangerous if you send passwords in the clear. Use SSH to set up a more secure way of transfering files, and especially for opening windows from a remote machine on a local console. The CS department's systems staff has good pages about SSH clients and using SSH is now a campus standard. They also have other platform notes about using SSH from a web browser or Windows.
Both makefiles and SSH now have many good tutorials and how-tos on the Web, one of the reasons the pages linked to above have not been updated in a while and don't have too much detail. Use your Google-fu to find out more.
Timing codes and parts of codes
1. General information about timing on a computer
2. Resource Utilization Info in Unix
3. Finding clock resolution and overhead
4. Timing simple operations
5. Common timers
6. The tarball clock_examples.tar contains two subdirectories called C and Fortran. Each has a simple timer function, a test driver that calls it, and a makefile that builds the executable. The makefile also has a "clean" target to remove all object files and the executable, as described in the page above about makefiles. Use this if you want a starting point for future projects.
7. A tarball has codes to find clock facts. It includes two subdirectories: overhead and resolution. They both have files called 'info', but all of the codes have been seen in class (as of 14 Sept).
8. Not necessary, but some useful Matlab functions is available. Put the m-files in it in a directory called .matlab in your home directory. First, though, read through them and see what you want. What is included there reflects my personal (lack of?) taste, and you may want to modify or ditch them.
Computer architecture and how to use it
Matlab notes. Wade through these with a Matlab window running next to you.
The f-word in scientific computing. The class notes are in three formats, but are all the same material.
1. Intro to Fortran (OpenOffice format)
2. Intro to Fortran (PowerPoint format)
3. Intro to Fortran (PDF)
4. tar archive containing small example Fortran codes, with a few caveats:
Getting a high performance LU factorization, and associated things

Edits to this page:

Started: 2009 Aug 31
Modified: Mon 31 Aug 2009, 11:21 AM to add the first day's notes
Modified: Tue 01 Sep 2009, 05:37 PM adding SSH, makefile, and timing stuff notes
Modified: Mon 14 Sep 2009, 02:21 PM to add in matlab utilities tarball
Modified: Wed 16 Sep 2009, 08:41 PM to add the architecture notes.
Modified: Tue 22 Sep 2009, 03:44 PM including five more Matlab pages
Modified: Tue 20 Oct 2009, 02:21 PM to include fortran notes/examples and to add the directory tree
Modified: Tue 20 Oct 2009, 02:42 PM to remind about the clocking examples
Modified: Thu 29 Oct 2009, 12:32 PM to add notes about LU factorization
Last Modified: Thu 29 Oct 2009, 12:32 PM