Note. This is the version of Mac Eye pertaining to Mac OSX 10.7 (Lion). It is archived for legacy reasons and no longer updated. For up to date information see here.
This page is maintained by James Wookey ( ).
This page is designed to provide a list of instructions, links and tips for setting up a MacOS X machine for use in the Earth Sciences (mostly seismology). It is not affiliated in any way with Bravo TV's Queer Eye for the Straight Guy, Apple Computer, Inc or any reputable distribution of Linux. Thanks to George Helffrich for the name, possibly inspired by this Joy of Tech cartoon. *The rebranding from "Linux Guy" to "Geophysics Guy" better reflects the current purpose of the page (and gave me an excuse to make a new logo).
Bristol-specific information now has its own local-access only page: Mac Eye for the Bristol Guy. More information on using Mac OS X generally in the department is also available from John Schumacher's webpage (this is also only available internally).
This information is provided in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Any views represented here are entirely personal; they do not reflect the views of the School of Earth Sciences, or the University of Bristol.
If you find anything here doesn't work, drop me an email. Also, if you have any packages, tips or advice you think should be on here, please let me know.
Library folder is now hidden in Finder. You can change this on the command like with:
chflags nohidden ~/LibraryIf you decide that, actually, you just cannot be trusted with being able to see the contents of your Library, you can rehide it with
chflags hidden ~/Library.
sudo. So to create the directory /usr/local2 use the command sudo mkdir /usr/local2. You will be prompted for a password; this is YOUR password (not any separate root one). If you are going to be doing a lot as root, you can type sudo su to login to root user. Remember, with great power comes great responsibility, and you can do untold damage to your machine as root so be careful. If you don't have administrator permissions on the machine you are setting up, I am afraid you might as well skip the rest of this page ...
sudo dscl . -create /users/joebloggs shell /bin/tcsh
substituting joebloggs for your username (the short Unix one, see above). I have had some reports of this not working. If it does not, it can be done with the NetInfo Manager in Utilities, or the command chsh. Be careful when changing directory services things, in my experience they can be temperamental.
.tcshrc or .cshrc file. An example of such a file is given here. Just copy it to your home directory and type mv -f tcshrc.txt .tcshrc. This contains basic paths, some helpful environmental variables and a bit of shell-fu to set window prompts and titles.
cd dOcUmEnTs will work as well as cd Documents. This means that files on a standard HFS+ cannot differ only by case. The filesystem is, however, case-preserving, which is useful if you are transferring files to and from systems like Linux or Solaris which are case sensitive. The wrinkle in this is that although the OS is case-insensitive, various things in the shell are not (like filename expansion). So ls doc* does not match the folder Documents. So in practice the user has to be 'case-aware', even if the filesystem is not!
$DISPLAY automatically) so if you run a command from Terminal or iTerm which requires an X11 window, X11.app starts automatically. In fact, it is not recommended that you launch X11 via the Dock Icon any more, because this causes set up problems. Also make sure it doesn't start at Login (see the Users pane in System Preferences). Also, avoid setting your $DISPLAY explicitly (for example in your .cshrc file).
defaults write com.apple.x11 wm_ffm trueYou should restart X11 after doing this.
MacPorts installs software under the /opt/local tree, which protects it from the predations of the OS and your own installs to, for example, /usr/local.
Fink installs software under its own /sw tree. This is a definite bonus since if you manage to mess up your Fink installed software you can just scratch the whole tree and start again!
tetex package. Other useful ports packages are gv and psutils.
sudo make install
make and configure. The default Apple-supplied version does not come with a Fortran compiler.
G77 can be built from source code for the Intel Macs by applying some patches. See George Helffrich's page for instructions. There is a binary built using these patches on hpc.sourceforge.net, and a package on Fink. Note: this is, as yet, untested by me on Lion, and is very likely to remain that way.
gfortran -o myprog myprog.f90 lib/mylib.a -lg2c -L/sw/lib
(this assumes that you have g77 installed from Fink). Order is important.
convert flag to your file open statement:
open(20,file='myfile.bin',convert='big_endian', form='unformatted') close(20)This can be used for both reading and writing.
convert='little_endian' is also valid.
For a great primer course in scientific python with a geosciences bent, take a look at Andrew Walker's python course for PhD students.
Git. This is a fast, distributed version control system originally developed by Linus Torvalds (the father of Linux). An OSX installer can be found at git-scm.com - follow the Mac OSX link and choose the most up to date i386 or x86_64 build. You can also host your projects free at github.com and bitbucket.org.
SourceTree. This is a free App which provides a very nice GUI for your Git, Mercurial and Subversion version control needs. It also allows access to web source control services like GitHub and BitBucket.
Message Passing Interface (MPI). This is a very popular variant of distributed computing parallelism, with libraries supporting languages including C, C++ and Fortran 95-2003. The easiest way to install this on your OSX machine is using OpenMPI distribution. There is a nice tutorial on how to install it here.
sudo fink install gmt
/usr/local). You will need to add the following lines to your .cshrc:
setenv TAUP_HOME /usr/local/TauP
set path = ($path ${TAUP_HOME}/bin)
(as of version 1.1.5 the CLASSPATH variable need not be set).
setenv CWPROOT /usr/local/SU
cd $CWPROOT/src
make install
make xtinstall
This should build all the binaries and put them in /usr/local/SU/bin. Note that I haven't built the optional Fortran, Motif and OpenGL codes, so those might need extra fiddling with the Makefile.config file, and/or extra third-party libraries.
MyFolder type:
hdiutil makehybrid -o MyImage.dmg MyFolderThis can then be burned in DiskUtility as normal. (Thanks to George Helffrich for this tip.) A hybrid format disk image can be created directly in DiskUtility, by using the drop down formats menu under the Menu Item New->Disk Image from Folder.
/System/Library/Frameworks/Kerberos.framework, and click install. Authenticate, and replace all files. When this is finished, ssh and afp should be working again. You may have to repeat this after subsequent Apple updates.
open mydoc.pdf
opens the preview application with the PDF mydoc loaded, and
open .
opens the current directory in Finder. You can also specify the action to take, see the man page for details.
One of the new features of Tiger is the Spotlight search function, which searches metadata associated with files. The command to use this from the command line is mdfind. So:
mdfind shoebox
lists all files with any metadata tag set to the value shoebox. The query can be limited by directory using the flag -onlyin. Thus
mdfind -onlyin /tmp shoebox
will only list files in (and under) the directory /tmp. For some odd reason this command doesn't understand "." to mean the current directory, so if you want to search from where you are use:
mdfind -onlyin `pwd` shoebox
The query can be limited to certain metadata tags only; for more details see Mac OS X Tiger for Unix Geeks.
If you go to the root directory in Finder, you will notice that you cannot see directories like /usr, /dev and so on, whereas you can in Terminal. This behaviour is controlled by HFS+ extended attributes. Mac OS X provides the utilities GetFileInfo and SetFile (located in /Developer/Tools) for viewing and setting these attributes from the command line. This can be quite useful (for example if you want to be able to see /usr in Finder). To do this type:
sudo SetFile -a v /usr
See the man pages for GetFileInfo and SetFile for details of all the attributes and metadata you can edit.
If you want to paste multiple PDF, PS or EPS files into a single document, use the following:
gs -dNOPAUSE -sDEVICE=pdfwrite -sOUTPUTFILE=new.pdf -dBATCH file1.pdf file2.pdf file3.eps ...
This generates the new combined file new.pdf