Installation mac
Contents
Installing the relax dependencies
The python-devel and scons packages are only required if the C modules need to be compiled for your system.
The Grace software is used for visualisation of 2D data sets.
The official way
The most reliable way to install relax on your system is to use the official Python releases. The steps are:
Python
First check if you have the latest Python 2.7 installed, before installing the newest. Search in Spotlight for Terminal, and write here
which python
python --version
If needed, download the latest 2.7 version from the Official Python website.
This should be the DMG file labelled as Python 2.7.x Mac OS X 64-bit/32-bit x86-64/i386 Installer (for Mac OS X 10.6 and later).
Open the DMG file, double click on the Python.mpkg file, and follow the instructions.
The Python binary should now be located at /usr/local/bin/python. This is actually a symbolic link pointing to /Library/Frameworks/Python.framework/Versions/2.7/bin/python.
Check out a relax branch
You can see the different relax branches here.. Subversion is necessary, and should be shipped with [ http://subversion.apache.org/packages.html#osx OS X].
which svn
svn --version
cd $HOME/Downloads
To check out the relax_disp or trunk branch using the subversion client, simply type:
svn co svn://svn.gna.org/svn/relax/trunk relax_trunk
svn co svn://svn.gna.org/svn/relax/branches/relax_disp relax_disp
If this svn command does not work, try:
svn co http://svn.gna.org/svn/relax/trunk relax_trunk
svn co http://svn.gna.org/svn/relax/branches/relax_disp relax_disp
SCons - building relax
This is required to build the relax C modules. Download the file form the SCons download site.
- Download the file called scons-2.x.x.tar.gz.
- Open this through the Finder to unpackage the archive into the ~/Downloads/scons-2.x.x/ directory.
- Open a terminal and type, replacing the x's with the current version, the following to get into the correct directory:
- Download the file called scons-2.x.x.tar.gz.
cd $HOME/Downloads/scons-2.x.x
Then compile by:
sudo python setup.py install
If you have several Python versions, then compile with the wished python interpreter by typing:
sudo /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install
This should install scons into /usr/local/bin/scons.
which scons
First try to build relax
To compile the C modules in relax, several packages must be in place, including the minfx package.
But we can just try to build relax now, and then solve the dependencies.
cd $HOME/Downloads/relax_trunk
# See bug: https://gna.org/bugs/index.php?22052
sed -i "" "s/archs = \['i386', 'ppc', 'x86\_64']/archs = \['i386', 'x86\_64'\]/g" sconstruct
# Then build
scons
You should get the message: The dependency 'minfx' has not been installed
Minfx and Bmrblib
Remember to check, if there are newer versions of minfx and bmrblib.
The minfx and bmrblib libraries can be installed on all Linux systems by typing:
cd $HOME/Downloads
curl http://download.gna.org/minfx/minfx-1.0.7.tar.gz -o minfx-1.0.7.tar.gz
tar -xzf minfx-1.0.7.tar.gz
cd minfx-1.0.6
sudo pip install -e .
cd ..
curl http://download.gna.org/bmrblib/bmrblib-1.0.3.tar.gz -o bmrblib-1.0.3.tar.gz
tar -xzf bmrblib-1.0.3.tar.gz
cd bmrblib-1.0.3
sudo pip install -e .
cd ..
Let's try to build again
cd $HOME/Downloads/relax_trunk
scons
If you get the message -bash: gcc: command not found, you need to install Apple Xcode.
Numpy
First check if you have numpy installed in the current python installation.
python
import numpy
numpy.__version__; numpy.__file__
# Exit python with: Ctrl+d
If needed, download the latest Numpy DMG file from the sourceforge download site.
This should be the DMG file numpy-1.x.x-py2.7-python.org-macosx10.x.dmg.
Open the DMG file, double click on the numpy-1.x.x-py2.7.mpkg file, and follow the instructions.
Scipy
First check if you have scipy installed in the current python installation.
python
import scipy
scipy.__version__; scipy.__file__
# Exit python with: Ctrl+d
If needed, download the latest Scipy DMG file from the sourceforge download site.
This should be the DMG file scipy-0.xx.x-py2.7-python.org-macosx10.3.dmg.
Open the DMG file, double click on the scipy-0.xx.x-py2.7.mpkg file or equivalent, and follow the instructions.
wxPython
First check if you have wxPzthon installed in the current python installation.
python
import wx
wx.__version__; wx.__file__
# Exit python with: Ctrl+d
If needed, download the wxPython Development 2.9 DMG file from the official wxPython website.
The link should be called wxPython2.9-osx-cocoa-py2.7.
Open the DMG file, double click on the wxPython2.9-osx-cocoa-py2.7.pkg file, and follow the instructions.
Mpi4py
This is for running on multi-processor machines, for the analyses in relax which support it. Download the file from the mpi4py download site.
Note, this will require an up to date version of XCode installed on your system, as the code will be compiled.
Download the file labelled as mpi4py-1.x.x.tar.gz.
Open this through the Finder to unpackage the archive into the ~/Downloads/mpi4py-1.x.x/ directory.
Open a terminal and type, replacing the x's with the current version, the following to get into the correct directory:
$ cd ~/Downloads/mpi4py-1.x.x
Then to be sure the correct Python version is being used, type:
$ sudo /Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install
Use of repositories
macports
Not explained yet. Please provide your solution, if you know it.
fink
Not explained yet. Please provide your solution, if you know it
homebrew
See this email thread.
Download and install Apple's Xcode. Install the "Command Line Tools" from inside Xcode. Install Homebrew by typing into your Terminal:
ruby -e "$(curl -fsSkL raw.github.com/mxcl/homebrew/go)"
Install python 2.7 including pip package manager, scons for relaxation compiling and wxPython for a native Mac GUI:
brew install python scons wxmac
Install numpy via pip (don't install scipy, as it causes problems with scons!)
pip install numpy
Minfx and Bmrblib
Remember to check if there are newer versions of minfx and bmrblib.
The minfx and bmrblib libraries can be installed on all Linux systems by typing:
wget http://download.gna.org/minfx/minfx-1.0.5.tar.gz
tar -xzf minfx-1.0.5.tar.gz
cd minfx-1.0.5
python setup.py install
cd ..
wget http://download.gna.org/bmrblib/bmrblib-1.0.3.tar.gz
tar -xzf bmrblib-1.0.3.tar.gz
cd bmrblib-1.0.3
python setup.py install
cd ..
Note that if you have multiple Python versions, the correct one must be specified. It is best to use the full Python path, for example:
/Library/Frameworks/Python.framework/Versions/2.7/bin/python setup.py install
Testing the Python installation
Before installing relax, it is best to be sure that the Python modules are functional by importing them:
$ python
Python 2.6.6 (r266:84292, Oct 12 2012, 14:23:48)
[GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2
>>> import wx
>>> wx.__version__; wx.__file__
'...'
>>> import bmrblib
>>> bmrblib.__version__; bmrblib.__file__
'...'
>>> import minfx
>>> minfx.__version__; minfx.__file__
'...'
Checking out a relax branch
If you would like to play with relax branch rather than the main relax downloads, the Subversion program should first be installed.
You can see the different branches here.
First the relax sources can be checked out of the source code repository and the C modules compiled:
cd /usr/local/
svn co svn://svn.gna.org/svn/relax/branches/relax_disp relax_disp
cd relax_disp
# See bug: https://gna.org/bugs/index.php?22052
sed -i "" "s/archs = \['i386', 'ppc', 'x86\_64']/archs = \['x86\_64'\]/g" sconstruct
# Then build
scons
# Optional building of the user manual, if a LaTeX installation is available.
scons user_manual_pdf
If the svn command does not work, try:
svn co http://svn.gna.org/svn/relax/branches/relax_disp relax_disp
Add relax to path
cd /usr/local/bin
ln -s /usr/local/relax_disp/relax .
Restart the terminal, to load the new variables.
Start relax in GUI mode
relax -g
TEST INSTALLATION
After an installation you should really run an Installation_test
Trouble shooting
Multiple Python versions
For more details, see Multiple Python versions.
You will need to check that the correct Python and SCons versions are used when running relax or compiling the C modules. This can be checked by typing the following:
$ sudo /usr/libexec/locate.updatedb
$ which python
$ locate python | grep '\/python$\|\/python...$' | grep bin | xargs ls -alh
$ which scons
$ locate scons | grep '\/scons$' | grep bin | xargs ls -alh
The first command updates the locate database, the which commands show which version of Python and SCons will be executed if python or scons are typed at the prompt, and the locate commands will show all installed versions of Python and SCons.
You may still have 'minfx' installation problems when compiling the C modules if multiple Python version are present.
So it is recommended to open the /usr/local/bin/scons file and change the first line from /usr/bin/env python to /usr/local/bin/python so that the correct Python version is used.
Alternatively you change your PATH environmental variable to have /usr/local/bin/ at the start. SCons is always an issue when multiple Python versions are installed.
