Installing EMAN2.2 on OSX from source with Anaconda
These instructions have been verified to work for several different people on several recent versions of OSX. Strongly encourage using this approach since it is compatible with the new binary approach.
This approach uses a Python distribution called Anaconda for all of the messy dependencies EMAN2 requires, including the Python interpreter itself. In addition, this means that if you want to use EMAN2 from Python with other Python libraries, you have a rich Anaconda environment where you can install any additional packages you like. Anaconda is cross-platform and we have found it to be a MUCH better choice than Mac-specific package managers like MacPorts.
PLEASE report any problems or update the page!
Completely remove any previous eman2 source folders, and check out a fresh copy of the source from GitHub:
mkdir src cd src git clone https://github.com/cryoem/eman2.git
Note: on the Mac it is important that you not clone eman2 directly into your home directory, since Mac filenames are normally not case-sensitive. EMAN2 is normally installed in $HOME/EMAN2. If you clone from GitHub into your home folder then $HOME/eman2 will also become the installation folder, and things will be hopelessly confused!
Install current Python2.x Anaconda from https://www.continuum.io/downloads (remember EMAN is Python2 not Python3).
- Download the command-line installer, not the graphical installer, since this gives you a choice of where to put the installed folder.
- Install Anaconda to $HOME/anaconda2
- If you use a different location, you will need to update that in all of the subsequent instructions.
- XCode is required!
If you can successfully run g++ --version from the command line, you should be all set and can skip to the next step.
- XCode is free and available from the App Store. It includes the command-line C++ compiler for the Mac.
- The first time you ever try and use the C++ compiler from the command-line it will complain if you have not run the XCode GUI, since it requires a click-through user agreement.
You may need to download additional tools from within XCode to get the command-line compiler working. See: http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/
- configure account to use this anaconda. I have a "useconda2" alias which does this (I just reset the entire PATH to avoid building up redundancies):
useconda2='export PYTHONPATH=$HOME/EMAN2/lib:$HOME/EMAN2/bin; export EMAN2DIR=$HOME/EMAN2; 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. 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=4and a couple are from other channels, eg:
conda install -c conda-forge boost boost-cpp fftw conda install -c cryoem ftglThe rest:
conda install bsddb freetype gsl hdf5 ipython jpeg libpng libtiff matplotlib numpy=1.11 pyopengl=3.0 scikit-learn scipy theano tk cmake openmpi
- Once all of this is done you're ready to start building:
cd (wherever you checked out the eman2 source) ccmake . c
- You can probably ignore any warnings you see at this point.
- CMake should find everything automatically, as long as you put a directory called anaconda2 in your home directory or in $HOME/EMAN2.
- If you put anaconda somewhere else, you will need to manually configure a bunch of locations. See troubleshooting below for tips.
Once the options are set as you like them. Press g to generate all of the makefiles
Again, ignore warnings for now, then from the command line: make -j4 (you can replace 4 with the number of cores on your machine)
If everything works, do a make install and you're done
If you get errors in compilation, you may want to run make again without the -j4 to more easily see the error messages. If you get errors you can't figure out, report them to the mailing list for help.
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.
Here is the list of anaconda packages (installed above) with versions known to work in Feb, 2017. If you are having problems, you can do a conda list and check for these:
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
If you are having ccmake configuration issues, here is the list of the relevant options from my configuration. Clearly you will need to adjust these for your own account name:
EMAN_INSTALL_PREFIX:PATH=/Users/stevel/EMAN2 ENABLE_DEBUG:BOOL=OFF ENABLE_DJBFFT:BOOL=OFF ENABLE_EMAN_CUDA:BOOL=OFF ENABLE_FFTW2:BOOL=OFF ENABLE_FFTW3:BOOL=ON ENABLE_FFTW_PLAN_CACHING:BOOL=ON ENABLE_FFT_CACHING:BOOL=OFF ENABLE_FTGL:BOOL=ON ENABLE_HDF5:BOOL=ON ENABLE_IOCACHE:BOOL=OFF ENABLE_JPEG:BOOL=ON ENABLE_MEMDEBUG:BOOL=OFF ENABLE_MEMDEBUG2:BOOL=OFF ENABLE_NATIVE_FFT:BOOL=OFF ENABLE_NFFT2:BOOL=OFF ENABLE_OPENGL:BOOL=ON ENABLE_OPTIMIZE_MACHINE:BOOL=OFF ENABLE_OPTIMIZE_MOUNTAIN_LION:BOOL=ON ENABLE_OPTIMIZE_PHI:BOOL=OFF ENABLE_OPTIMIZE_WINDOWS_VC:BOOL=OFF ENABLE_OPTIMIZE_X86_64:BOOL=OFF ENABLE_OPTPP:BOOL=OFF ENABLE_PNG:BOOL=ON ENABLE_PROFILE:BOOL=OFF ENABLE_RT:BOOL=ON ENABLE_SPARX_CUDA:BOOL=OFF ENABLE_STATIC_FTGL:BOOL=OFF ENABLE_TAO:BOOL=OFF ENABLE_TIFF:BOOL=ON BOOST_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include BOOST_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libboost_python.dylib FFTW3_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include FFTW3_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfftw3f.dylib FFTW3d_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include FFTW3d_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfftw3.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.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