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| 1. Install FFTW from source. Compile both normal (double) and --enable-single. This requires running ''configure'' and ''make install'' twice. While there are a dozen different versions available from anaconda, I didn't want to try and find one that had the necessary versions, so I just built it. If someone figures out one that works, let me know. You will also need --enable-shared and I used --prefix=$HOME (so you don't have to deal with the Mac's annoying security subsystem). | |
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| 1. Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. Unfortunately, since the current CMakeLists file doesn't search anaconda at the moment, this is a manual process: | 1. Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. CMake should find everything automatically with 3 exceptions, as long as you put a directory called anaconda2 in your home directory. Replace $HOME below with your actual home directory: |
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| BOOST_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/boost BOOST_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libboost_python.dylib FREETYPE_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/freetype2 FREETYPE_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfreetype.dylib FTGL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include FTGL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libftgl.2.dylib GSL_CBLAS_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include GSL_CBLAS_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgslcblas.dylib GSL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include GSL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgsl.dylib HDF5_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include HDF5_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libhdf5.dylib JPEG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include JPEG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libjpeg.dylib NUMPY_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/lib/python2.7/site-packages/numpy/core/include PNG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include PNG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpng.dylib PYTHON_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/python2.7 PYTHON_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpython2.7.dylib TIFF_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include TIFF_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libtiff.dylib ZLIB_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libz.dylib FFTW3_INCLUDE_PATH:PATH=/Users/stevel/include FFTW3_LIBRARY:FILEPATH=/Users/stevel/lib/libfftw3f.dylib FFTW3d_INCLUDE_PATH:PATH=/Users/stevel/include FFTW3d_LIBRARY:FILEPATH=/Users/stevel/lib/libfftw3.dylib |
PYTHON_INCLUDE_PATH:PATH=$HOME/anaconda2/include/python2.7 PYTHON_LIBRARY:FILEPATH=$HOME/anaconda2/lib/libpython2.7.dylib ZLIB_LIBRARY:FILEPATH=$HOME/anaconda2/lib/libz.dylib |
Installing EMAN2.2 on OSX with Anaconda
These instructions worked for me on Sierra (10.12). I expect they would also work on versions back several years, but cannot guarantee it.
PLEASE report any problems or update the page!
Install current Python2.x Anaconda from https://www.continuum.io/downloads (remember EMAN is Python2 not Python3). When installing put anaconda in your home directory and name it 'anaconda2'.
- Obviously you will need to have XCode installed on your Mac as well
- configure account to use this anaconda. I have a "useconda2" command which does this (I just reset the entire PATH to avoid building up redundancies):
useconda2='export PYTHONPATH=$HOME/EMAN2/lib:$HOME/EMAN2/bin; export PATH=$HOME/anaconda2/bin:$HOME/EMAN2/bin:.:$HOME/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Developer/usr/bin:/Applications/Chimera.app/Contents/MacOS'
- Install other necessary Anaconda modules (conda install). This includes specific versions for a few. I don't recall how many of these were already installed and how many I had to do. Note that some need a specific version, eg:
conda install qt=4 pyqt=4
and a couple are from other channels, eg:conda install -c conda-forge boost boost-cpp fftw conda install -c jmbell ftgl
The rest:conda install bsddb freetype gsl hdf5 ipython jpeg libpng libtiff matplotlib numpy=1.11 pyopengl scikit-learn scipy theano tk cmake
Here is the list of packages (installed above) with versions known to work in Feb, 2017. You shouldn't need to do anything with this, if you installed above:boost 1.63.0 py27_4 conda-forge boost-cpp 1.63.0 1 conda-forge fftw 3.3.5 0 conda-forge bsddb 1.0 py27_1 cmake 3.6.3 0 freetype 2.5.5 2 ftgl 2.1.3 2 jmbell gsl 2.2.1 0 hdf5 1.8.17 1 ipython 5.1.0 py27_0 ipython_genutils 0.1.0 py27_0 jpeg 9b 0 libpng 1.6.27 0 libtiff 4.0.6 3 matplotlib 1.5.3 np111py27_0 numpy 1.11.1 py27_0 pyopengl 3.0.2 py27_0 pyqt 4.11.4 py27_4 qt 4.8.7 4 scikit-learn 0.17.1 np111py27_2 scipy 0.18.1 np111py27_0 theano 0.8.2 py27_0 tk 8.5.18 0
- Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. CMake should find everything automatically with 3 exceptions, as long as you put a directory called anaconda2 in your home directory. Replace $HOME below with your actual home directory:
PYTHON_INCLUDE_PATH:PATH=$HOME/anaconda2/include/python2.7 PYTHON_LIBRARY:FILEPATH=$HOME/anaconda2/lib/libpython2.7.dylib ZLIB_LIBRARY:FILEPATH=$HOME/anaconda2/lib/libz.dylib
Once this was done (it really didn't take very long to do), everything works for me, including the GUI. While I haven't tested absolutely everything, I did go through a lot of the tutorial and everything seemed fine.