Compiling EMAN2 on Mac OS X with Homebrew
Contents
Homebrew is a package management system for Mac. It is under active development and has strict policies to protect the user from damage via software. They also seek to protect users from themselves by avoiding sudo commands as much as possible. It is recommended that you do NOT install homebrew alongside other package managers such as macports/fink.
The following install was successful on OS X 10.8 (Mountain Lion) and OS X 10.10 (Yosemite) and 10.11 (El Capitan). If for any reason this doesn't work for you, I recommend refreshing your terminal (1st) and restarting your computer (2nd) since many of the packages downloaded might require sourcing. If neither solve your specific problem, please send an e-mail to a member of the lab and we'll try to address it as soon as possible. Also, it may be necessary to turn off SIP (System Integrity Protection) before proceeding when installing on El Capitan. To do this, reboot your machine while holding [CMD]+[R], open a terminal from the utilities menu at the top of the screen, type "csrutil disable", hit enter, type reboot, and hit enter to restart with SIP disabled.
Additionally, a known problem of using pure homebrew is that Qt windows seem to possess abnormally large buttons. A way around this is to install Qt/PyQt from source.
Install homebrew
To install homebrew, simply paste the following line into your favorite Mac terminal emulator:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
To make sure everything is up to date, run:
brew update
To make sure everything is configured correctly, run the following command, addressing any warnings or errors before proceeding. Most of the warnings can be ignored, but for the smoothest install, it is better to address them sooner rather than later.
brew doctor
Additionally, add the following to your shell's 'rc' file to source homebrew programs ahead of the system's default versions:
export PATH=/usr/local/bin:$PATH
If you find you have already completed these instructions but are upgrading from OS X 10.8, 10.9, or 10.10, you will need to reinstall all homebrew packages or start from scratch. Luckily, there is an easy way to do the former:
brew list | xargs brew reinstall -v
This should reinstall all packages in their current versions.
Required Packages
Xcode
Starting with Mac OS X 10.7 and Xcode 4.3, the developer tools are distributed through the Mac App Store instead of an installer package.
You'll also need the command line tools, which you can install with:
xcode-select --install
CMake
CMake is a family of tools designed to build, test and package software. It is used to generate the Makefiles for compiling EMAN2. We install the homebrew version as follows:
brew install cmake
Qt4
Qt is a graphics library for cross-platform user interfaces.
brew install qt --with-developer --with-docs --HEAD
Boost
Boost is a set of useful, standardized libraries for C++. It is used to generate the Python-C++ interface in EMAN2. Homebrew comes with two 'boost' packages, and we'll need both to generate the libraries required for compiling EMAN2:
brew install boost --with-python brew install boost-python
To install with MPI support, simply run the following commands instead:
brew install boost --with-mpi --with-python brew install boost-python
GSL
The GNU Scientific Library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
brew install gsl
A personal concern is that there is no option to '--enable-float'; however, I have not run into any problems with this yet.
FFTW3
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). The most recent version is available from homebrew as follows:
brew install fftw
Berkeley DB (5.3.28)
The Oracle Berkeley DB family of open source, embeddable databases provides developers with fast, reliable, local persistence with zero administration. EMAN2 uses Berkeley DB as a mechanism for local storage of project metadata.
Oracle has made their most recent version very VERY proprietary. To install BDB, you need an account on the following website at which you can download BDB 5.3.28.
Once there, download "Berkeley_DB_5.3.28.tar.gz," then enter the following commands where you placed the download (preferably your source code directory).
tar -xzf db-5.3.28 cd db-5.3.28/build_unix ../../dist/configure make sudo make install
If you encounter errors during this process, I suggest trying the following:
cd db-5.3.28 cd src/dbinc curl -O https://raw.githubusercontent.com/narkoleptik/os-x-berkeleydb-patch/master/atomic.patch patch atomic.h < atomic.patch cd ../../build_unix ../dist/configure make sudo make install
Freetype and libPNG
On Mac OS X 10.8 and later, X11 and Freetype are no longer included by default. Even if you are using an earlier Mac OS X, I recommend installing your own Freetype. Homebrew offers the most recent version of freetype, but we'll need to explicitly include it in our configuration step later on.
brew install freetype
The PNG (Portal Network Graphics) format provides lossless-compressed image support. Although homebrew installs libpng as a dependency for freetype, it can be installed independently using the following command
brew install libpng
FTGL
FTGL is a free, open source library to enable developers to use arbitrary fonts in their OpenGL applications. We can install it as follows:
brew install ftgl
HDF5
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
brew tap homebrew/science brew install hdf5
SIP
Python's SIP (not to be confused with Mac OS X's SIP) is a tool that makes it very easy to create Python bindings for C and C++ libraries. It was originally developed to create PyQt, the Python bindings for the Qt toolkit, but can be used to create bindings for any C or C++ library.
brew install sip
PyQt4
PyQt4 provides Python bindings for Qt4. This software underlies every EMAN2 GUI application.
brew install pyqt
Required Python Modules
PIP
Pip is a package manager for python. To install it, use the system's own "easy_install" program
easy_install pip
Numpy
Numpy is an array manipulation package for python. To install, run
pip install numpy --upgrade
bsddb3
bsddb3 provides Python bindings for the Berkeley DB API.
Having previously defined the BERKELEYDB_DIR environment variable, we can install bsddb3 with pip very easily:
pip install bsddb3
PyOpenGL
PyOpenGL provides Python bindings for OpenGL. There is a pip package for it, available here, along with an acceleration package for optimization of certain graphics routines.
pip install PyOpenGL PyOpenGL-accelerate
IPython
IPython provides a rich toolkit to help you make the most out of using Python interactively. EMAN2 uses iPython for the "e2.py" interactive interpreter environment.
pip install ipython
Matplotlib
Matplotlib is a python 2D and 3D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments. It can be installed with the following line:
pip install matplotlib
For examples and inspiration, see: http://matplotlib.org/gallery.html
Readline
pip install gnureadline
Optional (Recommended) Packages
Readline
Readline facilitates command history parsing in python.
brew install readline
JPEG
Jpeg is a library for writing JPEG image files.
brew install jpeg
TIFF
Libtiff is a library for reading and writing TIFF image files.
brew install libtiff
For EMAN2 Developers
If you spend a lot of time developing EMAN2, you will likely want these packages
brew install git cvs doxygen gnu-indent cscope
Excellent documentation for GIT is available at: https://www.atlassian.com/git/
Cleaning up
Cleaning things up and ensuring that everything has been installed properly, run:
brew linkapps brew cleanup brew doctor
Most warnings observed when running 'brew doctor' are harmless, especially if you don't use homebrew extensively. Unless problems arise later on, we recommend ignoring them.
The QUICK version
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" brew update && brew doctor brew install qt --with-developer --with-docs --HEAD brew install cmake boost boost-python ftgl freetype readline sip pyqt brew tap homebrew/science && brew install hdf5 jpeg libtiff fftw gsl brew install git cvs doxygen gnu-indent cscope brew linkapps && brew cleanup && brew doctor sudo easy_install pip sudo -H pip install “ipython[all]” matplotlib spicy numpy gnureadline —upgrade sudo -H pip install PyOpenGL PyOpenGL-accelerate --upgrade
Download Berkeley DB 5.3.28.tar.gz (instructions above)
tar -xf db-5.3.28 cd db-5.3.28 cd src/dbinc curl -O https://raw.githubusercontent.com/narkoleptik/os-x-berkeleydb-patch/master/atomic.patch patch atomic.h < atomic.patch cd ../../build_unix ../dist/configure make sudo make install sudo -H pip install bsddb3 --upgrade
Get EMAN2 source code
EMAN2 is now hosted on GitHub. Here is a direct link to dowload the source. Just hit the "clone or download" button:
https://github.com/cryoem/eman2
Configure EMAN2
1. Go to 'build' and type
ccmake ../eman2
2. Link all libraries properly.
When using Homebrew, this phase takes a little more care to get right. I suggest comparing your screen to the one I've pasted below (using OS X 10.8):
BOOST_INCLUDE_PATH /usr/local/include BOOST_LIBRARY /usr/local/lib/libboost_python.dylib CMAKE_BUILD_TYPE CMAKE_OSX_ARCHITECTURES CMAKE_OSX_DEPLOYMENT_TARGET CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platf CMAKE_VERBOSE_MAKEFILE OFF EMAN_INSTALL_PREFIX /Users/jmbell/EMAN2 ENABLE_AUTODOC OFF ENABLE_BOUNDS_CHECKING OFF ENABLE_DEBUG OFF ENABLE_EMAN_CUDA OFF ENABLE_FFTW2 OFF ENABLE_FFTW3 ON ENABLE_FFTW_PLAN_CACHING ON ENABLE_FFT_CACHING OFF ENABLE_FTGL ON ENABLE_HDF5 ON ENABLE_IOCACHE OFF ENABLE_JPEG ON ENABLE_MEMDEBUG OFF ENABLE_MEMDEBUG2 OFF ENABLE_NATIVE_FFT OFF ENABLE_NFFT2 OFF ENABLE_OPENGL ON ENABLE_OPTIMIZE_MACHINE ON ENABLE_OPTIMIZE_MOUNTAIN_LION OFF ENABLE_OPTIMIZE_WINDOWS_VC OFF ENABLE_OPTIMIZE_X86_64 OFF ENABLE_OPTPP OFF ENABLE_PNG ON ENABLE_PROFILE OFF ENABLE_RT ON ENABLE_SPARX_CUDA OFF ENABLE_TIFF ON ENABLE_V4L2 OFF FFTW3_INCLUDE_PATH /usr/local/include FFTW3_LIBRARY /usr/local/lib/libfftw3f.dylib FREETYPE_INCLUDE_PATH /usr/local/include/freetype2 FREETYPE_LIBRARY /usr/local/lib/libfreetype.dylib FTGL_INCLUDE_PATH /usr/local/include FTGL_LIBRARY /usr/local/lib/libftgl.dylib GSL_CBLAS_INCLUDE_PATH /usr/local/include GSL_CBLAS_LIBRARY /usr/local/lib/libgslcblas.dylib GSL_INCLUDE_PATH /usr/local/include GSL_LIBRARY /usr/local/lib/libgsl.dylib HDF5_INCLUDE_PATH /usr/local/include HDF5_LIBRARY /usr/local/lib/libhdf5.dylib JPEG_INCLUDE_PATH /Library/Frameworks/UnixImageIO.framework/Headers JPEG_LIBRARY /usr/local/lib/libjpeg.dylib NUMPY_INCLUDE_PATH /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/l PNG_INCLUDE_PATH /Library/Frameworks/UnixImageIO.framework/Headers PNG_LIBRARY /usr/local/lib/libpng.dylib PYTHON_INCLUDE_PATH /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platf PYTHON_LIBRARY /usr/lib/libpython2.7.dylib TIFF_INCLUDE_PATH /Library/Frameworks/UnixImageIO.framework/Headers TIFF_LIBRARY /usr/local/lib/libtiff.dylib ZLIB_LIBRARY /usr/lib/libz.dylib
Build EMAN2
Once you're happy with the links, press 'c' to configure and then 'g' to generate the makefile.
8. Still inside build type:
make -j16 && make install
9. Add the EMAN2 folder (and the examples folder therein) to your PATH via the .bashrc file
export EMAN2DIR=${HOME}/username/EMAN2
export PATH=$EMAN2DIR/bin:$PATH
export PATH=$EMAN2DIR/examples:$PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EMAN2DIR/lib
export PYTHONPATH=$PYTHONPATH:$EMAN2DIR/lib:$EMAN2DIR/bin Once you refresh your shell by calling the shell in the terminal or by restarting your computer, everything should work properly. If the building process goes through without errors, the basic tests to see whether EMAN2 is actually installed properly, are
10. A. Run e2speedtest.py from the command line
10. B. Run e2.py from the command line
10. C. Run e2display.py from the command line (assuming you're not on a cluster)
If everything went well, the above should run without failure and you can begin using EMAN2. If not, please double check that you've followed all instructions. If you have, feel free to post to the EMAN2 google group for assistance.