Joakim's Mac OS X Setup

Below you will find my basic setup of my Mac running Mac OS X.

Note: This guide is intended for people at the Department of Physics, Stockholm Univeristy. It may prove useful for other pepole too, but some topics are clearly site and field specific.

NOTE: These instructions are for Mac OS X 10.6 Snow Leopard. If you for some strange reason install an earlier version, check out the (partly obsolete) old instructions for 10.1, 10.2, 10.3, 10.4 or 10.5.

Be sure to check my (not complete) list of compatibility issues at the end of this page.

Consider this as a tentative guide to how you might want to set up your Mac to get the most out of it as a physicist at Fysikum. In the following instructions I presume that you know how to configure your machine for the network (DHCP for laptops or static IP for stationary computers). If you have any questions, send me an e-mail.

1. Backup your hard drive.
   If you upgrade your Mac OS X from an earlier version, you should make a backup before you continue. If you have a spare hard drive, it is wise to make a bootable backup copy of your entire hard drive with a program like Carbon Copy Cloner or SuperDuper.
   
   
2. Partition your hard drive.
   If you want to use Unix/Linux programs, I strongly recommend having a separate partition for these. You can e.g. divide your harddisk into two parts, one with HFS Extended (Journaled, not case-sensitive) for Mac OS X and your usual user files and one with HFS Extended (Journaled, case-sensitive) for your Unix/Linux files. Partitioning is done by running the Mac OS X installer and choose 'Disk Utility' from one of the menues. Note that the Mac OS X start-up volume should not be formatted as case-sensitive, whereas your Unix/Linux partition should. The reason for this is that the system and some Applications don't work if you have your startup-volume formatted as a case-sensitive partition. For certain Unix/Linux programs, it is the other way around, some (even if it is rare) programs require a case-sensitive file system. Note that if you did not create this special partition from the start, but you realize later that you need it, you can always create a disk image formatted with whatever file system you want. It is not as convenient, but it works. (Note that the partitioning map should be GUID).
   
   
3. Install Mac OS X.
   Install Mac OS X onto your Mac OS X partition. If you upgrade from an earlier version, it is easier than it used to be to do this with Snow Leopard. The default 'Upgrade' option in the installer seems to work fine. If you have problems, you can of course always start off with a fresh install on a clean disk (even if the Snow Leopard disk is an upgrade disk, it seems to be possible to install on a fresh drive). Either way, be prepared that some programs do not work properly with Snow Leopard. See Apple's official compatibility list, or this more complete blog.
   
   Also choose a custom install and add the bits and pieces you prefer. If you want to be able to use X Windows, click to include 'X11' in your installation. If you are tight on space on your hard drive, you can deselect the languages and printer drivers you don't need to save some space. In general though, Snow Leopard takes much less space than Leopard, so you should be fine installing all the standard things.
   
   
4. Upgrade Mac OS X.
   Upgrade Mac OS X to the latest version by running 'System Preferences -> Software Update' until you have the latest Mac OS X version. Depending on how old your installation DVD is, you might have to run the Software update several times. Run it until it says that your system is upto-date.
   
   
5. Install iLife.
   If you have performed a completely fresh install, you need to install iLife (if you want it) from the original DVD that came with your Mac, or a later
   
   
6. Install Xcode.
   If you are going to program in e.g. C, C++ or Fortran or install programs from sources by compiling them, install Xcode by running the XcodeTools installer found in 'Optional Installs/Xcode Tools/' on the Install DVD.
   
   
7. Install the Fortran compiler.
   If you need Fortran, you can download the g77 Fortran compiler from Gaurav Khanna's computation tools web page. Follow the instructions on that page on how to install it. The g77 3.4 version seems to work fine with Snow Leopard. Note that you need to have root access to install the Fortran compiler. Either you can get this by preceding your commands by 'sudo'. You will then be asked about a password, which is your password (assuming you are classified as an Administrator which you probably are), or you can enable the root user by following these instructions. Only enable root if you know what you are doing!. To finish the Fortran installation, create a link from f77 to g77 to be compatible with some makefiles. Do this by typing
   
   sudo ln -s /usr/local/bin/g77 /usr/local/bin/f77
   
   At Guarav Khanna's page above, you can also find links to gfortran if you prefer that (you can have both g77 and gfortran installed simulatenously if you want).
   
   If you are on an Intel Mac, you could also consider Intel's Fortran compiler ifort. It is commercial, but they do have an academic licensing for about 2000 SEK. You can download a trial version from Intel if you want to give it a try. From my experience, ifort is about 35-40% faster than g77 and in most cases it is easy to compile with ifort if your programmes compile well with g77. With ifort, you can also compile 64-bit code that can give you even more efficient code on some machines (e.g. my Fortran programs compiled with 64-bit ifort on my Mac Pro is faster than the 32-bit versions, but on my old MacBook Pro (first Intel Core 2 Duo generation, they run with the same speed). Note that ifort does currently not officially support Snow Leopard, but at least the 32-bit version seems to work fine.
   
   Note that Guarav's page above, also contains information and links to c and c++ compilers (even if you got the standard installation when you installed Xcode tools).
   
   
8. Install cernlib and paw.
   If you need cernlib and paw, the easiest is to install them via fink. At least PAW works fine under Snow Leopard.
   
   
9. Install TeX.
   The TeX installation I kind of like most on Mac OS X is TeXShop which uses tetex as the TeX motor. Follow the instructions on darkwing.uoregon.edu/~koch/texshop/texshop.html to first install tetex and then TeXShop. The easiest is to follow the instructions there on how to get MacTeX from CTAN. You then get tetex and TeXShop in one simple go.
   
   
10. Install whatever else you like.
    Here is a little list of things I like to have installed:
• Emacs. The all classic text editor (free). It comes in a few different flavours, pick the one you prefer (I haven't found my favourite yet).
  • Carbon Emacs. A more classic version of Emacs (also based on Gnu Emacs) (this is the one I prefer and it seems to work fine under Leopard.)
  • Aquamacs. A Macier version of Emacs (based on Gnu Emacs)
• TextWrangler. Another nice text editor (free).
• Smultron. Yet another nice text editor (free and SWEDISH!)
• Norton Antivirus. As an employee of Stockholm University, you can download Norton Antivirus from here. However, Norton Antivirus currently does not work with Snow Leopard.
• Microsoft Office, Mathematica, etc. CDs are available from Christian Walck (or at least he knows where they can be found). Install and register with Christian Walck.
• LaTeXiT. Nice little application (included in the MacTeX installation above if you followed that install route for LaTeX) that lets you quickly write equations to include in e.g. Keynote. It has a nice touch that you can drag your equations from e.g. Keynote back into LaTeXiT to edit your equations. For this reason, I prefer this program instead of
• LaTeX Equation Editor. Similar application as LaTeXiT, but without the ability to edit your equations later (unless you have stored them in LaTeX Equation Editor's library).
• Subversion. Version control system (the successor of cvs). Subversion is also included with Snow Leopard.
• ClickToFlash. If you, like me, dislike Flash ads on web pages (they e.g. draw a lot of CPU power, giving you much worse battery performance), I can recommend installing ClickToFlash, which instead shows a grey box where the Flash ad is. You can then click on it to show it if you want to see it.
  
  
  
11. Install Kerberos and AFS.
    If you want to access our AFS disk system (and your home account if it is AFS), go to these instructions to install the needed programs (I have not checked that this works on Leopard yet).

Snow Leopard compatibility status

This is my (private) list of things that do work or that don't work under Snow Leopard (as of this writing). Note that I have not made extensive tests of these programs, I have just checked that the kind of things I typicall do work. Hence, treat this table with some care.

Links

• Versiontracker.Best resource on the net for Mac OS X software. If any of the links above are missing you can search for the software at Versiontracker.
• MacOSXHints. Hints and tips on various Mac OS X issues.
• OSX Page. Extensive list of software. Contains much more X Windows software than Versiontracker.

This page was last modified 2009-09-04 .