Transition to the New Astrophysics OS X System Setup

The old setup of OS X systems has been in use in Astrophysics since 2008, and is beginning to show its age. We are now moving users and systems over to a revised setup, which builds on the good aspects of the older setup, addresses some known problems, and leaves behind three years' accumulated clutter.

  • PLEASE NOTE: OS X Lion was released on 20th June 2011; system-security updates for OS X Leopard will cease fairly soon, if they haven't already. We will therefore be accelerating this transition, and will be giving priority to OS X systems still running Leopard.
  • UPDATE:As of this writing (March 2013), Mountain Lion (10.8) is out, Lion (10.7) is supported, Snow Leopard (10.6) is at best tolerated, and anybody still using Leopard (10.5) or earlier is in contravention of University rules if their system is connected to the University network. The boundaries are due to move up one notch when 10.9 is released, nominally in August 2013. We are therefore about to go through another update exercise, with a soft deadline of Easter, and a hard deadline of August.

This FAQ attempts to outline, for existing users, things which are done differently under the new system setup; information for new users is under development. Please contact us, either in person or by e-mail, for more information.

Please see also:

Why do we need to update?

  • Important: There were serious problems with data loss under the older system setup (see below).
  • Urgent: Many of the systems under the older setup are still running the Leopard version of OS X. Since the release of OS X Lion on 20th July 2011, system-security updates for OS X Leopard have ceased. This presents a security risk to the network as a whole.

Where’s my home directory?

This is now /home/yourname, which is by default directly on the fileserver; the contents will be whatever Home Sync last saved for you under the old system setup. (If you've elected for your system to have local home directories, it will be in /Volumes/Data/Users/yourname instead; but see next Question.) If you can’t live without (the latest versions of) your old home directory’s contents, you can copy them from their old location (/Volumes/Users/yourname), which will still be in place.

PLEASE NOTE: Blindly copying everything will overwrite one’s Library contents, which will break many things, very fast. Exceptions include one’s Safari bookmarks (~/Library/Safari/Bookmarks.plist), providing Safari has been closed. A truly marvellous command-line incantation to copy everything but ~/Library (and ~/.Trashes) is available on request, but is unfortunately too large to fit in this margin, and a tad too dangerous to be released from captivity.

What's this synchronisation window for?

It's our replacement for Home Sync, for those of you who have elected that their system has local home directories. In order to do backups, we need to have some way to synchronise the network and local versions of your home directory. This also means that, were you to log on at another system, your home-directory contents would be the same.

Please sit tight. This may take a wee while if your home directory is extensive, especially the first time. It's the most obvious downside of not having a network-mounted home directory.

Why can't I log in using SSH?

The first time you log on after a reboot, you may be told the system can’t find your home directory. This is to be expected, for technical reasons we can explain on request. Log off and back on, and all should be well.

How do I set up Apple’s mailer?

This needs to be done afresh; attempts to continue using your old setup will end in tears. Please see:

E-Mail in OS X

What about Time Machine and Home Sync?

Time Machine and Home Sync may work well on a laptop with a limited number of files, but proved in practice to not be sufficiently reliable when saving large amounts of material onto a fileserver. This has led to some serious data-loss incidents.

To address this, the Data partition under the new system setup is backed up to the server using a different and more robust method. (User-level tools are under development, but you should already be able to see a file called backuplist.txt in /Volumes/Data containing information about the available backups.) The need for Home Sync has completely gone away (see above).

Where has Self-Service gone?

It’s been moved to /Applications. Please check /Applications/Physics for other third-party software (eg AquaMacs EMACS, Cyberduck, Firefox, Skype, and Vine Server) which used to be under /Applications/Utilities or /Applications.

Where have all the packages in Self-Service gone?

Most of the entries under the older system setup were put there to help people update their systems in their own time, or are now frankly obsolete. If something appears to be missing, the latest available version may well already be present on your system: try looking under /Applications for it, or try invoking it by name at the command line (don’t forget any Activations you may need first), or try seeking it with the Applications Setup search facility. For example, running the command

Activate search gnuplot

shows that GNUplot is in Scisoft, so saying

Activate scisoft

should make GNUplot available at the command prompt in your current shell. It should also show that GNUplot is also available via a wrapper script which does the Activation internally, without disturbing your current shell's environment.

Some specifics:

  • X11: The version distributed with OS X Leopard was broken, and tended to hang the system. This is fixed in Snow Leopard.
  • C and Fortran compilers: We’re trying to slim down the available selection. Apple’s gcc and the gfortran from HPC are available at the command line without further ado; version 11.1 of ifort is available from the Development section in Self-Service (newer versions of ifort and icc will become available in due course). The versions of gcc and gfortran which accompany the OpenMPI libraries should be invoked by the wrapper scripts openmpicc, openmpif90 et al in any case.
  • Scisoft, and Starlink: These suites are installed by default, but have moved, and have taken their library and header directories with them. They should be Activated in the normal way.

    If you’ve linked your own compiled programs to libraries in these suites, you’ll need to recompile and relink them, using appropriate paths under the following directories. Please note that much of Scisoft, and all of Starlink, is now 64-bit-only.

    [**]Scisoft: /usr/local/scisoft/

    [**]Starlink: /Local/starlink-namaka/x86_64/

Why are there (eg) two AquaTerms?

This is a weird one. Please note that AquaTerm is here standing proxy for other instances of apparent duplication.

There’s one instance of AquaTerm in Scisoft, and a different one in the MacPorts collection (which we use to provide many widely-used programs). The fundamental reason for this is that Scisoft and MacPorts are designed and built in isolation from one another, and neither suite can assume that the other has been installed.

To ensure you’re getting the correct AquaTerm executable:

  • If you’re using a Scisoft program (such as SuperMongo) which is linked to the AquaTerm framework, say

    Activate scisoft

    at the command line first. Your desired program will then pick up Scisoft’s AquaTerm executable without further ado.

  • Programs directly available at the command prompt without needing Scisoft to be Activated will find MacPorts’s AquaTerm executable (if they need it) without needing Scisoft to be Activated. So don’t do that.

Please bear the above in mind if you need to link your own software against one or other of the AquaTerm framework libraries (for sufficiently generalised values of "AquaTerm" and of "framework").

And finally . . .

If you find something which is mission-critical to you is truly missing, discuss it with us, please, either in person or by sending e-mail to:

Wherever possible, we will install it on your system as a one-off, or add it into Self-Service for installation by other members of your Group, or update the build process to make it available to everybody.

Categories: Astrophysics | Historical