External Links
From Research Computing
| Table of contents |
Automated Logic
QED Manifesto (http://www.cs.ru.nl/~freek/qed/qed.html)
Home page of Freek Wiedijk (http://www.cs.ru.nl/~freek/)
Home page of John Harrison, developer of HOL light (http://www.cl.cam.ac.uk/users/jrh/)
Developing applications with OCAML (http://caml.inria.fr/pub/docs/oreilly-book/)
CAML (http://caml.inria.fr/)
Foundations group (http://www.cs.ru.nl/fnds/)
Computational Chemistry
Gaussian (http://www.gaussian.com/)
NWChem (http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
The General Atomic and Molecular Electronic Structure System (http://www.msg.ameslab.gov/GAMESS/GAMESS.html)
CHARMM (Chemistry at HARvard Molecular Mechanics) (http://yuri.harvard.edu/)
Molden (http://www.cmbi.ru.nl/molden/molden.html)
ChemViz Curriculum Support Resources (http://www.shodor.org/chemviz/overview/) Includes overview of computational chemistry.
Lecture notes on quantum chemistry (http://zopyros.ccqc.uga.edu/lec_top/lectures.html)
Computer Science and Computer Scientists
CUNY Graduate Center Ph.D. program in Computer Science (http://web.gc.cuny.edu/ComputerScience/)
Publications of Philippe Flajolet (http://algo.inria.fr/flajolet/Publications/publist.html)
Donald Knuth (http://www-cs-faculty.stanford.edu/~knuth/index.html)
Distributed Resource Management
NPACI Rocks Cluster Distribution (http://www.rocksclusters.org/)
The BioTeam (http://web.bioteam.net/metadot/index.pl) Check out their presentations on biocomputing.
The Sun Grid Engine Project (http://gridengine.sunsource.net/)
Cluster World (http://www.clusterworld.com/)
The openMosix Project (http://openmosix.sourceforge.net/)
Grid Computing
The Globus Alliance (http://www.globus.org/) The CUNY Grid is based on the Globus Toolkit.
Globus Documentation Project (http://gdp.globus.org/) Alpha version.
Portal-based user registration for globus certificates (http://www.grids-center.org/solutions/purse/)
MyProxy (http://grid.ncsa.uiuc.edu/myproxy/) MyProxy is a repository for X.509 Public Key Infrastructure (PKI) (http://www.ietf.org/html.charters/pkix-charter.html) security credentials (certificates and private keys).
Python Globus (http://dsd.lbl.gov/gtg/projects/pyGlobus/)
NSF middleware initiative (http://www.nsf-middleware.org/)
Ninf (http://ninf.apgrid.org/welcome.shtml) Hierarchical grid RPC API
NSF NMI Release 7 (http://www.nsf-middleware.org/Lists/NMIR7/AllItems.aspx)
IBM Grid Computing (http://www-1.ibm.com/grid/)
Grid.Org (http://www.grid.org/home.htm)
Distributed Net: grid computing (http://www.distributed.net)
IBM Grid Computing (http://www-130.ibm.com/developerworks/grid/)
Grid Computing Planet (http://www.gridcomputingplanet.com/)
Top 500 Supercomputing Sites (http://www.top500.org/)
Hardware
Standard Performance Evaluation Corporation (http://www.spec.org/) Go here for industry benchmarks.
Tom's Hardware (http://www.tomshardware.com/index.html)
Article on the Cell Processor (http://www.blachford.info/computer/Cells/Cell0.html)
Opengear (http://www.opengear.com/) Hardware for distributed computing (console servers)
LinuxDevices.com (http://www.linuxdevices.com/) Embedded linux devices
Article on opengear console servers (http://www.linuxdevices.com/articles/AT9848493652.html)
Internet Applications & Web Services
Software Engineering for Internet Applications (http://philip.greenspun.com/seia/). Explains how Google (http://www.google.com), Amazon (http://www.amazon.com) and eBay (http://www.ebay.com) serve so many simultaneous users.
Mastering the World Wide Web (http://www.cs.indiana.edu/classes/a348-dger/fall2002/notes/)
Apache Security (http://www.apachesecurity.net/index.html)
Jakarta Tomcat (http://jakarta.apache.org/tomcat/)
Apache Axis (http://ws.apache.org/axis/index.html)
webtechniques (http://www.webtechniques.com/) aka New.Architect. Source of PERL (http://www.perl.org) programing techniques.
The Absolute Minimum Every Software Developer Absolutely, Positively Must Know About Unicode and Character Sets (No Excuses!) (http://www.joelonsoftware.com/articles/Unicode.html)
Internet 2
Main Internet 2 site (http://www.internet2.edu)
ATM in a nutshell (http://www.hpc.gatech.edu/Internet2/atm/)
Linux
Linux Magazine Online (http://www.linux-mag.com/)
Distro Watch (http://distrowatch.com). LINUX/UNIX distributions
Linux World (http://www.linuxworld.com)
SUSE LINUX (http://www.novell.com/linux/suse/index.html)
Linux Online (http://www.linux.org)
The KNOPPIX Project (http://www.knoppix.com)
Debian Linux (http://www.debian.org)
Linux Documentation Project (LDP) (http://www.tldp.org/)
LinuxPlanet (http://www.linuxplanet.com/linuxplanet)
Linux Focus (http://www.tldp.org/linuxfocus/index.shtml)
Where Linux users go for help (http://www.linuxquestions.org/)
Newbiedoc (http://newbiedoc.sourceforge.net/) Debian Linux documentation by newbies for newbies.
SELinux
SELinux for Dummies (http://fedoraproject.org/wiki/SELinux/Dummies)
Overview of SELinux (http://www.redhat.com/v/swf/SELinux/) c/o http://www.redhat.com
RHEL 4 Selinux guide (http://www.redhat.com/docs/manuals/enterprise/RHEL-4-Manual/selinux-guide/index.html)
Linux System Administration
SysAdmin Magazine (http://www.samag.com/) For UNIX system administrators
Unix Backup and Recovery (http://safari.oreilly.com/?x=1&mode=section&sortKey=title&sortOrder=asc&view=&xmlid=1-56592-642-0&g=&catid=&s=1&b=1&f=1&t=1&c=1&u=1&r=&o=1&n=1&d=1&p=1&a=0&page=0)
Backup central (http://www.backupcentral.com/). Only the recovery matters.
LinuxPrinting.org (http://www.linuxprinting.org/)
SystemImager (http://www.systemimager.org/)
Basic Installation of PHP on a Unix System (http://www.onlamp.com/pub/a/php/2000/11/17/php_admin.html)
The Soothingly Seamless Setup of Apache SSL MySQL and PHP (http://www.devshed.com/c/a/PHP/The-Soothingly-Seamless-Setup-of-Apache-SSL-MySQL-and-PHP)
Linux, Apache, MySQL & PHP (LAMP) Setup Guide (http://www.linuxhelp.net/guides/lamp/)
Ganglia grid monitor (http://monad.gc.cuny.edu/ganglia). Username and password required.
NAMD wiki (http://www.ks.uiuc.edu/Research/namd/wiki/). Research computing aspires to this model.
Creating custom kernels with Debian's kernel-package system (http://newbiedoc.sourceforge.net/system/kernel-pkg.html)
Amanda: Advanced Maryland Automatic Network Disk Archiver (http://www.amanda.org)
Configuring Amanda (http://www.samag.com/documents/s=9402/sam0204a/)
A Unix Perspective on Oracle Archive Redo Log Files (http://www.samag.com/documents/s=9797/sam0507a/0507a.htm)
Bash prompt HOWTO (http://lantana.tenet.res.in/General_Info/Tech/HOWTO/Bash-Prompt-HOWTO.html)
Ipchains HOWTO (http://www.tldp.org/HOWTO/IPCHAINS-HOWTO.html)
Linux Documentation Project HOWTO index (http://www.tldp.org/HOWTO/HOWTO-INDEX/howtos.html)
Useful Debian Linux customizations (http://stp.ling.uu.se/~perweij/priv/main/debiannotes.html)
Open Source
SourceForge Open Source development (http://sourceforge.net/index.php)
Why Open Source Software? Look at the Numbers! (http://www.dwheeler.com/oss_fs_why.html)
How to Evaluate Open Source Software (http://www.dwheeler.com/oss_fs_eval.html)
The Practical Manager's Guide to Open Source (http://www.lulu.com/PracticalGuide)
No Software Patents! (http://www.nosoftwarepatents.com/) Excerpt: Copyright protects authors but doesn't hurt any honest person. Patents, in contrast, are 20-year monopolies that the government grants on broad and general ideas. Patents are potential weapons against all of us.
Against Intellectual Monopoly (http://www.dklevine.com/general/intellectual/against.htm) Book by economists David K. Levine (http://levine.sscnet.ucla.edu/) and Michele Boldrin (http://www.econ.umn.edu/%7Emboldrin/index.html) explains why "intellectual monopoly is costly, dangerous, and neither needed for, nor a necessary consequence of, innovation."
Programming, compilers and libraries
The Portland Group (http://www.pgroup.com/) Compilers for high-performance computing.
Latest PGI Users Guide (http://www.pgroup.com/doc/pgiug.pdf)
PGI compiler and tool documentation (http://www.pgroup.com/resources/docs.htm)
Netlib MPI library documentation (http://netlib.org/mpi/index.html)
MPI tutorials (http://www-unix.mcs.anl.gov/mpi/tutorial/)
MPICH-G2 (http://www3.niu.edu/mpi/) A grid-enabled implementation of the MPI v1.1 standard (http://www-unix.mcs.anl.gov/mpi/).
Concurrent Versions System (https://www.cvshome.org/)
ckpt (http://www.cs.wisc.edu/~zandy/ckpt/) A process checkpoint library
Software Development
The Eclipse open source Integrated Development Environment (http://www.eclipse.org/)
MagicDraw (http://www.magicdraw.com/) a visual UML (http://www.uml.org/) modeling and CASE tool.
Junit (http://www.junit.org/index.htm) Testing resources for extreme programming.
log4j (http://logging.apache.org/log4j/docs/index.html) open source logging tool developed under the Jakarta Apache project.
Jakarta commons project (http://jakarta.apache.org/commons/index.html) reusable java code.
Java AWT Reference (http://www.oreilly.com/catalog/javawt/book/index.html)
Chapter 3 from The Art of Project Management (http://www.oreilly.com/catalog/artprojectmgmt/chapter/ch03.pdf)
rxtx (http://users.frii.com/jarvi/rxtx/download.html) Serial I/O for java.
testdriven.com (http://www.testdriven.com/) Test driven development.
Solar Activity
Solar X-ray Flux:(Values: Normal, Active, M Class Flare, X Class Flare, Mega Flare) Higher activity is better for shortwave. Geomagnetic Field:
(Values: Quiet, Unsettled, Storm) Lower activity better is for shortwave; higher is worse.
Solar activity updated every 10 minutes from n3kl.org (http://www.n3kl.org/sun/noaa.html).
Statistics
Inter-University Consortium for Political and Social Research (http://www.icpsr.org)
Survey Documentation and Analysis (http://sda.berkeley.edu:7502/document.htm)
Tex and LaTeX
Kile (http://sourceforge.net/projects/kile) A KDE Latex editor. We recommend Kile for TeX processing on Linux.
MikTeX (http://www.miktex.org) We recommend MikTeX with WinEDT (http://www.winedt.com) for TeX processing on Windows.
TeXShop (http://www.uoregon.edu/~koch/texshop/) I use TeXShop on the Mac.
Kile RPMS (http://dag.wieers.com/packages/kile/) For Red Hat and Fedora Core.
CTAN (http://www.ctan.org) Comprehensive TeX Archive Network.
TeXlipse (http://texlipse.sourceforge.net/) Eclipse (http://www.eclipse.org/) 3.x plugin for LaTeX document preparation. This seems to be stalled as of 2006, and I've concluded that Kile is better. But this plugin, and plugins like it, have promise.
