Mac OS X for Astrophysicists

I've now got an Intel Mac, so I'll start marking out things that I know definitely work on it. i denotes something that I know works under Rosetta emulation, and i denotes something that I know has a native or universal binary. If there's no i it means I don't know (I'm yet to find anything that flat out doesn't work).

Recent changes: Reorganised X11 section, a few Leopard updates and misc other minor changes 16/11/07, link update 19/11/07, link update 3/12/07

Contents

1. Astronomy software
How to get standard astronomy software like IRAF.
2. About Xgrid
Information on the new OS X distributed computing tool.
3. X11
Tips for using X11 on OS X.
4. Standard tools
C compilers, X Windows, other tools you'd find with most Linux distributions.
5. Presentations
Tools for talks
6. Document preparation
LaTeX and the like
7. Other applications
Other applications you might find useful
8. Command line tips
Tips for interfacing the command line and the standard Mac OS X environment.
9. Useful links

Astronomy software

• IRAF
IRAF is available as a special Mac package from the maciraf page. These need to be installed as an 'iraf' user. This user would normally appear as one of the login options and with a home directory unless you use couple of little tricks.

Mac OS X doesn't show users for login unless their UID number is over 500. You can make the iraf user invisible in this way by doing the following:
1) Download all the packages and put them somewhere the iraf user (which we will create later) can get at them. Your 'Public' directory should be ideal for this.
2) Create the iraf user (see the maciraf installation page, or just use the System Preferences utility - it is very simple) and whilst in System Preferences make your 'Login Options' (under 'Accounts') the 'Name and password' option. Also make sure the new user is an administrator.
3) Open the Terminal and type 'nireport / /users uid'. This gives you a list of current UID numbers. Pick one below 500 that is not in the list. I chose 50.
4) From 'Netinfo Manager' in your Applications/Utilities folder go to 'users' and pick the 'iraf' user. Search for the 'uid' property and change it to your chosen number. Also, check that the 'gid' is set to 20 for the staff group (this was an issue with the maciraf package and Panther that may have been resolved now, but this should be fine to do anyway). Close Netinfo Manager.
5) Switch to the login window and log in as iraf.
6) Open the Terminal and fix your home directory permissions with:
cd ..
sudo chown -R iraf iraf
sudo chgrp -R staff iraf
and if sudo asks for a password use iraf's password.
7) Continue with the installation of iraf as normal.
8) If you want go back to System Preferences and change your 'Login Options' back to 'List of users'. 9) Go back to Netinfo Manager and set the iraf user's shell to /usr/bin/false. This step is necessary to hide the user in Tiger. 10) One last step to hide the iraf user's home directory in the Finder - make sure DevTools are installed (see below) and in the Terminal perform:
sudo /Developer/Tools/SetFile -a V /Users/iraf

• ESO-MIDAS
ESO-MIDAS has a native Mac OS X binary now but it can also be compiled from source. You'll want to install Motif libraries from Fink or similar beforehand (again, see below).
• ESO Scisoft
Scisoft is available for OS X from here and is regularly updated.
• IDL i
Not strictly astronomy software, but I'll include it here. IDL comes in a Mac OS X version. If you can't get a license for it then you might get away with GDL as an alternative. It implements a fair bit of IDL, but not all of it. A lot of the astrolib work (including READFITS and WRITEFITS). GDL is available via Fink (see below, unstable branch only, and problems have been reported compiling it from Fink) or download GDL from here.
• JObserve
Download JObserve from here. There's now an 'unsupported' Mac download available, or you can install it by following the 'everything else' instructions. If you choose that route you will need to edit the resulting jobserve.sh script as follows:
OSTYPE=`/bin/uname` to OSTYPE=`/usr/bin/uname`
Add the following before "*"):
"Darwin")
JAVA=/usr/bin/java
$JAVA -Djava.security.manager -Djava.security.policy=$JO_HOME/java.policy \
-cp $JOPATH edu.nrao.vla.jobserve.Observe -d $JO_HOME $*
;;
• Starlink i
A binary installation of Starlink and the source can be downloaded from here. There are now Intel binaries, and if you have any difficulties compiling it from the source I'm told by Brad Cavanagh (the release manager for Starlink on OS X) that if you have any difficulties with it you should be able to get it compiled by downloading g95, setting F77 and FC to 'g95' and proceeding with the instructions in the README file.
• AIPS
AIPS installs on Macs and there's a page of instructions here.
• GIPSY
Thanks to Erwin de Blok GIPSY has been ported to the Mac. It's available from here although the patches should make it into the main tree soon.
• MIIPS
Donald Gudehus's MIIPS package runs on OS X. Download from here.
• HEAsoft
HEAsoft (FTOOLS and XANADU) is available here for OS X.
• Stellarium i
Stellarium is a virtual planetarium that works on OS X. Not tried it myself yet but it looks like it could be a handy bit of software, especially if you're after some fancy graphics for outreach work or similar things.
• The UltimateAstroWidget i
The UAWis a handy Dashboard widget for astronomers. It gives a handy clock for where you're observing from, giving LST etc., as well as airmass plots, and a tool for figuring out the observability of an object at a given time and place.
• QLFits i
The same site also hosts QLFits, which lets you very handily inspect FITS headers from inside the Finder.

Xgrid

X11

• X11.app in Tiger i
Also on one of your DVDs should be the X11 package, which gives you an X server (look for the Optional Packages installer - scroll down the DVD contents). If not, get it from Apple if you are a Panther (10.3) user. It can mix your X11 windows in with your standard OS X ones, or it can run fullscreen. If you choose this option from X11.app's preferences then switch between your desktops with Command-Option A. The Command key is variously also called 'apple', 'clover', or 'pretzel'. This should be a good clue as to which one this is. The Option key is the one marked with a slanted symbol, normally left of the leftmost Command key and shared with 'alt'. If you choose the fullscreen option you'll want a suitable window manager, probably from Fink or DarwinPorts (below). Once you've got one installed do:
cp /private/etc/X11/xinit/xinitrc ~/.xinitrc
and edit the .xinitrc file with emacs, vi, or your chosen editor and replace 'exec quartz-wm' on the last line with 'exec wmaker', 'exec fvwm2' or whatever you have chosen.
Intel users - whilst X11 works almost entirely without problems there is one little bug that will drive you totally up the wall if you try running a remote emacs on certain other systems. There's a fix here thank goodness!
Note - don't try that fix on Leopard!
• X11 in Leopard
X11 got a fairly sizeable overhaul for Leopard. I've not yet installed Leopard, but here's a couple of useful links that might help out with the bugs that are in it:
• http://forums.macosxhints.com/showthread.php?t=80171
X11 in Leopard FAQ
• http://xquartz.macosforge.org
Xquartz Mac OS Forge page
• SSH
If you have problems such as being unable to paste or windows disappearing try invoking ssh as 'ssh -Y' rather than 'ssh -X'. This uses a newer ssh feature called 'trusted X11 forwarding'.
• Copying and pasting
The Mac OS X pasteboard is completely separate from the X11 clipboard. Within X11.app the highlight-to-copy and middle-click-to-paste behaviour works as you'd expect. In the native environment the Edit menu or Command-C/Command-V lets you copy and paste to the OS X pasteboard. To work between the two:
Paste from X11 to OS X - select your text in your X11 program to copy it to the X11 clipboard, then in the 'Edit' menu at the top of the screen select 'Copy' or use Command-C. Paste to your OS X application as normal.
Paste from OS X to X11 - a bit confusing as the 'Paste' menu option in X11.app is greyed out most of the time, but if you copy text it should automatically go to the X11 clipboard. From there, just middle-click or Control-V as normal. Alternatively, don't forget 'pbpaste' mentioned above.
• Changing the startup
Do 'cp /etc/xinit/xinitrc ~/.xinitrc' to give yourself a personal startup script you can edit (see below)
• Keeping quartz-wm features
quartz-wm is the window manager that gives X11 the Mac OS X look and feel. You may decide to change this for another window manager by editing a .xinitrc file but if you do this it is worth running 'quartz-wm --only-proxy' before your alternative window manager as this will let you use copy and paste as normal.
• Focus follows mouse
If you use quartz-wm then try at the command line the following:
'defaults write com.apple.x11 wm_ffm -bool true' to get focus-follows-mouse in your X windows.
'defaults write com.apple.x11 wm_click_through -bool true' to disable the way that a click will activate a window but not pass the click itself through to the application underneath.
Want it in Mac OS X itself? Have a look at Codetek Virtual Desktop linked above. Also, the Terminal program has an option for this, enabled with 'defaults write com.apple.Terminal FocusFollowsMouse -string YES' and disabled with 'defaults delete com.apple.Terminal FocusFollowsMouse'. It might be a bad idea to extend it to OS X applications generally since you'll inevitably want to use the menubar at the top at some point, and you could easily end up switching application en route!
• Nicer fonts in xterms
Try starting an xterm with the following options:
'xterm -fa Monaco -fs 11'
This starts it using a Monaco Freetype font with size 11.
• Proper detection of the DISPLAY variable in Tiger
Note - Leopard does things very differently. Don't use this on that system.
A standard OS X application won't know what your DISPLAY variable has been set to in X11. This means you can't start an X11 application from Terminal.app unless you use open-x11 described earlier. This script should pick up your DISPLAY setting and set it correctly, so you can source this in Terminal.app and then use X11 applications as if you were in an xterm.
if [ -e /tmp/.X11-unix/* ] then X11_FOLDER=/tmp/.X11-unix
currentUser=`(set \`whoami\`; echo $1)`
bb=`ls -l $X11_FOLDER | grep $currentUser`
bbb=${bb/*X/:}
usedDISPLAY=$bbb.0
export DISPLAY=$usedDISPLAY fi
Thanks to Dietrich Onnasch who originally posted this in comp.lang.idl-pvwave, and Nathan Nutter who provided a modification to help avoid errors when not running X11

Standard tools

• Developer tools i
Make sure you install the Developer Tools! If you didn't get an XCode CD/DVD then get it from Apple's Developer site after free registration. It's a big download, but essential as it has gcc and many other vital tools. Also, it has the X11 SDK you'll need to compile X11 software.
• Fink
Fink is a commonly used package manager for *nix software on OS X and is pretty well supported in the general Mac community. It is well documented and easy to use, and one of the best ways to get other window managers, LaTeX and most other standard X11 applications and the like.
• DarwinPorts i
DarwinPorts is another package manager for *nix software. It got off to a slower start than Fink, but many users are changing over due to various frustrations with Fink. I recently switched over, and have yet to find any complaint (other than emacs doesn't build with X support by default, see below). (Intel note - most packages reportedly work fine but it's not guaranteed all will)
• Emacs i
The default emacs on OS X is not compiled for X11. Either roll your own, grab one from Fink, DarwinPorts (do sudo port install emacs-devel +x11), or get a 'Carbonised' emacs for a native OS X feel (DarwinPorts users do sudo port install emacs-devel +carbon). If you install xemacs from Fink make sure to also install the xemacs-sumo-pkg package to get all the extras.
If you want a native version you might also try Aquamacs (a universal binary too), or there are older versions such as the carbon-based emacs package (v21.4) available from the yaced SourceForge site (Tiger users only), and Apple has a link to one here, and lastly a Cocoa-based Emacs.app is available from this SourceForge page. The Cocoa port probably integrates a little better with OS X than the Carbon ones, but the Carbon port may have other features you prefer.

Presentations

• Microsoft Office
Office is very commonly used and Powerpoint is available for the Mac. This is probably the most common presentation package, but I've never used it myself.
• Keynote i
Apple's own solution, Keynote (now part of iWork along with Apple's Pages word processor and the Numbers spreadsheet) is relatively cheap, simple but very powerful and capable of 3d fancy graphical changes that are guaranteed to ruin a talk just as well as any overly sugary Powerpoint twirl-and-fade. Also available with an educational discount, this is a real bargain and has excellent dual-head support for Powerbook owners. If you don't already have Office and aren't planning on getting it this is well worth the money. Vector graphics, like PDFs (which are now easily created from your PostScript files) drop in easily making it a doddle to drop in LaTeX typeset equations without any pixellation. It imports Powerpoint files reasonably well, and also exports nicely to PDF and Quicktime movie files.
• Salling Clicker
Essential for gadget freaks with Bluetooth-equipped Macs, the Salling Clicker lets you use a Bluetooth PDA or phone to control other applications, most usefully perhaps Powerpoint or Keynote. This means your mobile phone can be the remote control for your presentation. The fact that it lets you run iTunes and other applications from a distance is a bonus! It costs money, but not very much at all. (Note that apparently since Tiger some people do this without the extra software - I haven't needed to use Salling Clicker since upgrading, but it's still first-rate software)

Document preparation

• LaTeX i
LaTeX is available from Fink or DarwinPorts above, amongst other places (but if you've installed one of those anyway it's easiest to get it from there). Also note that Panther (10.3) and later can convert Postscript to PDF with a built-in distiller, and look out for applications like TexShop and iTexMac which are specially designed for preparing TeX-based documents. Alternatively your trusty emacs is readily available.
For typesetting equations for presentations etc. see LaTeXiT, Equation Service and Equation Editor.

• TeX FoG
If you have trouble remembering all the LaTeX commands for mathematical symbols you may find TeX FoG a handy tool. It lets you create the LaTeX code for an equation by clicking buttons for each symbol you need.
• Grapher i
Tiger comes with a surprisingly capable graphing application. It is also able to create LaTeX code for the equations it graphs.
• GLE
GLE has updated its installation methods to use autoconf - so you should be able to install this by using the same instructions as for Linux. Just make sure you install libtiff and libpng using either Fink or DarwinPorts.
• Tioga i
Tioga is a package written by Bill Paxton for creating figures and plots. It uses Ruby, PDF and Tex together to produce its output.
• TextWrangler i
As an alternative to emacs (above) or similar text editors, TextWrangler is getting excellent reviews. It's a cut-down version of BBEdit - a very powerful but expensive editor. TextWrangler will give syntax highlighting for most common languages as well as fit in neatly with OS X (providing features such as asking for authentication to save over files with restricted permissions).
• SubEthaEdit i
SubEthaEdit is another text editor with the usual syntax highlighting and other advanced features, but with one feature you won't find in other editors - collaborative editing. This might be useful if you happen to be writing a document with a coauthor who also has a Mac. You could both edit the same document at the same time, without having to email back and forth.

Other applications

• The GIMP i
The GIMP image editing tool is available as an OS X application package, and this is one of the few X11 tools I'd suggest not using Fink or DarwinPorts for. Gimp.app is a must-have.
• Tofu i
Tofu is an unusual program designed for reading large chunks of text. Rather than scrolling downwards it scrolls sideways. It sounds odd, but it works very well especially on those wide laptop screens. Very useful to have around for large ASCII text files.
• Calculator i
The OS X 10.3 (Panther) calculator has now been fixed. It's still got a few peculiarities though. For example, it can't raise a number to a non-integer power. The OS X 10.4 (Tiger) calculator is more fully featured - just make sure you run the full-blown application and don't use the much simpler Dashboard widget.
• Longhand i
Longhand is a powerful calculator that takes equations you type in and calculates them as you type. It supports a huge number of functions, matrices, complex numbers and lets you assign results to variables to use later. Very useful for quick bits of maths.
• Virtual desktop tools
Leopard of course now has Spaces built in, which provides virtual desktops, but for those using Tiger...
• Codetek Virtual Desktop
Codetek Virtual Desktop gives you a virtual desktop pager and the pro version has a few extra features like focus-follows-mouse. There's a 15 day demo but after that you'll need to pay $40 for it (pro) or $20 (lite).
• Desktop Manager
Like Codetek Virtual Desktop above, Desktop Manager gives you a virtual desktop pager. It doesn't have some of the features of the full version of Codetek's product, but it is free software. The webpage says it's only alpha quality at the moment and I've not tried it myself.
• VirtueDesktops i
VirtueDesktops is based on Desktop Manager, and looks like it's getting very popular amongst those that like virtual desktop applications.
• Space.app
Space.app is another free virtual desktop manager I've not tried, and doesn't seem to have seen any development for some years now.
• Adobe Reader
Whilst the built in Preview is very good for viewing PDF files (and the viewer I use most of the time) the reader from Adobe has a few extra tricks up its sleeve. For example, it can search PDFs on your hard disk for particular text, which can be handy when trying to dig out a reference from a folder full of papers. The new version of OS X (Tiger) has Spotlight which can do that sort of search much better, but if you don't have it then this reader can be very handy to have around. Adobe Reader will also let you view pdfs from inside a browser window - which again can be handy if you don't have Tiger which has the ability to do that straight out of the box.
• Skim
Skim lets you read PDFs and make notes on them too. Looks very handy.
• Cyberduck
The bizarrely-named Cyberduck is a nice simple FTP and SFTP program for transferring files. It's also free.
• Fugu i
If you want a graphical frontend to SFTP and SCP Fugu may be what you're after.

Command line tips

There's a number of commands to link your command line and the OS X environment. Here's a few very useful ones:

• 'open' will let you open standard file types in the right application from the command line, for example 'open paper.pdf' to open 'paper.pdf' in Preview or your default PDF viewer.
• 'open -a' lets you open a specific application from the command line, for example 'open -a mail' to start Apple's Mail application.
• 'open-x11' lets you open X11 applications without X11.app already running, eg 'open-x11 xclock'. Note - Leopard handles this automatically now, so no need to use this script.
• 'pbpaste' and 'pbcopy' send the pasteboard (or clipboard as it is called on other systems) to and from the command line. For example, to get a word count of a PDF document you could select all the text in Preview, copy it to the pasteboard and then in Terminal enter 'pbpaste | wc -w'. Alternatively you might want to get a text file into the pasteboard quickly using 'pbcopy < lotsoftext.txt'.

Useful links

• MacOSXHints.com
MacOSXHints.com has lots of tips and tricks for getting more out of your Mac. It's forums site is absolutely essential for support and has areas specifically for X11 and Unix-related problems, and many of the users there are quick to respond with excellent advice.
• X11 FAQs
There are X11 FAQs at the MacOSXHints Forums and also at Apple.
• Macsingularity.org
From Marcos Huerta, the man behind the IRAF package, comes this excellent site. In particular, check out the beginners' guide for astronomers here.
• Mac OS X for Physicists
Hitoshi Murayama's excellent page along much the same lines as this, but with a more particle physics bent.
• Mac OS X for Oceanographers and Atmospheric Scientists
Andy Jacobson's site covers a number of analysis tools along with the usual tips and standard apps.
• High Performance Computing for Mac OS X
Has information on all sorts of compilers and computation packages.
• Naomi Ridge's Professional Astronomy Software for Mac OS X page
This page has links to many more astronomy packages with OS X binaries or which compile easily in OS X. There's also a link to a mailing list which people might want to join.
• Jane Rigby's OS X for Astronomers page
Lots of handy tips to get you started.
• Andi Mahdavi's Mac OS X 10.3 Hints page
A number of tips here including astronomy software ones.
• MacResearcher
A community for Mac-using scientists.
• Mac IDL Tips and Tricks
A few tips for those using IDL on a Mac.