Installation on a Mac OS X

Table of Contents

• Installation on a Mac OS X

Installation notes

MacPorts

Homebrew

Which one ? Installation using MacPort

Installation on Mac OS X 10.10 Yosemite

Installation on Mac OS X 10.9 Mavericks

Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion Installation using Homebrew

Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion Installation on Mac OS X 10.6 Snow Leopard Installation on older Mac OS X Version Uninstalling OpenAlea Note for developpers Note for Python Scientists

Installation on a Mac OS X

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Installation notes

OpenAlea installation is done in two steps. install all dependencies required by OpenAlea as described in this page once dependencies installed, install OpenAlea as described in Building and Installing OpenAlea

To install dependencies on Mac OS X, openalea can rely on two package managers, namely Homebrew and Macports.

MacPorts

MacPorts is a standard Mac OS X tool to facilitate the process of installation of 3rd party programs and libraries. Please follow the instructions on MacPorts webpage to correctly install and setup MacPort installation.

Using MacPorts facilitates the process of installation of Openalea dependencies. Please be patient during the process, since some packages have to be compiled by MacPorts.

Install MacPorts To install OpenAlea dependencies with Macports, please have a look to section corresponding to your Mac OS X version (see for instance 10.9) MacPorts is recommend system. Documentation for homebrew is not officialy maintained and so can be outdated

Homebrew

Homebrew is a package management system that simplifies the installation of software on the Mac OS X operating system. It is a free/open source software project to simplify installation of other free/open source software. It is similar in aim and function to MacPorts and Fink (ref: wikipedia)

For the installation, follow these 3 steps:

Uninstall MacPorts if exists Install Homebrew To install OpenAlea dependencies with Homebrew, please have a look to section corresponding to your Mac OS X version (see for instance 10.9)

Which one ?

Using MacPorts or Homebrew for Openalea installation is not required, but strongly recommended. Both can be used, so choose the one you prefer but use only one !

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Installation using MacPort

Installation on Mac OS X 10.10 Yosemite

Because Mac OS X 10.10 is very young, these instructions will certainly change.

See installation for Mac OS X 10.9. Main changes is the renaming of the py27-pil module in py27-Pillow by MacPort.

3/15 sudo port install py27-Pillow

Installation on Mac OS X 10.9 Mavericks

Openalea works well on OS X 10.9 but several VPlant packages are not yet available. We are working on it to provide full support as soon as possible.

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If macport can't install py27-PyQGLViewer, install pyqglviewer from sources.

First download http://gforge.inria.fr/frs/download.php/file/34636/PyQGLViewer-0.13.tgz

Then unzip the file.

In the repertory PyQGLViewer: python configure.py make [ sudo ] make install

Install OpenAlea from sources

If it is not done automatically, update the PATH export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/ 2.7 /bin:$PATH

In OpenAlea and VPlants source directory, if exists, rename options_macports.py to options.py. If you work on image processing, you should install these libraries sudo port install tiff

# pylibtiff to read/write tiff images svn checkout https://pylibtiff.googlecode.com/svn/trunk/ pylibtiff-read-only cd pylibtiff-read-only python setup.py install cd -

# pyLSM to read lsm files easy_install pylsm

# Scikit-learn sudo port install py-scikit-learn

# Vtk only

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An upgrade of macport can cause a segmentation fault at the execution of openalealab and lpy, probably because boost has been compiled with a different compiler. To ensure that the same compiler is used everywhere, compile boost from sources (macport with -s option) and recompile both vplants and openalea: sudo port -s install boost

Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion

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Install OpenAlea from sources

Update the PATH export PATH=/opt/local/Library/Frameworks/Python.framework/Versions/ 2.7 /bin:$PATH

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Installation using Homebrew

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Update your paths to be able to run programs installed from Homebrew directly. Copy/paste this line at the end of your ~/.profile or ~/.bash_profile if it exists. export PATH=/usr/local/bin:$PATH Install Python :

# set up some taps and update brew brew tap homebrew/science # a lot of cool formulae for scientific tools brew tap homebrew/python # numpy, scipy brew update && brew upgrade

# install a brewed python brew install python pip install --upgrade setuptools pip install --upgrade pip brew linkapps Install dependencies

# Install Qt and PyQt brew install qt --with-d-bus --with-qt3support brew install sip pyqt

# install PIL, imagemagick, graphviz and other # image generating stuff (qt is nice for viewing) brew install imagemagick graphviz brew install freetype ln -s /usr/local/include/freetype2 /usr/local/include/freetype brew install pillow brew install matplotlib

# Useful python libraries pip install nose sphinx pyparsing dateutils pip install python-dateutil

6/15 #install scipy and numpy : brew install scipy

# Ann brew install https://raw.github.com/gag/homebrew-science/master/ann.rb

# ipython and notebook support brew install zmq pip install ipython[all]

# OpenAlea Dependencies brew install gnuplot pip install pyopengl pip install scikit-learn

# Install Boost.Python brew install boost brew install boost-python brew install homebrew/science/qhull brew install cgal eigen

# Install PyQGLViewer brew install qscintilla2 brew install https://raw.github.com/gbaty/homebrew-formula/master/pyqglviewer.rb sudo ln -s "/usr/local/Cellar/libqglviewer/2.5.1/QGLViewer.framework" "/Library/Frameworks/QGLViewer.framework" ln -s /usr/local/Cellar/libqglviewer/2.5.1/QGLViewer.framework /usr/local/ Frameworks/QGLViewer.framework

# Bison/Flex brew install bison brew install flex

brew install scons If you work on image processing, you should install these libraries brew install libtiff libpng giflib

# pylibtiff to read/write tiff images svn checkout https://pylibtiff.googlecode.com/svn/trunk/ pylibtiff-read-only cd pylibtiff-read-only python setup.py install cd -

# pyLSM to read lsm files pip install http://launchpad.net/pylsm/trunk/ 0.1 /+download/pylsm-0.1-r34.orig.tar.gz

# Scikit-learn pip install scikit-learn

# Vtk only brew install vtk --with-qt --with-python --with-pyqt

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All dependencies are now installed. You can now download OpenAlea, Vplant and ALinea sources. Then if downloaded from archives, decompress it. Finally go into source directory. In OpenAlea and VPlants source directory, if exists, rename options_brew_maverick.py to options.py.

If you have an error with libJPEG (and/or libTIFF, libPng, libGIF, ?) add to your ~/.profile:

IMGLIBS=/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ ImageIO.framework/Versions/A/Resources/ export DYLD_INSERT_LIBRARIES=$IMGLIBS /libJPEG.dylib:$IMGLIBS /libTIFF.dylib:$IMGLIBS / libPng.dylib:$IMGLIBS /libGIF.dylib

Installation on Mac OS X 10.7 Lion and 10.8 Mountain Lion

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Update your paths to be able to run programs installed from Homebrew directly. Copy/paste this line at the end of your ~/.profile. export PATH=/usr/local/bin:$PATH export PYTHONPATH=$HOME/local/lib/python2.7/site-packages:/usr/local/lib/ python2.7/site-packages/:$PYTHONPATH Then install Python

# set up some taps and update brew brew tap homebrew/science # a lot of cool formulae for scientific tools brew tap homebrew/python # numpy, scipy brew update && brew upgrade

# install a brewed python brew install python

# Install Qt and PyQt brew install qt --with-qt3support brew install sip pyqt

# install PIL, imagemagick, graphviz and other # image generating stuff (qt is nice for viewing) brew install imagemagick graphviz pip install pillow pip install nose sphinx pyparsing dateutils

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# install numpy and scipy

# install openblas (otherwise scipy's arpack tests will fail) brew install openblas brew install numpy --with-openblas brew install scipy --with-openblas

# If openblas doesn't compile : brew install numpy brew install scipy brew install ann brew install matplotlib

# ipython and notebook support brew install zmq pip install ipython[all]

# OpenAlea Dependencies brew install gnuplot pip install pyopengl

# Install Boost.Python brew install boost --build-from-source #option required for boost/python brew install qhull brew install cgal eigen

# Install PyQGLViewer brew install qscintilla2 brew install https://raw.github.com/pradal/homebrew/master/Library/Formula/ libqglviewer.rb brew install https://raw.github.com/pradal/homebrew/master/Library/Formula/ pyqglviewer.rb brew install scons If you have an error with libJPEG (and/or libTIFF, libPng, libGIF, ?) add to your ~/.profile:

IMGLIBS=/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ Frameworks/ImageIO.framework/Versions/A/Resources/ export DYLD_INSERT_LIBRARIES=$IMGLIBS/libJPEG.dylib:$IMGLIBS/libTIFF.dylib: $IMGLIBS/libPng.dylib:$IMGLIBS/libGIF.dylib

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Installation on Mac OS X 10.6 Snow Leopard

See Installation on a Mac OS X Snow Leopard

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Installation on older Mac OS X Version

Manuall Installation on old Mac OS X

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11/15 Uninstalling OpenAlea

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To uninstall OpenAlea, remove OpenAlea and all the config files rm ~/.pydistutils.cfg # if this file exists sudo vi /etc/bashrc # remove the line source ~/.openalea.sh if it exists # modify the ~/.profile # Remove all the eggs # Remove all the shared libraries

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Note for developpers

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If you happen to be a developer, please consider extending the Automated Dependency Builder to support Mac Os X.

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Note for Python Scientists Click to display ?

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Install Python 2.7 with HomeBrew Install scientific python stack (numpy, scipy, matplotlib): http://www.lowindata.com/2013/installing-scientific-python-on-mac-os-x http://joernhees.de/blog/2013/06/08/mac-os-x-10-8-scientific-python-with-homebrew/ edit 1426868450 [Note for Python Scientists]section 12834-

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