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Hermann Fomichev
Hermann Fomichev

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  • 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 10.5 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 or 10.4.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. 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 Retrospect.

  • 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 the Unix/Linux partition could be formatted with the UFS file system instead, but the performance of that is not very good on Mac OS X so it is better to stick to the case-sensitive version of HFS Extended. Also 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 for Intel Macs and Apple Partitioning Map for PowerPC Macs).

  • Install Mac OS X. Install Mac OS X onto your Mac OS X partition. If you upgrade from an earlier version, I strongly recommend that you either do an 'Archive and install' or a completely fresh 'Erase and install' (all your files will be erased, so be aware). The default 'Upgrade' option in the installer can cause several problems with old system files/additions lying around causing conflicts. You can of course give it a try, but be prepared that you might end up with problems. If you use the 'Erase and Install' and have a bootable backup of your hard drive, you can use the Migration Assistant (either during the installation process, or later by launching it manually) to transfer back the things you want from your old installation. For both the 'Archive and Install' and 'Erase and install' options, be prepared that some applications will not work without running the original installer again, so you should have these handy in that case. 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.

  • 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.

  • Install iLife. If you have performed an 'Erase and install' you need to install iLife (if you want it) from the original DVD that came with your Mac, or a later Install DVD for iLife if you have bought a more recent copy.

  • Install Xcode (before it was called Developer Tools). 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.

  • 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 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. 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).

  • Install cernlib and paw. If you need cernlib and paw, please follow the instructions below. a) For PowerPC Macs, download cernlib and paw from Keisuke Fujii's HEP page. He uses the APT/RPM package mangement system for installation. Follow the instructions on his page on how to install this and CERNLIB. Install cernlib in /cern as usual and add /cern/pro/bin to your path by editing your .cshrc file and add the line SETENV PATH "$PATH:/cern/pro/bin" If you now start an xterm window in X11 and type paw you should get paw running with graphics and all. Note that cernlib and paw on Keisuke's page (as of this writing, 2007-01-11) are not updated for Intel macs. However, the binary install of paw works anyway (under Rosetta), whereas using cernlib with your own routines don't work on Intel Macs as they are compiled for PowerPCs. b) For Intel Macs, I have compiled cernlib directly from source, following the instructions on Keisuke's page above (with some modifications to make it compile). I have compiled the needed libraries and cernlib itself. Not all things went through (not paw++ e.g.), but at least paw and cernlib seems to work as it should. I give no guarantees, but if you want to install my compiled version of cernlib for the Intel Mac, download and install the following: sudo tar zxvf libcompat-intel.tar.gz -C / sudo tar zxvf libblas-intel.tar.gz -C / sudo tar zxvf liblapack-intel.tar.gz -C / sudo tar zxvf cern2005-intel.tar.gz -C / This installs the needed libraries in /usr/local and cernlib is installed in /cern as usual. You need both Xcode tools, g77 and gfortran installed for this work. As above, you then need to add /cern/pro/bin to your path when you are finished.

  • 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 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.

  • 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.

  • 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). Seems to work fine with Leopard.

  • Configure crontab (optional). If you want to, you can configure cron such that it automatically runs some system maintenance scripts at convenient times. As root install a crontab file like the following: SHELL=/bin/sh #min hour mday month wday command 10 12 * * * sh /etc/daily 20 12 * * * sh /etc/weekly 30 12 * * 2 sh /etc/monthly Note that there should be tabs between all fields (except between sh and /etc...). This will keep your system sane and the locate database updated. If you don't like these jobs to run at the specified times (12.10, 12.20 and 12.30), change to your liking.

  • 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).



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