|
Size: 20245
Comment:
|
Size: 20248
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 10: | Line 10: |
| If you find yourself upgrading from OS X 10.8 to 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. You will then need to reinstall older versions of berkeley-db (5.3.28) and cmake (3.1.3) as shown below (replacing the package name as appropriate, of course). To do so you must first remove the existing version of these two programs created by the above reinstallation command. |
|
| Line 29: | Line 37: |
If you find yourself upgrading from OS X 10.8 to 10.9 or 10.10, you will need to reinstall all homebrew packages. Luckily, there is an easy way: {{{ brew list | xargs brew reinstall -v }}} This should reinstall all packages in their current versions. You will then need to reinstall berkeley-db as shown below, but you must first remove the existing version created by the above reinstall. You will also want to port an older version of cmake (3.1.3 for instance), which you can do following the instructions for berkeley-db (replacing the package name, of course). |
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). 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.
If you find yourself upgrading from OS X 10.8 to 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. You will then need to reinstall older versions of berkeley-db (5.3.28) and cmake (3.1.3) as shown below (replacing the package name as appropriate, of course). To do so you must first remove the existing version of these two programs created by the above reinstallation command.
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.
You'll also need the command line tools, which you can install with:
xcode-select --install
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 --with-all-languages 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
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
Optional (Recommended) Packages
Readline
We can easily install 'readline' to parse command history in python as follows:
brew install readline
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
XQuartz
Although not mandatory for running EMAN2, you'll probably need XQuartz at some point in your Mac computing career. It's easy to install via the .dmg file found here:
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/
For EMAN2 Developers
If you spend a lot of time developing EMAN2, you will likely want these packages
brew install doxygen gnu-indent cscope
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
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.
brew install pyqt
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
If this fails to work (it has for me in some cases), try restarting your terminal application and/or your computer. Alternatively, you could try unsetting your python path; however, an explanation of how to accomplish this is beyond the scope of this document.
PyOpenGL
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
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/Python 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.