Compiling EMAN2 on Mac OS X with Homebrew

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). If for any reason this doesn't work for you, please send an e-mail to jmbell@bcm.edu and I'll address it as soon as possible.

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 , run:

brew doctor

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

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.

If you have upgraded your system from a previous version of Mac OS X and/or a previous version of Xcode, make sure previous versions have been "cleanly" removed.

sudo /Developer/Library/uninstall-devtools --mode=all

Installing Xcode is a two step process. First, install Xcode from the Mac App Store. Second, open Xcode, and go to "Preferences" then "Downloads". Select "Command Line Tools" and click the "Install" button to the right. Wait for this to complete.

XQuartz

You'll probably need XQuartz. It's easy to install, but you can try not using it.

http://xquartz.macosforge.org/landing/

CVS/GIT

CVS and GIT are version control systems. You can install them as follows:

brew install git cvs mercurial

Excellent documentation for GIT is available at: https://www.atlassian.com/git/

GCC/LLVM

To compile EMAN2's C++ code, we need to download a compiler. Here we install the homebrew versions of gcc and llvm, which are more up-to-date than those available on Mac by default.

brew install gcc
brew install llvm --with-clang --with-asan

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

OpenGL

brew install glew glfw3

Qt4

Qt is a graphics library for cross-platform user interfaces.

brew install qt

If you need to incorporate additional qt features, check the output of

brew options qt

to see what else you can include.

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-mpi # or leave out the mpi option
brew install boost-build 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. You need an account on their website to download the package, and you need a license to use 6.0.1. Instead, we can use homebrew, but we need to get a previous version since homebrew defaults to 6.0.1 (as of March, 2015). I managed to find instructions on Stack Overflow (https://stackoverflow.com/questions/3987683/homebrew-install-specific-version-of-formula) that explain how to go about this and have reproduced them below:

brew tap homebrew/boneyard
brew versions berkeley-db # Copy the command after '5.3.28'
cd $( brew --prefix )
git checkout fdc17de /usr/local/Library/Formula/berkeley-db.rb
cd ${HOME}

Now we can install berkeley-db just as we would any other package.

brew install berkeley-db

Finally, add the following to your shell's 'rc' file to enable bsddb3 to know where berkeley-db is located:

export BERKELEYDB_DIR=/usr/local/BerkeleyDB.5.3

At this point, I suggest that you refresh your shell.

If you're using Yosemite, you'll just want to define the environment variable as /usr/local instead.

Freetype

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

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

PNG

The PNG (Portal Network Graphics) format provides lossless-compressed image support. Mac OS X 10.7 Lion ships with libpng 1.5, in which some deprecated features in the PNG API were removed. EMAN2 is being updated to use these new methods. For now, use libpng 1.2 if you are compiling on 10.7.

brew install libpng

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 install hdf5

JPEG

Library for writing JPEG image files. Though optional, it's very easy to install this package:

brew install jpeg

TIFF

Library for reading and writing TIFF image files. Install TIFF as follows:

brew install libtiff

Readline

We can easily install 'readline' to parse command history in python as follows:

brew install readline

Required Python Modules

Here we opt to use the homebrew version of python over the default install built against the system.

brew install python

This sets up a separate site-packages directory, installs 'pip' (a package management solution for Python), and allows us to 'build' our python library from scratch, incorporating only the components we want/need.

For further project specificity, we could opt for a virtual environment, which can be created after installing:

pip install vrtualenv

An explanation of the innerworkings of python virtual environments are beyond the scope of this document; however, you can find more information here: http://docs.python-guide.org/en/latest/dev/virtualenvs/

sip (4.12)

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 (4.8)

PyQt4 provides Python bindings for Qt4.

brew install pyqt

bsddb3 (5.3)

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 (3.0)

PyOpenGL provides Python bindings for OpenGL. There is a pip package for it, available here:

pip install PyOpenGL

For the sake of optimization, pip also possesses an acceleration package that you can install in addition:

pip install PyOpenGL-accelerate

iPython (0.10)

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

For more details about ipython and its many growing features, see: http://ipython.org/

If you're interested in any of the recent developments in reproducible research and web/cloud-based python programming, I suggest using the following line to install ipython

pip install "ipython[all]"

and checking out the 'Jupyter' project online: http://jupyter.org/

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

Homebrew has a version of readline; however, so does python. We install it here, too, for good measure.

pip install gnureadline

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.

Get EMAN2 source code

First, obtain the EMAN2 source either via a stable source release, the nightly source release, or using CVS (if you have access permissions; a CVS tutorial is beyond the scope of this document).

For a "From-Source-Officnato"

Download EMAN2 from the NCMI: http://ncmi.bcm.tmc.edu/ncmi/software/software_details?selected_software=counter_222

For an EMAN2 Developer

Next, check out eman2 from CVS:

1. Get account on blake and be cleared to access CVS

2. Set up CVS variables on .bashrc file:

export CVSROOT=username@blake.bcm.edu:/usr/local/CVS/CVS
export CVS_RSH=ssh

3. Make 'src' directory wherever you want the source code to be

mkdir ~/src

4. Inside src, make 'build' directory

cd ~/src && mkdir build

5. Inside src, download the source code

cd ~/src && cvs co 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_OSX_ARCHITECTURES                                                                                         
 CMAKE_OSX_SYSROOT                                                                                                /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk               
 CMAKE_VERBOSE_MAKEFILE           OFF                                                                            
 EMAN_INSTALL_PREFIX              /Users/jmbell/src/EMAN2/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_FTGL                      ON                                                                             
 ENABLE_HDF5                      ON                                                                             
 ENABLE_HDFIOCACHE                OFF                                                                            
 ENABLE_IOCACHE                   OFF                                                                            
 ENABLE_JPEG                      ON                                                                             
 ENABLE_LEOPARD                   OFF                                                                            
 ENABLE_MEMDEBUG                  OFF                                                                            
 ENABLE_MEMDEBUG2                 OFF                                                                            
 ENABLE_MOUNTAIN_LION             ON                                                                             
 ENABLE_NATIVE_FFT                OFF                                                                            
 ENABLE_NFFT2                     OFF                                                                            
 ENABLE_OPENGL                    ON                                                                             
 ENABLE_OPTPP                     OFF                                                                            
 ENABLE_PNG                       ON                                                                             
 ENABLE_PROFILE                   OFF                                                                            
 ENABLE_RT                        ON                                                                             
 ENABLE_SPARX_CUDA                OFF                                                                            
 ENABLE_TIFF                      ON                                                                             
 ENABLE_V4L2                      OFF                                                                            
 ENABLE_WINDOWS_VC                OFF                                                                            
 ENABLE_X86_64                    ON                                                                             
 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                                                   
 GL_INCLUDE_PATH                  /usr/local/include                                                             
 GL_LIBRARY                       /usr/local/lib/libgsl.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                /usr/local/include                                                             
 JPEG_LIBRARY                     /usr/local/lib/libjpeg.dylib                                                   
 NUMPY_INCLUDE_PATH               /usr/local/lib/python2.7/site-packages/numpy/core/include                      
 PNG_INCLUDE_PATH                 /usr/local/include                                                             
 PNG_LIBRARY                      /usr/local/lib/libpng.dylib                                                    
 PYTHON_INCLUDE_PATH              /usr/local/Frameworks/Python.framework/Headers                                 
 PYTHON_LIBRARY                   /usr/local/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.dylib     
 TIFF_INCLUDE_PATH                /usr/local/include                                                             
 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 -j24 && make install -j24

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                                                 

This should do it. 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.

brew install doxygen
brew install gnu-indent