Mac OS X for Astrophysicists


Since more and more astrophysicists are starting to use Macs as laptops for their work here is a beginner's guide to software you may want to look at and a few links to useful sites.

Oct 1st 2013: Time for a substantial overhaul and to trim out the really dated stuff. This may not leave much behind... I've also not checked how much of what is left still works. I started writing this page back in the 10.2 or 10.3 days so you can imagine a lot has changed. You should probably consider this page deprecated now!

Contents

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

Xgrid

Xgrid is a new tool in Mac OS X 10.4 (Tiger) which makes it easy to distribute heavy number crunching across a group of Macs (there is a preview version for 10.2.8 or later). It automatically detects available nodes and sends jobs to them, and does it all in the usual point-and-click interface (although you can work from the command line if you wish). Just give it your command line program and tell it how to vary the calling argument (e.g. 'myprocess -begin i -end j') and it'll send the job out and collect all the results for you. See also this 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 somewhat 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.
    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'.
  • 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.

    Standard tools


    Presentations

    For presentation software you have three or four options. You can use OpenOffice.org, or your usual TeX based solution you might use on a Linux machine. Alternatively the two big presentation packages on OS X are:

    Document preparation


    Other applications


    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:


    Useful links


    Additions, suggestions, comments etc to Edd.