URGE to Compute Wiki : Tools And Methods

Class archive

Day 1
Presentation
Day 2
Day 2 outline
Sample .bashrc
Day 2 Maple code
Day 2 Matlab/Octave code
Day 2 triples correlation
Day 3
Unix and Ubuntu Snippets (Dr. Carbonara)
Maple on linux.eng (Dr. Ringland)
Day 4
Tarball with latex/bibtex example (Dr. Ringland)
Other latex example (Dr. Carbonara)
Day 5
Outline
Tarball with latex/bibtexexample (Dr. Ringland)
Day 6 LaTeX for giving presentations
- Using the Seminar package to write presentations in LaTeX http://www.math.buffalo.edu/~biondini/var/latexseminarsample.tgz (Prof. Biondini)
- A more elaborate style: LaTeX Beamer (Dr. Jones),
  - beamer example tarball (local)
  - Some notes on Makefiles (example uses a Makefile to help automate steps in formatting the talk)
  - Norm Matloff's quick beamer tutorial (external link)
  - Wikipedia link (note parentheses around LaTeX in URL)
  - CTAN copy of full beamer user guide
  - /usr/share/doc/latex-beamer, (hopefully) the location in Ubuntu wherein lives the beamer documentation
Day 7 Conway's Life
PDF of Prof. Ringland's presentation
Day 8 Running batch jobs at CCR (March 16, 2009, Dr. Jones)
- CCR presentation on PBS
- On the U2 cluster, there are many sample PBS scripts in the directory /util/pbs-scripts, along with a README.txt file that describes them
- Day 8 announcements
Day 9 (March 30, 2009)
- Intro to shell scripting, (bash example, Bash-example_unix.txt) Mike Barry
- Matlab on U2 at CCR, Cynthia Cornelius
Day 10 (April 6, 2009)
- Unix shell scripting II http://copper.math.buffalo.edu/ugs/csums/unix_scripting_yearke/
  John Ringland
Day 11 (April 13, 2009)

Unix shell scripting III http://copper.math.buffalo.edu/ugs/csums/unix_scripting_yearke/
David Yearke, Director, Science and Engineering Node Services
OurExamples

Parallel Computing (Dr. Jones, 20090527-20090529)
Supplementary
Zotero

Zotero is a free Firefox extension for collecting, managing, and citing your research sources. John Ringland April 25, 2009, at 10:42 AM

Random number generator speeds

Please test your own random number generator for speed and enter the results below. For the "RNs per second per GHz", divide the number of RNs generated by the real time in seconds (on a machine where nothing much else is running) and by the speed of your CPU in GHz". (On Linux, type "cat /proc/cpuinfo" to get CPU info.)

Nominal distribution	Generator name	RNs per second per GHz	Test computer	Tester	Date
uniform in (0,1)	uni() (C++ Boost)	47 million	IBM laptop 1.7GHz, 1.25GB RAM	Chen Zhang	2/5/09
uniform in (0,1)	drand48 (C++ math.h)	15 million	IBM laptop 1.7GHz, 1.25GB RAM	Chen Zhang	2/5/09
uniform in [0,1)	Maple RandomTools[MersenneTwister] GenerateFloat64()	37 thousand	Intel P4 2.93GHz, 2.5GB RAM	John Ringland	2/5/09
uniform in (0,1)	rng.txt (Maple simple LCG )	16 thousand	Intel P4 2.93GHz, 2.5GB RAM	John Ringland	2/5/09
uniform in (0,1)	Octave rand()	160 thousand	Intel Core 2 Duo 1.6GHz	Steven Leuthe	3/13/09
uniform in (0,1)	Matlab rand()
binomial(n=200,p=0.5)	numerical recipes(using uni() from Boost)	0.2 million	IBM laptop 1.7GHz, 1.25GB RAM	Chen Zhang	2/5/09
poisson(mean=200.0)	numerical recipes(using uni() from Boost)	0.5 million	IBM laptop 1.7GHz, 1.25GB RAM	Chen Zhang	2/5/09
uniform in (0,1)*	Maple Statistics[Sample]()	14 million	Intel P4 2.40GHz, 2.0GB RAM	Matt Westley	2/9/09
uniform in (0,1)	Mathematica, Random[]	125 thousand	AMD Athlon Dual Core 3800+ 2.0GHz, 3.0GB RAM, Windows Vista	Benjamin Kanouse	2/10/09

*but it can generate from a lot of different distributions

LaTeX samples

Work in progress

Latex Mathematical Symbols

Tarball used in Feb 9 meeting

SYLLABUS brainstorming page

NOTE: The list of topics below should be related whenever possible to the current research projects, and labeled by the project mentors (Bayram: Ba, Biondini: Bi, Ringland: R, Sen: S). These topics will be broken up into one hour modules.

List of topics of interest followed (whenever possible) by the project it is needed for:

Operating system, Networking and hardware
- Ubuntu OS and open source software: GUI vs command line, file paths, permissions, file management, ssh, scp, OpenOffice, ...
- Basic networking concepts (enough for students to understand how to troubleshoot communication problems). For example: IP and MAC addressing; the concept of digital communications and packets; ports on the computers; security with IP tables as implemented with Firestarter;
- Basic facts about the hardware used in Computational Science: parts of a computer and how they affect the speed of computations;
Group work and communication software
- Web pages, Wikis, Skype, ...
Scientific typesetting and illustration
- Latex: Should we use Latex with a front end like Kile? Lyx?
- Vector graphics editing: Adobe Illustrator via VirtualBox/Windows
Programming
- Programming software: Matlab, Mathematica, Maple, C++.
- Parallel computing
- NEW TO ME: parallel computing using graphic cards (GPU computing).
On-line and in person research skills
- Journals, books, and other sources
- Bibliographic management: JabRef, bibtex
- How to evaluate Journals and Conferences (impact factor, publishing houses, etc.)