Mac OS X software installation and setup

Internet connection

To authenticate your machine over ethernet, launch the Terminal application /Applications/Utilities/Terminal.app and type

> ssh userID@10.100.0.1

You can then log in using your University of Alberta CCID. Your internet connection will be valid so long as the terminal session remains open.

For a permament connection, you will have to read off your machine's network ID (six hexademical pairs of the form 00:1d:4f:4a:15:51) and email it to . The ID can be found under System Preferences→Network. Click on the Advanced button on the Ethernet pane and select the Ethernet tab.

Email

To start, you will want to set up your mail client to work with your userID@ualberta.ca and userID@phys.ualberta.ca accounts. Follow the instructions here.

For ualberta.ca, the relevant IMAP servers are

incoming: imap.srv.ualberta.ca (SSL on Port 993 with password authentication)
outgoing: smtp.srv.ualberta.ca (SSL on default ports with no authentication)

For phys.ualberta.ca, they are

incoming: srv.phys.ualberta.ca (SSL on Port 993 with password authentication)
outgoing: relay.phys.ualberta.ca (SSL on default ports with password authentication)

These servers require Secure Sockets Layer (SSL) encryption.

Developer tools

The Mac OS X install disk 2 contains the developer tools. Just double click on the package. Otherwise, you can download the latest xcode package from http://connect.apple.com/. You'll need to register for an Apple Developer Connection account. Once you've registered, login and click Download Software and then Developer Tools. Find the link to the latest version of Xcode Tools.

To install the gcc compiler, run the .dmg file (currently xcode314_2809_developerdvd.dmg). Double clicking it will mount the disk image. Double clicking XcodeTools.mpkg will run the installer. gcc and a host of other development applications. gcc will be located at /usr/bin/gcc.

Software update

Run /Applications/System Preferences. Click on Software Update and apply all updates. Reboot. Repeat until no updates are found.

Readers and plugins

The flip4mac plugin allows for viewing of Windows Media files in QuickTime:
http://www.microsoft.com/windows/windowsmedia/player/wmcomponents.mspx

Apple's Preview application can handle almost all .pdf files, but some U of A forms will only work with Acrobat reader:
www.adobe.com/support/products/acrreader.html

Stuffit Expander is necessary to decompress .sit and .hqx files:
http://my.smithmicro.com/mac/stuffitexpander/index.html

LaTeX

Download MacTex-2008 distribution from http://www.tug.org/mactex/. Open the file MaxTex.dmg, which mounts a volume MacTex-2008. Inside that volumne, double-click on MacTex-2008.mpkg. Select custom install: Check TeXLive-2008 only.

Some other useful LateX-related applications:

TexShop is a very elegant latex front end:
http://www.uoregon.edu/~koch/texshop/
You'll have to set the following paths in TexShop/Preferences.../Engine.

(pdf)TeX: leave as /usr/texbin

Distiller (ghostscript): change /usr/local/bin to /sw/bin
BibDesk will manage your bibtex references: http://bibdesk.sourceforge.net/
Excalibur spell checker: http://excalibur.sourceforge.net/downloads.html
LaTeXit is a useful program for typesetting figures labels and equations for incusiong in PowerPoint or Keynote presentations:
http://www.apple.com/downloads/macosx/math_science/latexit.html

Install additional Mac software

Plot: http://plot.micw.eu/Main/HomePage
TextWrangler: http://www.barebones.com/products/textwrangler/download.shtml
When you install, check the box “install command line tools.” This will give you access to edit and twdiff from the command line.

Open a file in TextWrangler:
```
> edit filename
```
Open a new session without a file:
```
> edit -l 
```
Pipe something to TextWrangler:
```
> ls -la | edit
```
Accept stdin from the terminal; type Control-D to terminate:
```
> edit
```
Find and display file differences:
```
> twdiff file1 file2
> twdiff folder1 folder2
```

Install Unix tools

It's best to use Fink to manage all Unix installations. Fink stores everything in /sw rather than in /usr/local. Installation and removal of software is handled using the debian package manager.

Follow the Quick Start instructions at http://www.finkproject.org/download to download the binary distribution. Follow the instructions here to set up your local environment.

> tar -xvzf fink-0.28.1.tar.gz
> cd fink-0.28.1
> ./bootstrap
> fink selfupdate

Make sure that line is added to your .profile

. test -r /sw/bin/init.sh && . /sw/bin/init.sh

This should be done automatically by /sw/bin/pathsetup.sh. More detailed instructions here

Fink Commander is a nice graphical interface for managing package installation. (It is included in the .dmg file of the binary distribution.) To install it, just drop it into /Applications.

I suggest installing at least the following:

ghostscript
xpdf (gives you pdftops, which unlike ghostscript conversion, can embed fonts in eps)
imagemagick
aquaterm
gnuplot
grace
gmt (generic mapping tools)

For gnuplot, you'll want to create a .gnuplot file that configures aqua rather than X11 as the window manager:

echo "set terminal aqua" >> .gnuplot

Install web tools

A nice system for creating documentation is Sphinx, which is based on Python's docutils. It converts source files written in reStructuredText to html or to pdf via latex. It has full support for mathematical expressions.

$ sudo easy_install -U Sphinx

Kevin Beach