64-bit Fink for 10.8
From OS X Scientific Computing
Contents |
Upgrading from a 10.7 Fink install?
You don't have to do much, except issue
fink selfupdate
Make sure you have the 10.8 Xcode developer tools and the latest X11 installed (see Quick Start ).
If you are using my pre-compiled debian distribution, please issue the command
sudo perl -pi -e 's|10.7|10.8|g' /sw/etc/apt/sources.list
to enable use of the most current repository. I took the 10.7 repository off line (since I upgraded to 10.8, I have no way to maintain it).
Easy Quick Option: Jump-Start Install for 10.8 (and 10.7)
- Please refer to these "install What I Have" instructions.
- Install Xcode for 10.8/10.7 if you haven't yet done so.
- Then all you have to do (if you should so choose) is use my pre-compiled fink packages.
If you did this, no need to do anything else below. You are done!
Other Option: Bootstrap Install from sourcecode for greater control
You should install a 64-bit fink into /sw if you want to use any pre-compiled repositories (mine, or fink's).
How to Bootstrap-Install Fink-64bit
In a bash or zsh shell, issue the command
cvs -d:pserver:anonymous@fink.cvs.sourceforge.net:/cvsroot/fink login [just hit return when prompted for password]
cvs -z3 -d:pserver:anonymous@fink.cvs.sourceforge.net:/cvsroot/fink co -P fink
Then do
cd fink ; ./bootstrap /sw
The bootstrap configuration will ask you two questions that you must answer in the following way.
Pay attention, because the answer to the second question is NOT the default!
Fink must be installed and run with superuser (root) privileges. Fink can automatically try to become root when it's run from a user account. Since you're currently running this script as a normal user, the method you choose will also be used immediately for this script. Avaliable methods: (1) Use sudo (2) Use su (3) None, fink must be run as root Choose a method: [1] Your hardware is a 64bit-compatible intel processor, so you have the option of running Fink in 64bit-only mode. This is not recommended for most users, since many more packages are available for the default mode (which is mostly 32bit but includes some 64bit packages). Which mode would you like to use? (1) Default (mostly 32bit) (2) 64bit-only Choose a mode: [1] 2
When it is done, edit /sw/etc/fink.conf and change line 4 to look like this:
Trees: local/main stable/main stable/crypto
(Note that there is currently no unstable branch in 10.7, and it is being phased out for the earlier versions.)
Then issue
source /sw/bin/init.sh fink selfupdate-cvs fink -y update-all fink scanpackages
Install x86_64 versions of crystallography software
The normal, official Fink way is to compile everything yourself. If you are in a hurry, you might find it easier to use my unofficial pre-compiled Fink binary distribution.
Using my Pre-Compiled Fink Packages
For 10.8.X: If you put fink into /sw
First you need to edit the /sw/etc/apt/sources.list file and add the following line to the bottom of that file:
deb http://psbmini.ucsc.edu/fink_intel_10.8_64bit_sw stable main
That's all you need, but more detailed information is located here: Getting your fink installation to use packages that I have pre-compiled
Now you can install fink packages that I have pre-compiled using the apt-get command. Here is an example for installing coot:
fink scanpackages sudo apt-get update sudo apt-get dist-upgrade sudo apt-get install coot
Compiling it with Fink
This is the official Fink-approved way to do it:
To install coot, issue
source /sw/bin/init.sh fink install coot
To install ccp4, issue
source /sw/bin/init.sh fink install ccp4
You, or your shell startup files, need to issue
source /sw/bin/init.sh
before running these programs, or
source /sw/bin/init.csh
if you are a tcsh user.
