Installing various
useful tools for the Mac OS X
|
This
is a quick list of things I do when setting up a Mac, and is meant for internal
reference.
Eric
Salathe has a more comprehensive list at http://www.atmos.washington.edu/~salathe/osx_unix/
Also
Andy Jacobson has a good list at http://tazman.princeton.edu/osx/
Changing
the default shell
The
default shell type in OS X is bash, whereas on the seismo Suns it is
tcsh. To make things simpler I usually make the default tcsh. To do
this:
1.
In
the Applications/Utilities folder, start up NetInfo Manager
2.
Click
on _users_ and then your user login
3.
Click
the lock to make changes
4.
In
the _shell_ property, change to /bin/tcsh
5.
Click
the lock again and exit
Changing
uid in OS X
[Skip
this step for now – this is a placemarker for future implementation]
In
future when the Macs are mounted onto the Sun drives, this will be
necessary. Instructions, courtesy of Eric Salathe, are here:
http://www.atmos.washington.edu/~salathe/osx_unix/change_uid.html
To
find out your uid on the Suns, type this (on the Sun of course)
id
<login name>
Install
X11
[Contributed by Andrew Friedman]
X11 is automatically installed with 10.5.
The latest (unsupported) updates are at http://trac.macosforge.org/projects/xquartz/wiki/Releases
If you have OS 10.4:
1.
Go
to http://xanana.ucsc.edu/xtal/x11.html
2.
Download
X11.app and SDK for 10.4
3.
Install
both X11User.pkg and X11SDK.pkg
4.
Go
to the Applications/Utilities folder and pull the X11 icon over to the desktop
dock
5.
NOTE:
to tunnel X11 windows through ssh on a mac you need to use "ssh -Y"
6.
(suggested
by Charlie Koven) add the following lines to your .cshrc file so that you can
use X11 from terminal.app:
if ( $?DISPLAY == 0 ) then
setenv DISPLAY :0.0
endif
To
use X11 remotely [contributed by Charlie Koven]
To use X11 programs when logging in from
another computer, you need to set up ssh and sshd to forward the X11
connections. To do this, you have to modify two files: /etc/ssh_config and
/etc/sshd_config
/etc/ssh_config has a line that initially
says:
# ForwardX11 no
change this line (you have to use sudo to do
it) to:
ForwardX11 yes
(make sure you delete the # at the start of
the line)
/etc/sshd_config has a line that says:
#X11Forwarding no
change it to:
X11Forwarding yes
(again you need to sudo and make sure to
delete the #)
Then restart the computer (or restart the ssh daemon using kill
-HUP `cat /var/run/sshd.pid') and you should be able to use X11 programs
through your ssh connection.
Install
Xcode developer tools
1.
Go
to http://developer.apple.com/tools/xcode/
2.
Click
on Tools Download
3.
If
you aren_t registered yet, register – its free
4.
Download
Xcode 3.0 DMG and install if you have 10.5
5.
If
you have 10.4 instead, download Xcode 2.5 DMG. Also download the Xcode Legacy tools – found below – for
packages that need gcc3.1 to build
Install
Fink
Fink
is package management system to install various Unix software on your Mac
painlessly:
To
download:
1.
Go
to http://fink.sourceforge.net/download/index.php?phpLang=en
2.
Follow
the source release instructions for 10.5
3.
Download
and Install, and follow the web instructions (NOTE: if fink is already
installed in your setup, then all you need to do is to run the pathsetup – see
the web instructions). Generally, you need to set the path so that you
can see the installation, and also update fink.
4.
Type
_fink_ in the command line to see how to use it. _fink list_ shows the
list of all the applications you can get.
5.
Some
useful applications – ghostscript, gv, netcdf, xemacs, ncl
6.
Remember
to add /sw/bin to your path list in .cshrc so that the fink binaries will work
from the command line.
[Contributed by Andrew Friedman] You might have to reinstall Fink if you
upgrade to OS 10.5 - some earlier versions are not upgradable.
To download:
1.
Go to http://fink.sourceforge.net/download/index.php?phpLang=en
2.
Click on the Fink binary installer (for PowerPC, unless you have
the Intel mac). Follow the source release instructions for 10.5.
[Suggested
by Alexander Hansen]
You
might want to run something like
fink
list -it | grep -v " p " | grep -v "\[" | cut -f2 >
~/installed.txt
to
grab a list of all of your currently installed packages so that you can
reinstall them after you upgrade. Then
cat
~/installed.txt | xargs echo | xargs fink reinstall
Finally
(suggested by Charlie Koven): fink
commander is a nice GUI interface to fink.
Install
NETCDF
Before
you do, check to see if netcdf has been installed already. A typical
location is /usr/local/netcdf_. If it is in there already, there is
no need to install – you just need to make sure that your applications can see
it (see step 4)
OTHERWISE:
you can either go through fink, or install prepackaged binaries from the netcdf
website. Instructions for the latter:
1.
Go
to http://www.unidata.ucar.edu/software/netcdf/binaries.html. The current compiled
version will be called something like _darwin_...._macintosh_
2.
Download
it, and unzip (it should do so automatically; if not, use _unzip_ to unzip and
_tar xvf ?_ to untar.
3.
You_ll
see a folder called something like _netcdf-3.6.1_. These contain the
binaries of netcdf. You can put them anywhere you like, so long as your
applications know where they are. If you don_t have admin status, you_ll
have to put it somewhere in your home directory. If you have superuser,
/usr/local/netcdf-3.6.1 (or whatever it is called) is typical
4.
Make
sure that the netcdf binaries can be accessed: in .cshrc in your home
directory (make one if you don_t have one), add these lines (anywhere):
setenv PATH
/usr/local/netcdf-3.6.1/bin:$PATH
setenv NETCDF_LIB
/usr/local/netcdf-3.6.1/lib
setenv NETCDF_INC
/usr/local/netcdf-3.6.1/include
To activate this immediately, type _source
.cshrc_. In subsequent logins, it_ll automatically read the .cshrc to
modify the PATH (to check, do an _env_ in the command line)
5. You can check to see that netcdf works
by doing a _ncdump_ on a netcdf file.
Install
NCO (netcdf operator)
These contain useful utilities
for netcdf files. Fink carries it, though currently as an unstable
version. (Next line copied from the fink website) _To configure Fink to
use unstable, edit /sw/etc/fink.conf, add unstable/main and unstable/crypto to
the Trees: line, and then run fink selfupdate; fink index; fink
scanpackages_. Afterwards, type _fink install nco_ and follow the
instructions. Note that you will need Xcode installed to compile the
package, and the compilation takes time (allow for an evening, and make sure
you have good internet connection)
Matlab
Installation
1.
Install
X11 BEFORE installing Matlab
2.
If
a previous matlab version is installed, uninstall it. For uninstall
directions, go to http://www.mathworks.com/support/solutions/data/1-19VJS.html?solution=1-19VJS
3.
Install
Matlab disks. You_ll need the current license file for group use (the
installation will ask for it), please ask Charley Paffenbarger for them.
The current MATLAB version is R2006a; you_ll need the appropriate license
version for them.
Matlab
Netcdf Toolbox
1.
Go
to http://mexcdf.sourceforge.net/ and click on _download
instructions_
2.
Download
the SNCTOOLS and netCDF Toolbox. I generally download both even though
they say one is OK. Untar it, and create a subdirectory in your home
directory called Matlab (so: /Users/<yourlogin>/Matlab/). Move the
snctools and netcdf_toolbox subdirectories there.
3.
Download
precompiled MEXNC. Generally, find the latest version for OS X. It
may not be the one for your version of MATLAB, but it should work. Untar,
and then move the subdirectory to /Users/<yourlogin>/Matlab/.
4.
Start
MATLAB, and type _pathtool_. You_ll see a window with a couple of
paths. Click on _Add with Subfolders_ and add the
/Users/<yourlogin>/Matlab/ path into it. Save.
5.
This
should be it!
MATLAB
mapping utility: M_MAP
http://www.eos.ubc.ca/~rich/map.html
See
the website for installation instructions. Basically, you need to get the matlab subroutines and make
sure the path to them is visible to MATLAB.
Grads
This
is a useful mapping program made by COLA/IGES. To install:
1.
Download
the binaries (full distribution) from http://www.iges.org/grads/downloads.html
2.
Untar
– you_ll see a grads folder called grads-xxx (xxx=version)
3.
You
can place this folder anywhere, but I usually move the grads-xxx folder to
/usr/local/.
4.
Modify
the .cshrc file by adding these lines:
setenv
PATH /usr/local/grads-1.9b4/bin:$PATH
setenv
GADDIR /usr/local/grads-1.9b4/data
5.
I_m
also used to calling GRADS by typing _grads_ so I also put an alias in .cshrc:
alias grads gradsnc
6. That should be
it!
Ferret
(suggested by Charlie Koven)
Andy
Jacobson has a version of ferret
for osx.
Latex
(suggested by Charlie Koven)
·
Install
all the latex binaries (either through Fink, or through I-installer. The advantage of I-installer is that it installs the latex
binaries in directories that Texshop and Latex Equation Editor expect; if you
only have the fink version you will have to change the paths in the preferences
boxes of those applications.)
·
Then
get TexShop as a front end.
·
And
get bibdesk for managing your
bibtex database. It does most of
what you’d use Endnote for, and its free.
·
To
avoid powerpoint not displaying equations properly, use Latex Equation Editor
as a substitute for the MS equation editor: it transforms latex code into
either .pdf or .tiff files (which you can put in your powerpoint and trust that
they'll work).
Aquamacs
Emacs (suggested by Charlie Koven)
·
An
aqua-native version of emacs, called aquamacs
emacs. Nicer looking than the X11 version. If you use it, but you want to be able to open documents
from the command line, add the following line to your .cshrc:
alias
emacs "open -a /Applications/Aquamacs\ Emacs.app/ "
iTerm
(suggested by Charlie Koven)
Textwrangler
(suggested by Abby Swann)
a
great free text editor: a quote from their website: “Among other things, it can
open files from (and save them) to remote FTP servers, offers a significantly
more powerful grep engine, supports multi-byte and non-Roman text files, can
perform Find Differences on pairs of files, and can be invoked from the Unix
command line”
http://www.barebones.com/products/textwrangler/